Contacts of the helix formed by residues 548 - 578 (chain F) in PDB entry 1GO4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 548 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 3.9 10.8 - - + -
152B ASP* 3.2 35.8 + - - +
544F HIS* 3.6 9.7 + - - -
545F MET 3.0 21.4 + - - +
546F SER 3.8 6.3 + - - -
547F LEU* 1.3 75.0 - - - +
549F PRO* 1.3 75.2 - - + +
550F THR* 2.8 34.2 + - - -
551F SER* 2.9 17.3 + - - +
552F VAL* 2.9 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 549 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 4.1 5.4 - - - +
61B LEU* 3.9 15.0 - - + -
64B TYR* 3.3 41.5 - - + -
150B SER* 3.2 14.9 + - - +
151B PHE* 3.5 31.4 - - + +
548F ASN* 1.3 88.5 - - + +
550F THR* 1.3 56.5 + - - +
552F VAL* 3.7 6.8 - - + +
553F ALA* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 550 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B VAL 4.9 0.3 + - - -
89B SER* 3.9 19.6 + - - +
91B ILE* 6.0 2.0 - - + -
94B GLY* 6.6 0.4 - - - -
150B SER* 3.4 13.1 + - - -
151B PHE* 2.8 35.3 + - - -
152B ASP* 3.7 7.1 + - + +
173B GLN* 6.4 0.2 - - - +
548F ASN* 2.8 15.3 + - - -
549F PRO* 1.3 72.4 - - - +
551F SER* 1.3 65.0 + - - +
553F ALA* 3.3 1.4 + - - +
554F ARG* 2.9 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 551 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546F SER 3.3 17.6 + - - -
547F LEU* 3.6 7.8 - - - +
548F ASN* 2.9 35.2 + - - -
550F THR* 1.3 77.4 - - - +
552F VAL* 1.3 59.8 + - - +
554F ARG* 3.7 7.2 - - - +
555F GLN* 2.9 31.1 + - - +
558F ARG* 5.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 552 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLU* 6.3 3.8 - - + -
547F LEU* 5.0 10.8 - - + -
548F ASN 2.9 29.2 + - - +
549F PRO* 3.7 7.2 - - + +
551F SER* 1.3 80.1 + - - +
553F ALA* 1.3 63.5 + - + +
555F GLN* 3.2 8.3 + - - +
556F ARG* 3.0 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 553 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE* 3.6 35.2 - - + -
150B SER* 4.4 3.6 - - - +
549F PRO 3.0 18.9 + - - +
550F THR 3.9 2.7 - - - +
552F VAL* 1.3 77.8 - - - +
554F ARG* 1.3 63.2 + - - +
556F ARG* 3.3 11.2 + - - +
557F LEU* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 554 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE* 3.0 27.7 + - + +
92B GLU 2.8 30.1 + - - -
93B SER 3.8 2.0 + - - -
94B GLY* 3.8 19.3 - - - +
95C GLU* 3.3 34.5 + - - -
177C ASN* 6.0 2.2 - - - +
550F THR* 2.9 40.3 + - + +
551F SER* 3.7 6.7 - - - +
553F ALA* 1.3 75.4 - - - +
555F GLN* 1.3 63.1 + - - +
557F LEU* 3.0 10.3 + - - +
558F ARG* 3.0 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 555 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551F SER 2.9 18.2 + - - +
552F VAL* 3.4 7.6 - - - +
554F ARG* 1.3 77.8 - - - +
556F ARG* 1.3 57.6 + - + +
558F ARG* 3.1 42.2 + - - +
559F GLU* 2.9 53.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 556 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLU* 5.3 10.7 - - - +
552F VAL* 3.0 42.1 + - + +
553F ALA* 3.7 11.5 - - - +
554F ARG 3.3 0.2 - - - -
555F GLN* 1.3 78.0 - - + +
557F LEU* 1.3 57.2 + - - +
559F GLU* 3.3 15.4 + - - +
560F ASP* 2.7 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 557 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE* 3.4 30.3 - - + +
92B GLU* 3.6 50.0 - - + +
553F ALA 3.1 14.0 + - - +
554F ARG* 3.0 11.5 + - - +
556F ARG* 1.3 76.9 - - + +
558F ARG* 1.3 63.9 + - + +
560F ASP* 3.2 16.8 + - + +
561F HIS* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 558 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551F SER 5.1 1.0 + - - -
554F ARG* 3.0 26.0 + - - +
555F GLN* 3.1 61.9 + - - +
557F LEU* 1.3 78.5 - - + +
559F GLU* 1.3 57.4 + - - +
561F HIS* 3.4 6.1 + - - +
562F SER* 3.0 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 559 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555F GLN* 2.9 46.3 + - - +
556F ARG* 3.8 16.6 - - - +
557F LEU 3.2 0.2 - - - -
558F ARG* 1.3 74.8 - - - +
560F ASP* 1.3 62.5 + - - +
562F SER* 4.1 5.9 - - - +
563F GLN* 3.1 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 560 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556F ARG* 2.7 29.8 + - - +
557F LEU* 3.2 17.8 + - + +
559F GLU* 1.3 80.7 - - - +
561F HIS* 1.3 58.7 + - - +
563F GLN* 3.5 14.0 + - - +
564F LEU* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 561 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLU* 2.8 36.8 + - + +
147C VAL* 5.6 10.3 - - + +
557F LEU 3.0 15.2 + - - +
558F ARG* 3.9 5.8 - - - +
560F ASP* 1.3 76.6 - - - +
562F SER* 1.3 61.9 + - - +
564F LEU* 3.3 14.7 + - + +
565F GLN* 3.0 63.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 562 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558F ARG* 3.0 17.1 + - - +
559F GLU* 4.1 6.1 - - - -
561F HIS* 1.3 75.5 + - - +
563F GLN* 1.3 61.1 + - - +
565F GLN* 3.8 15.0 + - - +
566F ALA* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 563 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559F GLU 3.1 19.6 + - - +
560F ASP* 3.7 14.4 - - - +
562F SER* 1.3 77.4 - - - +
564F LEU* 1.3 58.7 + - - +
566F ALA* 3.3 6.7 - - + +
567F GLU* 3.0 52.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 564 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLU* 6.0 1.6 - - - +
561E HIS* 5.4 15.0 - - + +
564E LEU* 6.0 2.9 - - + -
560F ASP 3.1 17.9 + - - +
561F HIS* 3.5 16.6 - - + +
563F GLN* 1.3 76.1 - - - +
565F GLN* 1.3 70.2 + - + +
567F GLU* 3.4 6.6 + - + +
568F CYS* 3.1 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 565 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C GLU 6.0 0.2 + - - -
561F HIS* 3.0 50.1 + - + +
562F SER* 3.8 14.9 + - - +
563F GLN 3.4 0.2 - - - -
564F LEU* 1.3 80.2 - - + +
566F ALA* 1.3 58.5 + - - +
568F CYS* 3.4 5.4 + - - +
569F GLU* 3.0 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 566 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562F SER 2.9 18.5 + - - +
563F GLN* 3.3 11.2 - - + +
564F LEU 3.1 0.2 - - - -
565F GLN* 1.3 74.2 - - - +
567F GLU* 1.3 68.6 + - + +
569F GLU* 3.2 7.7 + - - +
570F ARG* 3.0 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 567 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563F GLN* 3.0 38.8 + - + +
564F LEU* 3.9 9.0 - - + +
566F ALA* 1.3 75.8 - - - +
568F CYS* 1.3 59.3 - - - +
570F ARG* 3.2 19.4 + - - +
571F LEU* 2.8 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 568 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564E LEU* 4.1 24.7 - - - -
564F LEU* 3.1 36.6 + - - +
565F GLN* 3.7 6.5 - - - +
567F GLU* 1.3 81.3 - - - +
569F GLU* 1.3 56.9 + - - +
571F LEU* 3.9 9.8 - - - +
572F ARG* 3.0 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 569 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565F GLN* 3.0 19.5 + - - +
566F ALA* 3.7 6.4 - - - +
568F CYS* 1.3 76.9 - - - +
570F ARG* 1.3 58.4 + - - +
572F ARG* 2.9 32.4 - - + +
573F GLY* 3.1 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 570 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566F ALA 3.0 16.2 + - - +
567F GLU* 3.6 17.8 + - - +
569F GLU* 1.3 73.1 - - - +
571F LEU* 1.3 69.5 + - - +
572F ARG 2.9 1.1 - - - -
573F GLY* 2.8 12.9 + - - -
574F LEU* 3.1 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 571 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564E LEU* 5.5 5.8 - - + -
568E CYS* 4.3 23.1 - - - -
571E LEU* 5.6 4.7 - - + -
567F GLU 2.8 20.1 + - - +
568F CYS* 3.9 9.2 - - - +
570F ARG* 1.3 76.5 - - - +
572F ARG* 1.3 62.4 + - - +
574F LEU* 3.3 17.1 + - + +
575F LEU* 3.1 53.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 572 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568F CYS 3.0 17.1 + - - +
569F GLU* 2.9 30.4 - - + +
571F LEU* 1.3 78.2 - - - +
573F GLY* 1.3 59.2 + - - +
575F LEU* 3.8 8.8 + - - +
576F ARG* 3.3 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 573 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569F GLU 3.1 5.6 + - - -
570F ARG* 2.8 14.5 + - - -
572F ARG* 1.3 73.2 - - - +
574F LEU* 1.3 56.3 + - - -
576F ARG* 2.9 9.9 + - - +
577F ALA* 2.7 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 574 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570F ARG* 3.1 35.8 + - + +
571F LEU* 3.5 19.1 - - + +
573F GLY* 1.3 76.0 - - - +
575F LEU* 1.3 67.0 + - + +
576F ARG 2.9 0.9 + - - -
577F ALA* 3.0 5.0 + - + +
578F MET* 2.8 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 575 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571E LEU* 3.9 27.4 - - + -
571F LEU* 3.1 40.7 + - + +
572F ARG* 4.0 7.6 - - - +
574F LEU* 1.3 78.5 - - + +
576F ARG* 1.3 60.5 + - - +
578F MET* 3.3 24.8 - - - +
579F GLU 4.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 576 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572F ARG* 3.3 14.1 + - - +
573F GLY* 2.9 13.1 + - - +
574F LEU 2.9 0.8 + - - -
575F LEU* 1.3 78.1 - - - +
577F ALA* 1.3 68.9 + - - +
578F MET 3.4 0.3 + - - -
579F GLU 3.7 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 577 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573F GLY 2.7 19.9 + - - +
574F LEU* 3.8 4.5 - - + +
576F ARG* 1.3 77.2 - - - +
578F MET* 1.3 52.7 + - - +
579F GLU* 2.7 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 578 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575E LEU* 6.2 4.7 - - - -
574F LEU* 2.8 25.9 + - + +
575F LEU* 3.3 16.9 - - - +
576F ARG 3.3 0.2 - - - -
577F ALA* 1.3 74.4 - - - +
579F GLU* 1.3 73.0 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il