Contacts of the helix formed by residues 548 - 578 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D TYR* 3.9 7.6 - - + +
152D ASP* 3.5 32.6 + - - +
544H HIS* 3.8 9.1 - - - -
545H MET 2.6 24.1 + - - +
546H SER 3.7 3.0 + - - -
547H LEU* 1.3 74.8 - - - +
549H PRO* 1.3 80.8 - - + +
550H THR* 3.3 12.8 + - - +
551H SER* 2.8 40.5 + - - -
552H VAL* 2.7 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 549 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D TYR* 4.0 12.3 - - - +
61D LEU* 4.8 2.5 - - + -
64D TYR* 3.3 33.9 - - + +
150D SER* 3.4 8.7 - - - +
151D PHE* 3.1 44.0 - - + +
548H ASN* 1.3 89.3 - - + +
550H THR* 1.3 54.0 + - - +
552H VAL* 3.0 6.0 + - + +
553H ALA* 2.7 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 550 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D VAL 4.8 0.2 + - - -
89D SER* 4.0 12.4 + - - +
150D SER* 3.0 14.7 + - - +
151D PHE* 2.8 37.0 + - - -
152D ASP* 3.6 6.9 + - + +
548H ASN* 3.3 8.4 + - - -
549H PRO* 1.3 77.3 - - - +
551H SER* 1.3 64.4 + - - +
553H ALA* 3.9 1.2 - - - +
554H ARG* 3.0 58.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 551 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546H SER 3.5 12.4 + - - -
547H LEU* 4.6 1.7 - - - -
548H ASN* 2.8 42.9 + - - -
550H THR* 1.3 76.7 - - - +
552H VAL* 1.3 64.0 + - - +
554H ARG* 3.2 10.1 + - - +
555H GLN* 3.1 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 552 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D GLU* 6.6 0.4 - - + -
547H LEU* 5.2 4.0 - - + -
548H ASN 2.7 32.4 + - - +
549H PRO* 3.5 8.1 - - + +
551H SER* 1.3 68.0 - - - +
553H ALA* 1.3 57.3 + - - +
554H ARG 3.0 1.8 - - - -
555H GLN* 2.7 36.0 + - + +
556H ARG* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 553 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D ILE* 3.9 23.6 - - + +
150D SER* 4.0 20.4 - - - +
549H PRO 2.7 19.1 + - - +
550H THR 3.9 3.8 - - - +
552H VAL* 1.3 73.1 - - - +
554H ARG* 1.3 60.4 - - - +
556H ARG* 3.5 26.9 - - - +
557H LEU* 3.7 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 554 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D SER* 4.2 4.8 + - - -
90D ASN 4.0 5.7 + - - -
91D ILE* 3.9 25.3 + - + +
92D GLU 5.6 0.9 - - - -
93D SER 4.5 0.6 + - - -
94D GLY* 2.7 42.9 + - - -
150D SER* 5.6 1.2 - - - -
550H THR* 3.0 41.3 + - - +
551H SER* 3.3 13.0 - - - +
552H VAL 3.0 0.2 - - - -
553H ALA* 1.3 75.0 - - - +
555H GLN* 1.3 61.1 + - - +
557H LEU* 3.6 7.5 - - + +
558H ARG* 2.8 50.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 555 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551H SER* 3.2 31.4 + - - +
552H VAL* 2.7 17.8 + - + +
554H ARG* 1.3 78.5 - - - +
556H ARG* 1.3 56.1 + - - +
557H LEU 3.0 0.7 + - - -
558H ARG* 3.3 23.6 + - - +
559H GLU* 2.9 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 556 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552H VAL* 2.9 37.7 + - + +
553H ALA* 3.5 12.3 - - - +
555H GLN* 1.3 72.7 - - - +
557H LEU* 1.3 56.6 + - - +
559H GLU* 3.4 16.1 + - - +
560H ASP* 4.0 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 557 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D ILE* 3.9 15.0 - - + +
92D GLU* 3.9 46.0 - - + +
553H ALA 3.7 8.1 - - - +
554H ARG* 3.6 11.9 - - + +
556H ARG* 1.3 75.1 - - - +
558H ARG* 1.3 64.6 - - + +
559H GLU 3.3 1.1 - - - +
560H ASP* 3.4 5.7 + - - +
561H HIS* 2.9 67.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 558 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554H ARG* 2.8 45.1 + - - +
555H GLN* 3.3 23.5 - - - +
557H LEU* 1.3 86.1 - - + +
559H GLU* 1.3 64.1 + - + +
561H HIS* 3.3 5.0 + - - +
562H SER* 3.1 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 559 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555H GLN* 2.9 36.4 + - + +
556H ARG* 3.4 18.7 + - + +
558H ARG* 1.3 75.9 - - + +
560H ASP* 1.3 52.2 + - - +
562H SER* 2.7 12.3 + - - -
563H GLN* 2.6 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 560 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556H ARG* 4.0 26.2 - - - +
557H LEU* 3.4 11.3 + - - +
559H GLU* 1.3 73.3 - - - +
561H HIS* 1.3 66.4 + - + +
563H GLN* 3.5 21.2 + - - +
564H LEU* 2.8 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 561 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D GLU* 5.8 5.5 + - + -
561G HIS* 5.4 12.8 - + - -
564G LEU* 5.7 9.0 - - + -
557H LEU* 2.9 49.7 + - + +
558H ARG* 3.8 5.6 - - - +
560H ASP* 1.3 79.7 - - + +
562H SER* 1.3 56.8 + - - +
564H LEU* 4.3 13.4 - - + +
565H GLN* 3.4 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 562 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558H ARG 3.1 13.7 + - - -
559H GLU* 2.7 16.7 + - - -
561H HIS* 1.3 78.9 - - - +
563H GLN* 1.3 57.4 + - - -
565H GLN* 3.4 6.1 + - - +
566H ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 563 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559H GLU* 2.6 27.4 + - + +
560H ASP* 3.5 35.9 + - - +
562H SER* 1.3 70.8 - - - +
564H LEU* 1.3 55.0 + - - +
566H ALA* 3.1 6.9 + - - +
567H GLU* 2.7 55.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 564 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564G LEU* 5.8 3.4 - - + -
568G CYS* 4.2 25.4 - - - -
571G LEU* 5.6 3.4 - - + -
560H ASP 2.8 17.6 + - - +
561H HIS* 4.3 12.8 - - + +
563H GLN* 1.3 77.7 - - - +
565H GLN* 1.3 64.6 + - - +
567H GLU* 3.3 6.0 + - + +
568H CYS* 3.0 43.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 565 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561H HIS 3.4 19.8 + - - +
562H SER* 3.4 7.1 + - - +
563H GLN 3.3 0.2 - - - -
564H LEU* 1.3 82.6 - - - +
566H ALA* 1.3 62.7 + - - +
568H CYS* 3.5 6.0 + - - +
569H GLU* 3.3 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 566 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562H SER 2.9 18.4 + - - +
563H GLN* 3.4 7.2 - - - +
565H GLN* 1.3 75.5 - - - +
567H GLU* 1.3 56.1 + - + +
569H GLU* 2.9 9.7 + - - +
570H ARG* 2.7 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 567 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563H GLN* 2.7 38.6 + - - +
564H LEU* 3.9 5.8 - - + +
566H ALA* 1.3 72.9 - - + +
568H CYS* 1.3 58.3 + - - +
570H ARG* 4.0 26.0 - - - +
571H LEU* 2.8 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 568 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571G LEU* 4.3 22.0 - - - -
564H LEU* 3.0 43.0 + - - +
565H GLN* 3.7 7.2 - - - +
567H GLU* 1.3 75.7 - - - +
569H GLU* 1.3 57.4 + - - +
571H LEU* 4.2 4.0 - - - +
572H ARG* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 569 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565H GLN 3.3 8.8 + - - +
566H ALA* 2.9 10.8 + - - +
568H CYS* 1.3 78.7 - - - +
570H ARG* 1.3 60.6 + - - +
572H ARG* 3.2 35.1 + - - +
573H GLY* 2.8 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 570 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566H ALA* 2.7 26.5 + - - +
567H GLU* 3.6 23.4 - - - +
569H GLU* 1.3 71.8 - - - +
571H LEU* 1.3 66.0 + - - +
573H GLY* 2.8 13.7 + - - -
574H LEU* 3.1 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 571 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571G LEU* 6.2 4.3 - - + -
575G LEU* 4.9 23.1 - - + -
567H GLU 2.8 20.3 + - - +
568H CYS* 4.2 3.8 - - - +
570H ARG* 1.3 75.0 - - - +
572H ARG* 1.3 63.0 + - - +
574H LEU* 3.2 18.6 + - + -
575H LEU* 3.0 47.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 572 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568H CYS 2.9 21.7 + - - +
569H GLU* 3.3 32.9 + - - +
570H ARG 3.1 0.2 - - - -
571H LEU* 1.3 78.2 - - - +
573H GLY* 1.3 57.1 + - - +
575H LEU* 3.4 9.2 + - - +
576H ARG* 2.9 52.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 573 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569H GLU* 2.8 14.6 + - - -
570H ARG* 2.8 9.8 + - - -
572H ARG* 1.3 76.7 - - - +
574H LEU* 1.3 56.3 + - - -
576H ARG* 2.9 8.9 + - - +
577H ALA* 2.8 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 574 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570H ARG* 3.1 25.5 + - + +
571H LEU* 3.6 20.6 - - + +
573H GLY* 1.3 72.7 - - - +
575H LEU* 1.3 63.9 + - + +
577H ALA* 3.0 24.7 + - + +
578H MET* 3.3 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 575 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584G VAL* 6.3 2.5 - - + -
571H LEU* 3.0 45.8 + - + +
572H ARG* 3.7 7.6 - - - +
574H LEU* 1.3 76.8 - - + +
576H ARG* 1.3 57.9 + - - +
578H MET* 2.8 45.0 - - + +
579H GLU 4.4 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 576 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572H ARG* 2.9 39.5 + - + +
573H GLY* 3.3 11.9 - - - +
575H LEU* 1.3 74.7 - - - +
577H ALA* 1.3 71.1 + - - +
578H MET 3.3 0.5 + - - -
579H GLU* 3.4 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 577 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573H GLY 2.8 11.7 + - - +
574H LEU* 3.0 17.3 - - + +
576H ARG* 1.3 76.7 - - - +
578H MET* 1.3 53.6 + - + +
579H GLU* 2.6 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 578 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574H LEU* 3.3 28.7 - - + +
575H LEU* 2.8 41.4 - - + +
577H ALA* 1.3 73.7 - - + +
579H GLU* 1.3 67.0 + - - +
----------------------------------------------------------
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