Contacts of the helix formed by residues 554 - 563 (chain N) in PDB entry 5G04
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 MET 554 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516N ILE* 3.5 45.3 - - + +
519N TYR* 3.4 31.2 - - + -
520N ARG* 4.5 1.3 - - + -
542N VAL* 3.9 17.7 - - + +
545N LEU* 3.6 30.7 - - + -
549N PHE* 6.3 0.4 - - + -
550N GLY 6.0 1.1 - - - +
551N GLU* 3.1 26.2 + - + +
553N PRO* 1.3 81.7 - - + +
555N HIS* 1.3 63.1 + - - +
556N PHE 3.3 1.8 - - - -
557N CYS* 3.2 39.5 + - + +
558N GLU* 3.3 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 555 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LYS* 2.9 37.5 - - + +
551N GLU* 3.1 15.8 + - - +
552N ALA* 3.7 15.5 - - - +
553N PRO 3.4 0.4 - - - -
554N MET* 1.3 77.3 - - - +
556N PHE* 1.3 63.0 + - - +
558N GLU* 3.3 21.3 + - + +
559N VAL* 3.3 26.6 + - + +
600N PHE* 5.3 8.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 556 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520N ARG* 3.1 48.7 - - - +
552N ALA 4.7 0.8 + - - +
553N PRO* 3.7 9.1 + - + +
555N HIS* 1.3 77.4 - - - +
557N CYS* 1.3 58.0 + - - +
559N VAL* 3.5 12.5 - - - +
560N MET* 3.5 17.0 - - - +
599N GLU 3.5 20.2 - - - -
600N PHE* 3.2 58.5 - + - -
601N TRP 5.5 0.7 - - - -
602N PRO* 5.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 557 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519N TYR* 3.6 14.1 - - - -
520N ARG* 3.3 38.0 - - - +
523N LEU* 3.5 31.9 - - + +
538N GLU* 4.7 0.9 - - - +
542N VAL* 4.1 8.5 - - + -
554N MET* 3.2 37.0 + - + +
555N HIS 3.2 0.4 - - - -
556N PHE* 1.3 76.9 - - - +
558N GLU* 1.3 64.1 + - - +
560N MET* 3.3 18.9 + - - +
561N LEU* 3.8 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 558 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538N GLU* 3.5 12.6 - - - +
539N ILE* 3.4 55.1 + - + +
542N VAL* 3.4 33.7 - - + +
543N GLU* 5.3 3.1 - - - +
551N GLU* 5.2 3.9 - - - +
554N MET 3.3 3.5 + - - +
555N HIS* 3.3 16.9 + - + +
557N CYS* 1.3 78.4 - - - +
559N VAL* 1.3 63.5 + - - +
561N LEU* 3.2 16.5 + - - +
562N LYS* 3.4 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 559 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LYS 5.3 6.7 - - - +
40B PRO* 6.0 5.2 - - + -
555N HIS* 3.3 23.2 + - + +
556N PHE 3.5 10.8 - - - +
558N GLU* 1.3 75.0 - - - +
560N MET* 1.3 67.0 + - - +
562N LYS* 3.1 33.6 - - + +
563N ASP* 3.1 34.6 - - - +
597N SER* 5.9 0.2 - - - -
600N PHE* 3.5 43.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 560 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520N ARG* 5.6 9.4 - - + +
523N LEU* 4.8 6.5 - - + -
524N ALA* 6.0 3.8 - - - +
527N LEU* 3.1 21.3 - - + +
556N PHE* 3.5 15.9 - - + +
557N CYS* 3.3 13.6 + - - +
558N GLU 3.2 0.8 - - - -
559N VAL* 1.3 80.5 - - - +
561N LEU* 1.3 66.9 + - + +
563N ASP* 3.2 42.1 + - + +
564N MET 3.7 0.7 + - - -
597N SER* 3.3 10.5 - - - +
600N PHE* 3.1 30.3 - - + +
601N TRP* 3.2 48.7 - - + +
602N PRO* 5.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 561 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523N LEU* 3.6 29.2 - - + -
526N ARG* 6.0 2.2 - - + -
527N LEU* 3.5 32.3 - - + -
533N PHE* 5.4 0.3 - - - -
534N SER* 3.3 42.2 - - - +
535N PRO* 5.8 2.5 - - + +
538N GLU* 3.2 46.2 - - + +
539N ILE* 6.5 0.7 - - + -
557N CYS 4.3 0.2 - - - +
558N GLU 3.2 6.6 + - - +
560N MET* 1.3 75.7 - - + +
562N LYS* 1.3 58.4 + - - +
564N MET* 2.6 26.5 + - + +
565N ALA* 3.4 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 562 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 5.9 0.6 - - - +
40B PRO* 5.7 5.3 - - - +
43B ASP* 3.9 19.6 + - - -
558N GLU 3.4 6.5 + - - +
559N VAL* 3.1 39.5 - - + +
561N LEU* 1.3 77.7 - - - +
563N ASP* 1.3 64.1 + - - +
564N MET 3.4 0.4 - - - -
565N ALA* 3.2 11.5 + - + +
566N ASP* 2.8 47.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 563 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TRP* 5.3 5.1 + - + +
527N LEU* 5.7 0.2 - - + -
559N VAL* 3.1 29.2 + - - +
560N MET* 3.2 22.4 - - + +
561N LEU 3.3 0.2 - - - -
562N LYS* 1.3 82.4 - - - +
564N MET* 2.8 31.0 - - + +
566N ASP* 3.2 11.2 + - - +
567N SER* 2.8 33.7 + - - -
595N ILE* 3.8 19.6 - - - +
596N LEU* 4.9 2.2 - - - -
597N SER* 3.1 38.9 + - - +
601N TRP* 5.6 1.1 - - - +
----------------------------------------------------------
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