Contacts of the helix formed by residues 31 - 39 (chain A) in PDB entry 4G98
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 SER 31 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG 3.2 8.7 + - - -
28A ALA 3.0 19.7 + - - -
30A ASN* 1.3 78.4 - - - +
32A GLU* 1.3 60.5 + - - +
33A PHE 4.4 0.7 - - - -
34A MET* 3.0 17.7 + - - +
35A ARG* 2.8 26.7 + - - +
211A ILE* 4.9 13.5 - - - -
214A PHE* 3.5 28.7 - - - +
215A GLU* 5.3 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASN 3.6 1.2 + - - -
31A SER* 1.3 71.9 - - - +
33A PHE* 1.3 58.3 + - - +
35A ARG* 3.3 32.8 + - - +
36A ASN* 2.9 35.9 + - - +
215A GLU* 6.3 0.2 - - - +
218A GLN* 3.8 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 3.2 0.8 + - - -
32A GLU* 1.3 80.1 - - - +
34A MET* 1.3 88.9 + - + +
36A ASN* 3.5 4.2 + - + +
37A PHE* 2.9 36.7 + + - +
42A VAL* 4.6 11.9 - - + -
46A GLY* 3.7 24.2 - - - -
50A VAL* 4.1 24.9 - - + -
214A PHE* 3.9 30.5 - + + +
217A LEU* 4.5 15.0 - - + -
218A GLN* 3.2 26.7 - - - +
221A LEU* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA 3.7 9.0 - - - +
29A GLU 3.5 14.4 - - - +
31A SER* 3.0 19.3 + - - +
33A PHE* 1.3 115.9 - - + +
35A ARG* 1.3 57.6 + - - +
37A PHE* 3.6 15.3 - - + +
38A GLN* 2.7 40.5 + - - +
50A VAL* 5.1 2.2 - - + -
147A LEU* 4.6 13.0 - - - -
214A PHE* 3.4 35.2 - - + -
301A HEM 3.8 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU 3.8 1.5 + - - +
30A ASN* 3.1 44.5 + - - +
31A SER 2.8 13.6 + - - +
32A GLU* 3.6 35.8 + - - +
34A MET* 1.3 75.3 - - - +
36A ASN* 1.3 67.0 + - - +
38A GLN* 3.3 12.3 + - - +
39A LYS* 3.1 48.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU* 2.9 20.2 + - - +
33A PHE* 3.6 6.3 - - + +
35A ARG* 1.3 79.3 - - - +
37A PHE* 1.3 62.5 + - - +
39A LYS* 3.3 21.2 + - - +
41A GLN* 2.9 57.7 + - + +
42A VAL* 5.8 1.1 - - - -
218A GLN* 3.9 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 2.9 34.0 + + + +
34A MET* 3.6 19.3 - - + +
36A ASN* 1.3 76.2 - - - +
38A GLN* 1.3 54.8 + - - +
40A GLY* 2.8 24.1 + - - -
41A GLN 4.0 0.2 + - - -
42A VAL* 4.0 30.1 + - + +
47A PHE* 4.0 25.6 - + - -
50A VAL* 5.3 4.3 - - + -
147A LEU* 3.6 52.9 - - + -
150A ILE* 3.2 26.2 - - + +
151A ALA* 4.0 16.8 - - + -
167A PHE* 5.4 4.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 3.0 37.7 + - - +
30A ASN* 5.5 1.8 + - - -
34A MET 2.7 16.2 + - - +
35A ARG* 3.3 11.8 + - - +
37A PHE* 1.3 74.7 - - - +
39A LYS* 1.3 59.8 + - + +
40A GLY 3.4 0.9 + - - -
147A LEU* 4.8 3.6 - - + -
150A ILE* 3.7 25.7 - - + +
301A HEM 3.1 46.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 3.1 37.7 + - - +
36A ASN* 3.5 19.8 - - - +
37A PHE 3.1 0.6 + - - -
38A GLN* 1.3 75.8 - - + +
40A GLY* 1.3 59.3 + - - +
41A GLN* 3.6 27.4 + - + +
----------------------------------------------------------
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