Contacts of the helix formed by residues 197 - 206 (chain O) in PDB entry 5XS0
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 GLU 197 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192O LYS* 2.4 32.3 + - - +
194O GLN* 5.4 0.3 + - - -
195O ASP 3.4 4.2 + - - +
196O LEU* 1.3 78.1 - - - +
198O PRO* 1.3 66.3 - - - +
199O SER 3.5 2.0 - - - -
200O VAL* 3.2 20.3 + - + +
201O GLU* 2.9 27.2 + - - +
42P ALA* 3.4 16.9 - - + +
45P GLN* 2.7 30.1 + - - +
77P GLU* 4.8 12.9 + - - +
78P MET* 4.2 19.1 - - + -
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Residues in contact with PRO 198 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194O GLN* 5.6 2.2 - - - +
196O LEU* 3.7 24.9 - - + +
197O GLU* 1.3 88.0 - - - +
199O SER* 1.3 58.7 + - - +
201O GLU* 3.3 7.7 + - + +
202O GLU* 2.9 29.9 + - - +
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Residues in contact with SER 199 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197O GLU 3.5 0.4 - - - -
198O PRO* 1.3 79.4 - - - +
200O VAL* 1.3 64.1 + - - +
202O GLU* 3.3 12.7 + - - +
203O ALA* 3.0 24.9 + - - +
38P ALA* 4.1 13.1 - - - +
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Residues in contact with VAL 200 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197O GLU* 3.2 26.9 + - + +
198O PRO 3.2 0.4 - - - -
199O SER* 1.3 79.5 - - - +
201O GLU* 1.3 63.5 + - - +
203O ALA* 3.4 2.4 + - - +
204O ARG* 2.9 50.1 + - - +
35P GLU* 4.8 2.8 - - + +
38P ALA* 3.5 38.6 - - + +
39P ILE* 3.5 22.9 - - + +
42P ALA* 4.0 10.1 - - + -
77P GLU 4.8 2.5 - - - +
78P MET* 3.6 5.2 - - + +
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Residues in contact with GLU 201 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196O LEU* 4.9 12.1 - - + -
197O GLU 2.9 17.2 + - - +
198O PRO* 3.7 7.6 - - + +
200O VAL* 1.3 76.1 - - - +
202O GLU* 1.3 58.5 + - - +
204O ARG* 3.3 22.0 + - - +
205O TYR* 2.9 32.4 + - + +
77P GLU* 5.1 3.3 + - - +
36Q TYR* 3.4 25.0 + - - -
37Q GLN* 4.5 13.8 + - - +
40Q GLN* 3.4 21.0 + - - +
41Q LYS* 6.3 0.9 - - - +
44Q ARG* 4.8 9.8 + - - +
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Residues in contact with GLU 202 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198O PRO 2.9 16.5 + - - +
199O SER* 3.7 11.2 + - - +
201O GLU* 1.3 74.6 - - - +
203O ALA* 1.3 66.7 + - - +
204O ARG 3.2 0.2 + - - -
205O TYR* 3.3 7.1 + - + +
206O ASN* 3.0 42.9 + - - +
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Residues in contact with ALA 203 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199O SER* 3.0 17.8 + - - +
200O VAL 3.8 2.2 - - - +
202O GLU* 1.3 77.9 - - - +
204O ARG* 1.3 57.1 + - - +
206O ASN* 3.4 9.0 + - - +
207O SER* 3.0 26.0 + - - -
32P THR* 4.3 3.5 + - - -
34P GLU* 3.6 23.6 - - + +
35P GLU* 3.5 33.4 - - - +
38P ALA* 4.6 0.9 - - + -
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Residues in contact with ARG 204 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200O VAL* 2.9 35.8 + - - +
201O GLU* 3.4 20.5 + - - +
203O ALA* 1.3 76.3 - - - +
205O TYR* 1.3 61.5 + - - +
207O SER* 2.9 24.6 + - - -
208O CYS* 3.4 13.3 - - - -
35P GLU* 2.9 30.5 + - - +
39P ILE* 4.4 0.2 - - - +
77P GLU 3.6 5.1 + - - -
78P MET 2.4 36.8 + - - -
79P PHE* 3.4 20.6 + - - +
80P GLY 3.8 2.2 - - - +
82P ASN* 5.4 1.8 - - - -
116P LYS* 4.0 11.9 - - - +
36Q TYR* 2.7 46.2 + - + +
40Q GLN* 3.7 9.7 - - - +
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Residues in contact with TYR 205 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201O GLU* 2.9 22.7 + - + +
202O GLU* 3.7 7.2 - - + +
204O ARG* 1.3 77.0 - - - +
206O ASN* 1.3 75.9 + - - +
207O SER 3.3 0.9 + - - -
208O CYS* 3.5 13.8 + - - +
33Q ALA* 3.4 48.7 - - + +
34Q GLU* 4.4 8.7 + - - +
36Q TYR* 4.4 9.5 - + - -
37Q GLN* 3.7 41.5 + - + +
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Residues in contact with ASN 206 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202O GLU* 3.0 37.8 + - - +
203O ALA* 3.6 6.3 - - - +
205O TYR* 1.3 92.5 - - - +
207O SER* 1.3 57.6 + - - +
208O CYS 3.3 5.2 + - - +
34P GLU* 5.3 8.1 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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