Contacts of the helix formed by residues 197 - 206 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192T LYS* 2.4 32.8 + - - +
195T ASP 3.4 4.6 + - - +
196T LEU* 1.3 76.9 - - - +
198T PRO* 1.3 66.7 - - - +
199T SER* 3.4 4.0 + - - -
200T VAL* 3.2 20.0 + - + +
201T GLU* 2.9 28.4 + - - +
42U ALA* 3.3 21.0 - - + +
45U GLN* 2.7 25.0 + - - +
77U GLU* 4.5 15.5 + - - +
78U MET* 4.2 17.6 - - + +
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Residues in contact with PRO 198 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194T GLN* 5.4 5.8 - - - +
196T LEU* 3.6 27.8 - - + +
197T GLU* 1.3 88.0 - - - +
199T SER* 1.3 65.6 + - - +
201T GLU* 3.4 7.4 + - + +
202T GLU* 3.1 23.4 + - - +
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Residues in contact with SER 199 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197T GLU* 3.4 2.4 + - - -
198T PRO* 1.3 80.3 - - - +
200T VAL* 1.3 64.0 + - - +
202T GLU* 3.5 10.3 + - - +
203T ALA* 3.2 23.7 + - - +
38U ALA* 4.2 10.1 - - - +
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Residues in contact with VAL 200 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197T GLU* 3.2 33.5 + - + +
199T SER* 1.3 76.2 - - - +
201T GLU* 1.3 65.7 + - - +
203T ALA* 3.3 2.6 + - - +
204T ARG* 2.9 53.2 + - - +
35U GLU* 5.0 2.6 - - + +
38U ALA* 3.5 37.7 - - + +
39U ILE* 3.7 21.3 - - + +
42U ALA* 4.0 5.6 - - + -
77U GLU 4.6 2.5 - - - +
78U MET* 3.7 4.5 - - + +
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Residues in contact with GLU 201 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196T LEU* 5.1 7.4 - - + -
197T GLU 2.9 17.4 + - - +
198T PRO* 3.7 7.9 - - + +
200T VAL* 1.3 77.1 - - - +
202T GLU* 1.3 59.3 + - - +
204T ARG* 3.8 10.2 + - - +
205T TYR* 2.9 31.8 + - + +
77U GLU* 5.3 0.9 + - - +
36V TYR* 3.2 34.9 + - - -
37V GLN* 4.0 22.6 + - - +
40V GLN* 4.1 13.2 + - - +
41V LYS* 5.9 2.7 - - - -
44V ARG* 4.3 17.1 + - - +
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Residues in contact with GLU 202 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198T PRO 3.1 15.9 + - - +
199T SER* 3.8 8.1 - - - +
200T VAL 3.2 0.2 - - - -
201T GLU* 1.3 75.4 - - - +
203T ALA* 1.3 65.3 + - - +
205T TYR* 3.1 7.8 + - + +
206T ASN* 2.8 41.6 + - - +
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Residues in contact with ALA 203 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199T SER 3.2 14.8 + - - +
200T VAL 3.9 3.1 - - - +
202T GLU* 1.3 79.0 - - - +
204T ARG* 1.3 60.7 + - - +
206T ASN* 3.5 10.0 + - - +
207T SER* 3.3 19.6 + - - -
32U THR* 4.6 1.7 + - - -
34U GLU* 3.7 44.0 - - + +
35U GLU* 3.8 9.7 + - - +
38U ALA* 4.3 3.8 - - + -
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Residues in contact with ARG 204 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200T VAL* 2.9 35.8 + - - +
201T GLU* 3.8 10.3 + - - +
203T ALA* 1.3 75.7 - - - +
205T TYR* 1.3 60.2 + - - +
207T SER* 2.9 20.1 + - - -
208T CYS* 3.3 14.9 - - - -
35U GLU* 3.1 34.0 + - - +
77U GLU 3.4 6.5 + - - -
78U MET 2.6 36.0 + - - -
79U PHE* 3.4 14.1 + - - +
80U GLY* 3.3 14.6 - - - +
82U ASN* 5.4 1.1 - - - -
116U LYS* 3.8 15.7 - - - +
36V TYR* 2.4 48.3 + - + +
40V GLN* 3.8 6.5 - - - +
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Residues in contact with TYR 205 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201T GLU* 2.9 23.4 + - + +
202T GLU* 3.1 8.0 + - - +
204T ARG* 1.3 75.6 - - - +
206T ASN* 1.3 75.3 + - - +
207T SER 3.3 0.3 + - - -
208T CYS* 3.5 12.9 + - - -
33V ALA* 3.5 44.7 - - + +
34V GLU* 4.7 11.7 + - - +
36V TYR* 4.7 5.5 - + - -
37V GLN* 2.9 46.6 + - + +
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Residues in contact with ASN 206 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202T GLU* 2.8 34.7 + - - +
203T ALA* 3.8 9.1 - - - +
204T ARG 3.2 0.2 - - - -
205T TYR* 1.3 89.5 - - - +
207T SER* 1.3 59.1 + - - +
208T CYS 3.4 4.4 + - - +
34U GLU* 5.3 7.6 - - + +
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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