Contacts of the helix formed by residues 197 - 206 (chain U) in PDB entry 1H2I
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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192U LYS* 2.5 34.9 + - - +
195U ASP 3.3 14.3 + - - +
196U LEU* 1.3 75.5 - - - +
198U PRO* 1.3 65.1 - - - +
199U SER 3.4 2.4 + - - -
200U VAL* 3.2 18.4 + - + +
201U GLU* 2.9 28.2 + - - +
42V ALA* 3.7 22.4 - - + +
45V GLN* 3.3 17.5 + - - +
77V GLU* 4.5 13.8 + - - +
78V MET* 4.1 13.6 - - + +
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Residues in contact with PRO 198 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196U LEU* 3.1 29.6 - - + +
197U GLU* 1.3 86.9 - - - +
199U SER* 1.3 58.6 + - - +
201U GLU* 3.5 7.3 + - + +
202U GLU* 3.1 27.3 + - - +
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Residues in contact with SER 199 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197U GLU* 3.3 1.2 + - - -
198U PRO* 1.3 77.7 - - - +
200U VAL* 1.3 63.4 + - - +
202U GLU* 3.3 12.6 + - - +
203U ALA* 2.9 29.8 + - - +
34V GLU* 4.9 1.4 - - - +
38V ALA* 3.8 16.3 + - - +
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Residues in contact with VAL 200 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197U GLU* 3.2 17.4 + - + +
199U SER* 1.3 75.2 + - - +
201U GLU* 1.3 65.6 + - - +
202U GLU 2.9 1.5 + - - -
203U ALA* 3.2 1.8 + - - +
204U ARG* 2.9 55.5 + - - +
35V GLU* 4.8 1.7 - - + +
38V ALA* 3.6 39.3 - - + +
39V ILE* 3.8 13.7 - - + +
42V ALA* 4.2 13.7 - - + -
77V GLU 4.5 1.8 - - - +
78V MET* 3.4 16.8 - - - +
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Residues in contact with GLU 201 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L TYR* 2.8 38.4 + - - -
37L GLN* 4.1 16.8 - - - +
40L GLN* 4.2 10.3 - - - +
41L LYS* 5.4 3.3 - - - +
44L ARG* 5.1 13.8 + - - +
196U LEU* 5.7 7.2 - - + -
197U GLU 2.9 17.9 + - - +
198U PRO* 3.8 9.0 - - + +
200U VAL* 1.3 76.5 - - - +
202U GLU* 1.3 58.8 + - - +
204U ARG* 3.8 12.1 + - - +
205U TYR* 3.1 26.4 + - + +
77V GLU* 5.8 0.8 - - - +
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Residues in contact with GLU 202 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198U PRO 3.1 17.7 + - - +
199U SER* 3.4 13.3 - - - +
200U VAL 2.9 1.4 - - - -
201U GLU* 1.3 75.3 - - - +
203U ALA* 1.3 67.0 + - - +
204U ARG 3.0 0.9 - - - -
205U TYR* 2.8 18.1 + - + +
206U ASN* 2.9 28.6 + - - +
34V GLU* 5.1 5.5 - - - +
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Residues in contact with ALA 203 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199U SER 2.9 19.5 + - - +
200U VAL 3.8 2.5 - - - +
202U GLU* 1.3 72.7 - - - +
204U ARG* 1.3 62.0 + - - +
206U ASN* 3.2 5.6 + - - +
207U SER* 3.0 20.8 + - - -
32V THR* 4.3 4.5 + - - -
34V GLU* 3.5 32.6 + - + +
35V GLU* 3.4 35.2 - - - +
38V ALA* 4.5 2.9 - - + -
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Residues in contact with ARG 204 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L TYR* 2.8 39.4 + - - +
40L GLN* 4.5 1.0 + - - -
200U VAL* 2.9 36.2 + - - +
201U GLU* 3.8 15.7 + - - +
203U ALA* 1.3 74.8 - - - +
205U TYR* 1.3 58.4 + - - +
207U SER* 2.7 32.8 + - - +
208U CYS* 3.7 7.2 - - - -
35V GLU* 2.8 60.2 + - - +
39V ILE* 4.2 0.6 - - - +
76V ASN 4.5 0.4 + - - -
77V GLU 3.0 27.7 + - - -
78V MET 3.3 16.0 + - - -
79V PHE* 3.5 22.4 - - - +
80V GLY* 3.5 7.9 - - - +
82V ASN* 5.0 2.0 - - - +
116V LYS* 3.8 11.9 - - - +
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Residues in contact with TYR 205 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L ALA* 3.3 38.5 - - + +
34L GLU* 4.2 11.8 + - - +
36L TYR* 4.5 9.9 - + - -
37L GLN* 3.1 41.7 + - + -
201U GLU* 3.1 15.2 + - + +
202U GLU* 2.8 14.8 + - + +
204U ARG* 1.3 76.2 - - - +
206U ASN* 1.3 68.9 + - - +
207U SER 3.5 0.5 + - - -
208U CYS* 3.8 14.6 + - - +
209U ARG* 2.6 36.4 + - - -
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Residues in contact with ASN 206 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202U GLU* 2.9 37.6 + - - +
203U ALA 3.5 6.7 - - - +
204U ARG 3.0 0.2 - - - -
205U TYR* 1.3 83.0 - - - +
207U SER* 1.3 60.2 + - - +
208U CYS 3.3 1.7 + - - -
209U ARG* 3.6 41.1 + - - +
32V THR* 5.2 1.3 - - - +
34V GLU* 3.8 24.3 + - - +
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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