Contacts of the helix formed by residues 197 - 206 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192C LYS* 2.7 38.0 + - - +
195C ASP 3.5 2.6 + - - +
196C LEU* 1.3 78.3 - - - +
198C PRO* 1.3 65.7 - - - +
199C SER* 3.5 8.4 + - - -
200C VAL* 3.0 26.8 + - + +
201C GLU* 2.9 26.6 + - - +
204C ARG* 5.6 0.2 + - - -
42D ALA* 3.6 20.4 - - - +
45D GLN* 3.4 16.6 + - - +
77D GLU* 4.5 12.1 + - - +
78D MET* 4.1 16.4 - - + -
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Residues in contact with PRO 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C GLN* 5.2 4.5 - - - +
196C LEU* 3.4 29.4 - - + +
197C GLU* 1.3 87.1 - - - +
199C SER* 1.3 67.3 + - - +
201C GLU* 3.0 15.8 + - + +
202C GLU* 3.0 16.1 + - - +
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Residues in contact with SER 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C GLU* 4.5 7.4 + - - -
198C PRO* 1.3 79.1 - - - +
200C VAL* 1.3 67.6 + - - +
202C GLU* 3.6 10.4 - - - +
203C ALA* 3.4 22.5 + - - +
34D GLU* 5.3 0.3 - - - +
38D ALA* 4.0 13.2 + - - +
42D ALA* 5.9 0.3 - - - +
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Residues in contact with VAL 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C GLU* 3.0 26.8 + - + +
198C PRO 3.0 0.6 - - - -
199C SER* 1.3 82.1 + - - +
201C GLU* 1.3 60.1 + - - +
202C GLU 3.3 0.2 + - - -
203C ALA* 3.5 3.1 + - - +
204C ARG* 2.9 61.5 + - - +
35D GLU* 4.8 1.6 - - + +
38D ALA* 3.9 34.1 - - + +
39D ILE* 4.0 11.4 - - + -
42D ALA* 3.9 12.6 - - + -
77D GLU 4.3 2.0 - - - +
78D MET* 3.3 12.8 - - - +
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Residues in contact with GLU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C LEU* 5.6 7.5 - - + +
197C GLU 2.9 16.5 + - - +
198C PRO* 3.0 10.1 + - + +
200C VAL* 1.3 70.8 - - - +
202C GLU* 1.3 70.1 + - - +
204C ARG* 3.4 16.9 + - - +
205C TYR* 2.9 25.6 + - + +
77D GLU* 4.6 6.5 - - - +
36E TYR* 2.7 43.6 + - - -
37E GLN* 5.4 4.9 - - + +
40E GLN* 3.6 16.6 - - - +
41E LYS* 6.5 0.7 - - - -
44E ARG* 4.7 13.1 + - - +
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Residues in contact with GLU 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C PRO 3.0 13.8 + - - +
199C SER* 3.6 13.5 - - - +
201C GLU* 1.3 73.5 - - - +
203C ALA* 1.3 67.3 + - - +
205C TYR* 2.7 22.4 + - - +
206C ASN* 2.9 28.4 + - - +
34D GLU* 4.9 6.1 - - - +
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Residues in contact with ALA 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C SER 3.4 13.3 + - - +
200C VAL 3.7 3.4 - - - +
202C GLU* 1.3 80.3 - - - +
204C ARG* 1.3 67.1 + - - +
206C ASN* 3.2 10.4 + - - +
207C SER* 3.5 10.6 + - - -
32D THR* 4.7 1.9 + - - -
34D GLU* 3.7 31.8 + - + +
35D GLU* 3.6 34.9 - - - +
38D ALA* 4.4 3.6 - - + -
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Residues in contact with ARG 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C VAL* 2.9 44.4 + - - +
201C GLU* 3.5 19.9 + - - +
202C GLU 2.8 3.6 + - - -
203C ALA* 1.3 71.5 - - - +
205C TYR* 1.3 54.2 + - - +
207C SER* 2.6 39.4 + - - +
208C CYS* 3.9 5.4 + - - -
35D GLU* 2.9 42.9 + - - +
39D ILE* 4.2 0.8 - - - +
76D ASN 4.4 0.4 + - - -
77D GLU 2.8 29.1 + - - -
78D MET 3.2 16.0 + - - -
79D PHE* 3.6 17.5 - - - +
80D GLY* 3.6 7.4 - - - +
82D ASN* 5.1 1.3 - - - +
116D LYS* 4.3 9.4 - - - +
36E TYR* 2.8 38.7 + - + -
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Residues in contact with TYR 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C GLU* 2.9 15.9 + - + +
202C GLU* 2.7 16.0 + - - +
204C ARG* 1.3 76.6 - - - +
206C ASN* 1.3 60.3 + - - -
207C SER 3.1 4.7 + - - -
208C CYS* 3.8 8.7 + - - +
209C ARG* 3.5 34.7 + - - -
33E ALA* 3.4 48.1 - - + +
34E GLU* 4.5 7.2 + - - +
36E TYR* 4.5 10.9 - + - -
37E GLN* 3.1 37.8 + - + -
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Residues in contact with ASN 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C GLU* 2.9 34.5 + - - +
203C ALA 3.7 6.1 - - - +
204C ARG 2.9 2.8 + - - -
205C TYR* 1.3 80.0 - - - +
207C SER* 1.3 58.2 + - - +
209C ARG* 3.4 44.8 + - - +
32D THR* 5.5 0.5 - - - +
34D GLU* 3.8 25.8 + - - +
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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