Contacts of the helix formed by residues 197 - 206 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192S LYS* 2.8 40.3 + - - +
195S ASP 3.4 4.7 + - - +
196S LEU* 1.3 79.7 - - - +
198S PRO* 1.3 55.4 - - - +
199S SER* 3.6 6.3 + - - -
200S VAL* 3.2 17.5 + - + +
201S GLU* 2.8 34.0 + - - +
42T ALA* 3.5 25.8 - - + +
45T GLN* 3.3 21.7 + - - +
77T GLU 4.5 14.5 + - - +
78T MET* 4.5 8.7 - - + -
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Residues in contact with PRO 198 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194S GLN* 5.8 0.9 - - - +
196S LEU* 3.4 29.4 - - + +
197S GLU* 1.3 83.3 - - - +
199S SER* 1.3 67.7 + - - +
201S GLU* 3.1 8.5 + - + +
202S GLU* 3.0 26.3 + - - +
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Residues in contact with SER 199 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197S GLU* 5.0 5.7 + - - -
198S PRO* 1.3 78.3 - - - +
200S VAL* 1.3 66.1 + - - +
202S GLU* 3.1 22.5 + - - +
203S ALA* 3.2 14.0 + - - +
34T GLU* 5.2 0.5 - - - +
38T ALA* 4.1 12.5 - - - +
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Residues in contact with VAL 200 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197S GLU* 3.2 19.8 + - + +
199S SER* 1.3 80.8 + - - +
201S GLU* 1.3 61.8 + - - +
203S ALA* 3.5 2.3 + - - +
204S ARG* 3.1 39.6 + - - +
35T GLU* 4.8 1.4 - - + +
38T ALA* 3.5 39.0 - - + +
39T ILE* 3.9 11.7 - - + +
42T ALA* 3.9 17.5 - - + -
77T GLU 4.4 2.5 - - - +
78T MET* 3.4 28.0 - - - +
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Residues in contact with GLU 201 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196S LEU* 5.0 9.4 - - + +
197S GLU 2.8 17.2 + - - +
198S PRO* 3.1 9.8 + - + +
200S VAL* 1.3 79.1 - - - +
202S GLU* 1.3 56.9 + - - +
204S ARG* 3.4 14.6 + - - +
205S TYR* 2.8 30.7 + - + +
77T GLU* 5.3 1.6 - - - +
36U TYR* 3.2 32.0 + - - -
37U GLN* 4.7 11.4 - - - +
40U GLN* 4.4 11.2 - - - +
41U LYS* 5.5 2.8 - - - +
44U ARG* 4.7 15.7 + - - +
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Residues in contact with GLU 202 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198S PRO 3.0 17.5 + - - +
199S SER* 3.1 13.7 + - - +
201S GLU* 1.3 70.6 - - - +
203S ALA* 1.3 62.1 + - - +
204S ARG 2.9 1.6 - - - -
205S TYR* 2.8 7.5 + - - +
206S ASN* 2.5 52.8 + - - +
34T GLU* 4.4 7.5 - - - +
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Residues in contact with ALA 203 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199S SER 3.2 12.2 + - - +
200S VAL 3.9 2.9 - - - +
202S GLU* 1.3 81.0 - - - +
204S ARG* 1.3 61.7 + - - +
206S ASN* 3.3 3.6 + - - +
207S SER* 3.2 21.0 + - - -
32T THR* 4.5 2.6 + - - -
34T GLU* 3.4 31.3 + - + +
35T GLU* 3.2 39.5 - - - +
38T ALA* 4.4 3.6 - - + -
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Residues in contact with ARG 204 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197S GLU 5.6 0.2 + - - -
200S VAL* 3.1 28.1 + - - +
201S GLU* 3.5 17.4 + - - +
202S GLU 2.9 0.6 - - - -
203S ALA* 1.3 75.1 - - - +
205S TYR* 1.3 65.6 + - - +
207S SER* 2.5 23.3 + - - +
208S CYS* 3.8 9.1 + - - -
35T GLU* 2.7 46.8 + - - +
39T ILE* 4.3 0.4 - - - +
76T ASN 4.6 0.2 + - - -
77T GLU 3.1 25.9 + - - -
78T MET 3.4 18.6 + - - -
79T PHE* 3.7 20.2 - - - +
80T GLY* 3.7 7.7 - - - +
82T ASN* 5.0 1.3 - - - +
116T LYS* 4.1 10.3 - - - +
36U TYR* 2.6 43.3 + - + +
40U GLN* 4.7 1.2 + - - -
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Residues in contact with TYR 205 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201S GLU* 2.8 23.6 + - + +
202S GLU* 2.8 12.2 + - - +
204S ARG* 1.3 72.2 - - - +
206S ASN* 1.3 62.4 + - - +
207S SER 2.9 6.2 + - - -
208S CYS* 3.3 13.4 + - - +
209S ARG* 3.2 52.3 + - - -
33U ALA* 3.7 23.4 - - + +
34U GLU* 4.9 6.5 + - - +
36U TYR* 4.8 10.9 - + - -
37U GLN* 2.8 52.0 + - + -
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Residues in contact with ASN 206 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202S GLU* 2.5 44.3 + - - +
203S ALA 3.5 5.2 - - - +
205S TYR* 1.3 73.5 - - - +
207S SER* 1.3 57.1 + - - +
208S CYS 3.7 0.2 - - - -
209S ARG* 4.1 37.0 + - - +
32T THR* 5.6 0.5 - - - +
34T GLU* 3.7 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