Contacts of the helix formed by residues 197 - 208 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192M LYS* 2.7 36.6 + - - +
195M ASP 3.3 4.6 + - - +
196M LEU* 1.3 73.5 - - - +
198M PRO* 1.3 65.8 - - - +
199M SER* 3.4 11.0 + - - -
200M VAL* 3.2 17.2 + - + +
201M GLU* 2.9 29.9 + - - +
42N ALA* 3.7 21.9 - - + +
45N GLN* 3.0 23.5 + - - +
77N GLU* 4.6 10.9 + - - +
78N MET* 4.0 21.3 - - + -
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Residues in contact with PRO 198 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194M GLN* 5.5 4.9 - - - +
196M LEU* 3.5 23.1 - - + +
197M GLU* 1.3 90.9 - - - +
199M SER* 1.3 62.8 + - - +
201M GLU* 3.8 6.0 - - + +
202M GLU* 3.0 41.8 + - - +
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Residues in contact with SER 199 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197M GLU* 4.1 13.2 + - - -
198M PRO* 1.3 78.3 - - - +
200M VAL* 1.3 64.6 + - - +
202M GLU* 3.6 11.3 + - - +
203M ALA* 3.0 26.9 + - - +
34N GLU* 5.3 0.7 - - - +
38N ALA* 4.0 13.3 + - - +
42N ALA* 5.5 1.0 - - - +
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Residues in contact with VAL 200 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197M GLU* 3.2 15.6 + - + +
199M SER* 1.3 81.5 + - - +
201M GLU* 1.3 60.3 + - - +
202M GLU 3.1 0.2 - - - -
203M ALA* 3.0 3.5 + - - +
204M ARG* 2.9 46.9 + - - +
35N GLU* 4.8 1.5 - - + +
38N ALA* 3.6 38.4 - - + +
39N ILE* 3.7 15.9 - - + +
42N ALA* 4.0 14.1 - - + -
77N GLU 4.4 1.6 - - - +
78N MET* 3.3 28.3 - - - +
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Residues in contact with GLU 201 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196M LEU* 5.3 8.2 - - + +
197M GLU 2.9 16.4 + - - +
198M PRO* 3.8 8.3 - - + +
200M VAL* 1.3 75.9 - - - +
202M GLU* 1.3 59.0 + - + +
204M ARG* 3.3 25.6 + - - +
205M TYR* 2.9 28.6 + - - +
77N GLU* 3.5 25.1 - - - +
36O TYR* 2.6 34.0 + - - -
40O GLN* 3.6 10.2 - - - +
44O ARG* 3.9 16.1 + - - +
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Residues in contact with GLU 202 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198M PRO* 3.0 30.3 + - + +
199M SER* 3.7 11.1 - - - +
201M GLU* 1.3 79.4 - - + +
203M ALA* 1.3 57.3 + - - +
205M TYR* 3.1 7.8 + - - +
206M ASN* 2.9 42.8 + - - +
34N GLU* 5.5 1.1 - - - +
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Residues in contact with ALA 203 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199M SER 3.0 13.9 + - - +
200M VAL 3.0 8.5 + - - +
202M GLU* 1.3 76.6 - - - +
204M ARG* 1.3 62.3 + - - +
206M ASN* 3.4 2.4 + - - +
207M SER* 3.1 22.5 + - - -
32N THR* 4.7 1.4 + - - -
34N GLU* 3.7 33.4 + - + +
35N GLU* 3.6 30.4 - - - +
38N ALA* 4.2 4.9 - - + -
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Residues in contact with ARG 204 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200M VAL* 2.9 25.4 + - - +
201M GLU* 3.4 25.8 + - - +
203M ALA* 1.3 72.5 - - - +
205M TYR* 1.3 70.0 + - - +
207M SER* 2.5 25.9 + - - +
208M CYS* 3.1 11.0 + - - +
35N GLU* 2.7 46.6 + - - +
39N ILE* 4.2 0.8 - - - +
77N GLU 2.9 28.1 + - - -
78N MET 3.2 16.6 + - - -
79N PHE* 3.4 22.5 + - - +
80N GLY* 3.4 9.7 - - - +
82N ASN* 5.2 1.6 - - - +
116N LYS* 4.2 10.5 - - - +
36O TYR* 2.9 36.3 + - + +
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Residues in contact with TYR 205 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201M GLU 2.9 14.7 + - - +
202M GLU* 3.4 10.3 - - - +
204M ARG* 1.3 81.6 - - - +
206M ASN* 1.3 69.3 + - - +
207M SER 2.9 3.8 + - - -
208M CYS* 3.1 17.6 + - - +
209M ARG* 3.6 36.1 + - - +
33O ALA* 4.6 20.9 - - + +
34O GLU* 5.9 0.9 - - - -
36O TYR* 5.3 9.3 - + + -
37O GLN* 3.0 41.8 + - + -
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Residues in contact with ASN 206 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202M GLU* 2.9 31.7 + - - +
203M ALA 3.8 1.6 - - - +
204M ARG 3.3 0.4 - - - -
205M TYR* 1.3 81.2 - - - +
207M SER* 1.3 57.6 + - - +
209M ARG* 3.4 38.0 + - - +
34N GLU* 3.7 32.1 + - - +
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Residues in contact with SER 207 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203M ALA 3.1 11.5 + - - -
204M ARG* 2.5 25.1 + - - +
206M ASN* 1.3 76.0 - - - +
208M CYS* 1.3 58.2 + - - +
209M ARG 2.7 28.8 + - - +
32N THR* 3.6 38.2 - - - +
35N GLU* 4.0 7.9 + - - -
116N LYS* 5.2 3.1 + - - -
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Residues in contact with CYS 208 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204M ARG* 3.1 9.6 + - - -
205M TYR* 3.1 10.9 + - - +
207M SER* 1.3 79.9 + - - +
209M ARG* 1.3 59.1 + - - +
116N LYS* 6.2 1.8 - - - -
30O GLN* 6.0 1.8 - - - -
31O TYR 4.7 7.4 - - - -
33O ALA* 3.3 46.0 + - + +
36O TYR* 4.4 22.4 - - - -
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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