Contacts of the helix formed by residues 197 - 208 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192R LYS* 2.8 30.6 + - - +
195R ASP 3.6 8.3 + - - +
196R LEU* 1.3 81.7 - - - +
198R PRO* 1.3 64.8 - - - +
199R SER* 3.3 9.5 + - - -
200R VAL* 3.1 18.9 + - + +
201R GLU* 2.9 26.4 + - - +
42S ALA* 3.5 22.7 - - + +
45S GLN* 3.1 20.9 + - - +
77S GLU* 4.6 9.9 + - - +
78S MET* 4.3 15.5 - - + -
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Residues in contact with PRO 198 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196R LEU* 3.1 28.7 - - + +
197R GLU* 1.3 85.9 - - - +
199R SER* 1.3 58.7 + - - +
201R GLU* 3.5 6.2 + - + +
202R GLU* 3.1 26.7 + - - +
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Residues in contact with SER 199 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197R GLU* 4.4 9.7 + - - -
198R PRO* 1.3 75.0 - - - +
200R VAL* 1.3 72.4 + - - +
202R GLU* 3.1 12.2 + - - +
203R ALA* 2.9 29.5 + - - +
34S GLU* 5.2 0.5 - - - +
38S ALA* 4.2 12.3 + - - +
42S ALA* 5.7 0.5 - - - +
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Residues in contact with VAL 200 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197R GLU* 3.1 21.9 + - + +
199R SER* 1.3 83.7 + - - +
201R GLU* 1.3 62.6 + - - +
203R ALA* 3.3 2.9 + - - +
204R ARG* 2.8 56.7 + - - +
35S GLU* 4.9 1.1 - - + +
38S ALA* 3.6 38.1 - - + +
39S ILE* 3.9 12.8 - - + +
42S ALA* 4.1 10.1 - - + -
77S GLU 4.2 3.8 - - - +
78S MET* 3.4 14.4 - - - +
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Residues in contact with GLU 201 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196R LEU* 5.4 9.4 - - + -
197R GLU 2.9 15.6 + - - +
198R PRO* 3.8 9.6 - - + +
200R VAL* 1.3 78.3 - - - +
202R GLU* 1.3 56.8 + - - +
204R ARG* 3.5 13.3 + - - -
205R TYR* 3.1 30.0 + - + +
77S GLU* 4.9 4.4 - - - +
36T TYR* 2.9 39.2 + - - -
37T GLN* 4.8 9.4 - - - +
40T GLN* 3.9 16.4 - - - +
41T LYS* 6.0 2.3 - - - +
44T ARG* 5.0 13.8 + - - +
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Residues in contact with GLU 202 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198R PRO 3.1 13.2 + - - +
199R SER* 3.3 13.7 - - - +
200R VAL 3.0 0.6 - - - -
201R GLU* 1.3 74.2 - - - +
203R ALA* 1.3 68.6 + - - +
204R ARG 3.0 2.4 + - - -
205R TYR* 3.3 4.4 + - - +
206R ASN* 3.1 42.7 + - - +
34S GLU* 4.9 8.7 - - - +
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Residues in contact with ALA 203 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199R SER 2.9 15.1 + - - +
200R VAL 3.8 3.4 - - - +
202R GLU* 1.3 75.3 - - - +
204R ARG* 1.3 61.7 + - - +
206R ASN* 3.5 2.8 + - - +
207R SER* 3.2 21.0 + - - -
32S THR* 4.4 2.9 + - - -
34S GLU* 3.5 30.1 + - + +
35S GLU* 3.3 38.0 - - - +
38S ALA* 4.3 5.6 - - + -
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Residues in contact with ARG 204 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200R VAL* 2.8 34.7 + - - +
201R GLU* 3.5 13.3 + - - +
203R ALA* 1.3 74.4 - - - +
205R TYR* 1.3 61.7 + - - +
207R SER* 2.6 30.8 + - - +
208R CYS* 3.6 6.2 + - - -
35S GLU* 2.7 55.5 + - - +
39S ILE* 4.1 1.2 - - - +
76S ASN 4.5 0.2 + - - -
77S GLU 2.9 28.7 + - - -
78S MET 3.1 22.6 + - - -
79S PHE* 3.4 21.6 + - - +
80S GLY* 3.5 7.1 - - - +
82S ASN* 5.0 1.6 - - - +
116S LYS* 4.1 9.4 - - - +
36T TYR* 2.8 41.8 + - + +
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Residues in contact with TYR 205 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201R GLU* 3.1 18.4 + - + +
202R GLU* 3.3 3.8 + - - +
204R ARG* 1.3 77.7 - - - +
206R ASN* 1.3 71.3 - - - +
207R SER 3.3 0.7 + - - -
208R CYS* 3.4 17.4 + - - +
209R ARG* 3.3 39.0 + - - +
33T ALA* 3.2 44.4 - - + +
34T GLU* 4.3 8.7 - - - +
36T TYR* 4.5 12.5 - + + -
37T GLN* 3.1 36.2 + - + -
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Residues in contact with ASN 206 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202R GLU* 3.1 41.3 + - - +
203R ALA 3.8 4.5 - - - +
205R TYR* 1.3 83.7 - - - +
207R SER* 1.3 60.8 + - - +
208R CYS 3.3 0.4 - - - -
209R ARG* 3.4 48.3 + - - +
34S GLU* 4.1 20.3 + - - +
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Residues in contact with SER 207 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203R ALA 3.2 11.8 + - - -
204R ARG* 2.6 17.8 + - - +
206R ASN* 1.3 74.7 - - - +
208R CYS* 1.3 64.1 + - - +
209R ARG 3.0 12.9 + - - -
32S THR* 4.0 28.6 - - - +
35S GLU* 3.8 18.1 + - - -
116S LYS* 4.3 8.5 + - - -
30T GLN* 5.4 2.1 - - - +
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Residues in contact with CYS 208 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204R ARG* 3.9 10.1 - - - -
205R TYR 3.4 3.6 + - - +
206R ASN 3.3 0.8 - - - -
207R SER* 1.3 88.3 + - - +
209R ARG* 1.3 59.9 + - - +
30T GLN* 5.3 8.1 - - - +
31T TYR* 4.4 9.6 - - - +
32T THR* 4.2 1.9 - - - -
33T ALA* 3.3 44.2 + - + +
36T TYR* 4.3 23.6 - - - -
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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