Contacts of the helix formed by residues 1189 - 1196 (chain A) in PDB entry 5IYB
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 ASP1189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1184A THR* 3.8 9.6 - - + +
1186A VAL* 2.7 43.7 + - - +
1188A GLU* 1.3 80.3 - - - +
1190A GLN* 1.3 64.2 + - - +
1191A GLU 3.1 0.9 - - - -
1192A TRP* 2.9 38.9 + - + +
1193A VAL* 3.6 8.6 + - + +
1211A LEU* 5.2 0.3 - - - +
1213A ARG* 4.1 19.3 + - - -
1256A VAL* 5.6 4.0 - - - +
1258A ARG* 3.4 31.5 + - + +
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Residues in contact with GLN1190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1181A PRO 3.9 3.8 - - - +
1182A GLN* 4.0 19.4 + - - +
1183A SER* 4.3 2.6 - - - +
1184A THR* 3.8 24.0 + - + +
1187A ALA* 3.1 20.9 + - - +
1188A GLU 3.1 1.4 - - - -
1189A ASP* 1.3 78.7 - - - +
1191A GLU* 1.3 62.4 + - - +
1193A VAL* 3.2 30.2 + - - +
1194A ASN* 3.3 9.7 + - - +
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Residues in contact with GLU1191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188A GLU 3.9 3.6 + - - +
1189A ASP 3.0 0.8 + - - -
1190A GLN* 1.3 76.5 - - - +
1192A TRP* 1.3 74.7 + - + +
1194A ASN* 3.1 11.4 + - + +
1195A VAL* 2.8 32.9 + - + +
199U LYS* 4.1 25.1 - - - +
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Residues in contact with TRP1192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188A GLU* 2.8 32.5 - - + -
1189A ASP* 2.9 31.0 + - + +
1191A GLU* 1.3 79.7 - - + +
1193A VAL* 1.3 55.8 + - + +
1195A VAL* 3.6 9.4 - - + -
1196A TYR* 2.3 56.3 + + + +
1246A ILE* 5.5 4.9 - - + -
1247A PHE 3.9 21.3 - - - -
1248A ASN* 3.2 26.0 - - + +
1249A ASP 5.0 0.2 - - - +
1252A ALA* 5.7 5.4 - - + -
1254A LYS* 5.4 4.9 - - + -
1256A VAL* 3.6 26.1 + - + +
1258A ARG* 5.2 16.3 - - + +
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Residues in contact with VAL1193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1181A PRO* 3.4 32.5 - - + +
1182A GLN* 3.2 50.7 - - + +
1184A THR* 4.8 2.5 - - + -
1189A ASP* 4.0 10.3 - - + +
1190A GLN* 3.2 22.4 + - - +
1192A TRP* 1.3 77.5 - - + +
1194A ASN* 1.3 62.4 + - - +
1196A TYR* 4.1 4.7 - - - +
1197A TYR* 3.2 23.9 + - - +
1258A ARG* 4.8 7.9 - - - +
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Residues in contact with ASN1194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190A GLN* 3.3 6.3 + - - +
1191A GLU* 3.1 15.7 + - + +
1193A VAL* 1.3 77.8 - - - +
1195A VAL* 1.3 58.0 + - - +
1197A TYR* 2.9 34.5 - - - -
199U LYS* 4.5 15.1 + - - +
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Residues in contact with VAL1195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1191A GLU* 2.8 22.9 + - + +
1192A TRP* 3.1 16.8 - - + +
1194A ASN* 1.3 77.9 - - - +
1196A TYR* 1.3 70.1 + - + +
1197A TYR* 5.1 0.2 - - - -
1198A GLU* 3.1 22.9 - - - +
147U MET* 5.5 1.0 - - - +
192U ARG* 3.4 34.8 - - + +
195U ILE* 5.9 4.7 - - + -
196U SER* 5.3 12.1 - - - -
199U LYS* 3.6 23.3 - - + +
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Residues in contact with TYR1196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1182A GLN* 5.2 2.9 + - - -
1192A TRP* 2.3 55.9 + + + +
1193A VAL* 3.3 7.8 + - - +
1195A VAL* 1.3 84.1 - - + +
1197A TYR* 1.3 59.5 + - - +
1198A GLU* 3.4 3.1 - - - -
1199A MET* 3.9 28.3 + - + +
1204A VAL* 5.7 4.5 - - - +
1246A ILE* 3.7 42.4 - - + -
1247A PHE* 2.1 55.4 + + - -
1248A ASN* 5.0 0.9 - - - -
189U ASN* 5.3 0.2 - - - -
192U ARG* 3.7 32.5 + - - -
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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