Contacts of the helix formed by residues 1194 - 1199 (chain M) in PDB entry 6G0L
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 SER1194 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1024M LYS* 2.6 40.7 + - - +
1190M TYR* 4.0 17.9 + - - +
1191M GLY 3.7 10.6 + - - -
1192M TYR 3.2 1.8 + - - -
1193M GLY* 1.3 74.0 - - - +
1195M TRP* 1.3 62.2 - - - +
1196M THR* 3.2 5.8 + - - +
1197M GLN* 3.6 20.9 + - - +
1198M ILE* 3.3 21.8 + - - +
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Residues in contact with TRP1195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I T 5.6 2.5 - - - -
1183M LEU* 4.1 17.7 - - + -
1192M TYR* 5.3 4.3 - + - -
1193M GLY* 3.1 32.0 + - - +
1194M SER* 1.3 73.4 - - - +
1196M THR* 1.3 65.3 + - + +
1197M GLN 3.2 2.1 + - - -
1198M ILE* 3.8 28.4 - - + +
1199M ARG* 3.3 28.8 + - - +
1210M ILE* 4.1 31.9 - - + +
1249M GLY 5.4 1.1 - - - -
1250M ALA* 3.4 32.8 + - + -
1253M LEU* 3.6 27.1 - - + -
1254M GLY* 3.4 30.5 - - - -
1257M VAL* 3.8 20.4 - - + -
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Residues in contact with THR1196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193M GLY 6.1 0.2 - - - +
1194M SER* 4.5 2.3 - - - -
1195M TRP* 1.3 79.8 - - + +
1197M GLN* 1.3 87.6 + - - +
1199M ARG* 3.9 9.1 - - - +
1200M ASP* 3.0 27.0 - - - +
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Residues in contact with GLN1197 (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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1190M TYR* 3.6 49.2 + - + +
1194M SER* 3.6 19.3 + - - +
1195M TRP 3.2 0.2 - - - -
1196M THR* 1.3 108.7 + - - +
1198M ILE* 1.3 63.8 + - - +
1199M ARG 3.4 0.4 - - - -
1200M ASP* 3.5 7.0 + - - +
1201M ASP* 3.2 23.2 + - - +
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Residues in contact with ILE1198 (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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1183M LEU* 4.8 6.7 - - + +
1186M GLY* 4.3 31.0 - - - +
1187M VAL* 4.7 8.3 - - + +
1190M TYR* 5.1 4.5 - - + -
1191M GLY 4.8 6.3 - - - +
1193M GLY 6.2 0.2 - - - +
1194M SER 3.3 21.8 - - - +
1195M TRP* 3.6 37.3 + - + +
1197M GLN* 1.3 78.3 - - - +
1199M ARG* 1.3 62.4 + - - +
1201M ASP* 3.3 20.8 + - - +
1204M LEU* 3.8 14.6 - - + +
1206M ILE* 3.8 29.6 - - + +
1210M ILE* 3.8 7.6 - - + -
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Residues in contact with ARG1199 (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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295M ARG* 2.5 65.9 + - - +
303M SER* 4.3 6.3 + - - -
1195M TRP* 3.3 18.7 + - - +
1196M THR* 3.9 12.6 - - - +
1198M ILE* 1.3 77.9 - - - +
1200M ASP* 1.3 66.9 + - - +
1201M ASP 3.4 1.8 + - - +
1206M ILE 4.5 4.9 - - - +
1207M THR* 4.4 14.5 + - - +
1210M ILE* 3.7 52.4 + - + +
1211M PHE* 5.1 10.3 - - - +
1212M LEU* 6.1 5.4 - - - +
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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