Contacts of the helix formed by residues 1194 - 1200 (chain W) 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 TRP1194 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1186W VAL* 5.0 7.9 - - - +
1191W TYR* 3.6 33.8 - + - -
1192W GLY* 3.2 51.1 + - - +
1193W SER* 1.3 71.0 + - - +
1195W THR* 1.3 62.9 + - - +
1196W GLN 3.3 1.6 - - - -
1197W ILE* 3.7 25.4 - - + +
1198W ARG* 2.9 28.6 + - - +
1209W ILE* 4.4 3.6 - - + +
1211W LEU* 3.7 23.2 - - + +
1249W ALA* 3.8 38.6 - - + -
1250W ILE* 6.5 0.2 - - + -
1252W LEU* 3.4 37.0 - - + +
1253W GLY* 4.1 6.1 - - - -
1256W VAL* 6.3 0.2 - - - +
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Residues in contact with THR1195 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295W ARG* 3.7 29.0 + - - +
1193W SER* 5.0 3.4 - - - +
1194W TRP* 1.3 72.4 - - - +
1196W GLN* 1.3 79.0 + - + +
1198W ARG* 4.1 7.4 + - - +
1199W ASP* 2.9 34.6 + - - +
1211W LEU* 3.7 15.5 - - - +
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Residues in contact with GLN1196 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023W LYS* 5.0 1.8 + - - -
1189W TYR* 3.5 52.2 - - + +
1193W SER* 2.9 35.4 + - - +
1194W TRP 4.5 0.2 - - - +
1195W THR* 1.3 87.9 - - + +
1197W ILE* 1.3 60.3 + - - +
1199W ASP* 4.1 3.6 - - - +
1200W ASP* 3.3 17.0 + - - +
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Residues in contact with ILE1197 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1181W LYS 5.9 0.2 - - - -
1182W LEU* 4.6 17.5 - - + +
1185W GLY* 3.4 28.5 - - - +
1186W VAL* 3.6 17.7 - - + +
1189W TYR* 3.6 20.9 - - + -
1190W GLY 4.4 2.5 - - - +
1193W SER 3.6 18.2 - - - +
1194W TRP* 3.5 24.5 + - + +
1195W THR 3.2 0.4 - - - -
1196W GLN* 1.3 76.3 - - - +
1198W ARG* 1.3 66.7 + - - +
1199W ASP 3.5 0.2 + - - -
1200W ASP 3.5 5.9 + - - -
1203W LEU* 3.0 38.7 - - + +
1205W ILE* 3.5 12.7 - - + +
1209W ILE* 4.9 4.7 - - + -
1252W LEU* 5.8 0.2 - - + -
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Residues in contact with ARG1198 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295W ARG* 2.4 49.3 - - - +
302W THR* 5.5 0.2 + - - -
303W SER* 2.7 24.8 + - - -
304W GLN* 4.5 0.6 - - - +
1194W TRP 2.9 16.2 + - - +
1195W THR* 3.2 9.9 + - - +
1197W ILE* 1.3 78.7 - - - +
1199W ASP* 1.3 75.1 + - - +
1200W ASP 3.5 2.1 + - - +
1205W ILE* 3.7 3.0 - - - +
1206W THR* 3.1 65.7 + - - +
1209W ILE* 3.2 56.1 - - + -
1211W LEU* 5.2 5.3 - - - +
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Residues in contact with ASP1199 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295W ARG* 4.4 6.5 - - - +
305W LEU* 3.2 57.9 + - + +
324W ALA* 4.5 5.9 - - - +
1195W THR* 2.9 24.8 + - - +
1196W GLN* 4.1 3.8 - - - +
1198W ARG* 1.3 104.1 + - - +
1200W ASP* 1.3 70.9 + - - +
1201W PRO* 3.1 6.3 - - - +
1206W THR* 4.9 6.6 + - - -
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Residues in contact with ASP1200 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305W LEU* 5.8 0.4 - - - -
1188W LYS* 2.9 26.3 + - - -
1189W TYR* 3.0 23.4 + - + +
1196W GLN 3.3 16.1 + - - +
1197W ILE 3.7 8.7 - - - +
1198W ARG 3.4 4.8 - - - +
1199W ASP* 1.3 79.8 - - - +
1201W PRO* 1.3 81.7 - - - +
1202W PHE* 3.4 16.7 - - - +
1203W LEU* 3.3 28.2 + - + +
1204W GLY* 3.9 8.1 + - - -
1206W THR* 5.4 2.1 - - - +
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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