Contacts of the helix formed by residues 1194 - 1199 (chain O) in PDB entry 6IY3
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 GLN1194 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1006O LYS* 5.1 3.2 - - - +
1008O GLU* 5.2 11.1 - - - +
1178O VAL* 4.8 4.4 - - - +
1180O ILE* 4.5 10.7 - - - +
1189O GLN 4.5 0.4 - - - +
1190O ASP* 2.9 44.5 + - - +
1191O LEU* 6.1 0.4 - - + -
1193O ALA* 1.3 79.8 - - - +
1195O ASP* 1.3 56.2 + - - +
1196O ARG 3.2 0.4 - - - -
1197O ALA* 3.2 8.3 + - - +
1198O HIS* 3.0 48.4 + - + +
1206O VAL* 5.5 0.5 - - - +
1208O ILE* 3.3 54.5 - - - +
1210O ARG* 5.2 7.4 + - - +
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Residues in contact with ASP1195 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794O MET* 4.5 26.7 - - + +
996O LYS* 4.5 7.5 + - - -
1168O LEU* 6.1 2.9 - - + -
1190O ASP 4.6 0.2 - - - -
1191O LEU* 2.9 41.2 - - - +
1192O GLN* 3.0 10.3 + - - +
1194O GLN* 1.3 73.2 - - - +
1196O ARG* 1.3 63.6 + - - +
1197O ALA 3.1 2.4 + - - -
1198O HIS* 3.6 25.5 + - + +
1199O ARG* 3.5 25.5 + - + +
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Residues in contact with ARG1196 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107O LEU* 4.3 11.4 - - + -
1109O PHE* 4.6 9.9 - - + -
1161O LEU* 4.6 10.9 - - - +
1162O SER 5.3 1.0 + - - -
1163O THR 4.8 4.0 + - - -
1165O ALA 3.4 26.1 + - - -
1166O GLY* 4.6 1.6 - - - -
1167O GLY 4.2 0.8 - - - +
1168O LEU* 3.6 34.2 - - - +
1170O LEU* 3.6 50.3 - - + +
1171O ASN 4.9 3.8 - - - +
1172O LEU* 2.8 36.4 - - - +
1192O GLN* 2.9 40.5 + - - +
1193O ALA* 3.8 17.0 - - - +
1194O GLN 3.2 1.0 - - - -
1195O ASP* 1.3 78.1 - - - +
1197O ALA* 1.3 57.5 + - - +
1199O ARG* 5.1 1.6 - - - +
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Residues in contact with ALA1197 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003O LEU* 4.4 1.7 - - - +
1107O LEU* 4.7 12.1 - - + -
1172O LEU* 4.6 2.2 - - + -
1173O GLN* 5.1 5.2 - - - +
1175O ALA* 4.2 20.9 - - + +
1176O ASP* 5.6 0.7 - - - -
1178O VAL* 5.0 5.4 - - + -
1193O ALA 4.7 0.4 + - - -
1194O GLN 3.2 6.6 + - - +
1195O ASP 3.1 0.2 - - - -
1196O ARG* 1.3 80.5 - - - +
1198O HIS* 1.3 60.2 + - - +
1199O ARG* 3.2 8.6 + - - +
1202O GLN* 3.8 23.3 - - + +
1206O VAL* 4.2 26.5 - - + +
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Residues in contact with HIS1198 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996O LYS* 2.8 25.7 + - - +
1003O LEU* 3.4 27.9 - - + +
1005O ASP 4.4 4.7 - - - -
1006O LYS* 3.4 41.4 - - + +
1194O GLN* 3.0 53.1 + - + +
1195O ASP* 3.6 20.3 + - - +
1197O ALA* 1.3 76.7 - - - +
1199O ARG* 1.3 65.2 + - - +
1206O VAL* 4.0 19.1 - - + +
1208O ILE* 4.0 12.1 - - - +
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Residues in contact with ARG1199 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794O MET* 5.6 15.5 - - + +
795O GLY* 6.4 2.7 - - - -
996O LYS* 4.7 6.1 - - - +
1003O LEU* 4.6 9.0 - - - +
1171O ASN* 3.1 37.3 + - - +
1172O LEU 3.3 22.4 + - - +
1173O GLN* 3.2 26.4 + - + +
1195O ASP* 3.5 19.3 + - + +
1196O ARG* 4.5 2.5 - - - +
1197O ALA 3.2 6.3 - - - +
1198O HIS* 1.3 82.6 - - - +
1200O ILE* 1.3 102.9 + - + +
1201O GLY 3.5 1.7 + - - -
1202O GLN* 4.2 5.9 + - - +
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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