Contacts of the helix formed by residues 1175 - 1179 (chain M) in PDB entry 3F5P
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 PRO1175 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1135M ASP* 4.4 2.2 - - - +
1139M ARG* 3.0 31.2 - - - +
1173M LEU 3.4 5.1 - - - +
1174M LEU* 1.3 93.4 - - + +
1176M VAL* 1.3 65.5 + - - +
1177M ARG 3.2 1.1 + - - +
1178M TRP* 3.4 35.8 + - + +
1179M MET* 4.0 9.1 + - - +
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Residues in contact with VAL1176 (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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1174M LEU 4.2 7.4 - - - +
1175M PRO* 1.3 67.0 - - - +
1177M ARG* 1.3 62.2 + - + +
1178M TRP 2.9 10.8 + - - -
1179M MET* 3.0 31.0 + - - +
1184M LEU* 4.1 17.3 - - + +
1218M ASN* 4.1 42.4 - - + +
1221M VAL* 4.3 17.8 - - + +
1222M LEU* 4.2 22.4 - - + +
1225M VAL* 5.6 0.9 - - - +
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Residues in contact with ARG1177 (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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1175M PRO* 3.2 2.0 - - - +
1176M VAL* 1.3 77.6 - - + +
1178M TRP* 1.3 82.4 + - + +
1179M MET 3.6 1.1 - - - -
1196M TRP* 5.3 0.5 + - - -
1200M VAL* 4.1 13.0 - - - +
1211M GLN* 3.3 34.7 + - - +
1212M PRO* 3.2 18.7 + - + +
1213M TYR* 3.1 60.9 + - + -
1216M LEU 3.0 29.6 + - - -
1217M SER* 3.6 1.2 - - - +
1218M ASN* 2.8 37.8 + - - +
1221M VAL* 3.8 14.4 - - + +
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Residues in contact with TRP1178 (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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1088M LYS* 5.3 10.8 - - - -
1134M ARG 5.7 1.7 - - - +
1135M ASP 6.0 2.0 - - - +
1136M LEU 3.5 14.6 - - - +
1137M ALA* 3.3 26.8 - - + +
1139M ARG* 4.2 15.0 - - - +
1175M PRO* 3.4 30.9 + - + +
1176M VAL 3.0 0.8 - - - -
1177M ARG* 1.3 99.8 - - + +
1179M MET* 1.3 63.5 + - - +
1196M TRP* 3.6 9.7 - - - -
1197M SER* 2.9 30.4 + - - +
1200M VAL* 3.3 28.7 - - + +
1204M GLU* 2.6 40.9 + - - -
1211M GLN* 5.5 3.1 - - + -
1212M PRO* 3.7 22.9 - - + -
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Residues in contact with MET1179 (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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1134M ARG 5.7 2.0 - - - +
1174M LEU* 4.3 24.7 - - + +
1175M PRO 4.0 6.1 - - - +
1176M VAL* 3.0 24.9 + - - +
1177M ARG 5.1 0.7 - - - -
1178M TRP* 1.3 79.5 - - - +
1180M SER* 1.3 64.2 + - - +
1181M PRO 3.9 0.2 - - - -
1183M SER* 3.6 33.4 - - - +
1184M LEU* 3.4 38.5 - - + +
1187M GLY* 5.6 0.7 - - - -
1189M PHE* 3.9 26.2 - - + -
1196M TRP* 3.2 13.2 + - - -
1197M SER* 5.0 0.2 - - - -
1213M TYR* 5.6 0.2 + - - -
1225M VAL* 4.2 4.9 - - - +
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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