Contacts of the helix formed by residues 1175 - 1179 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1135T ASP* 4.4 3.8 - - - +
1139T ARG* 3.2 31.9 - - - +
1173T LEU 3.4 6.7 - - - +
1174T LEU* 1.3 90.7 - - + +
1176T VAL* 1.3 65.0 + - - +
1177T ARG* 3.2 4.1 + - + +
1178T TRP* 3.4 33.9 + - + +
1179T MET* 3.7 10.3 - - - +
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Residues in contact with VAL1176 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1174T LEU 4.0 7.9 - - - +
1175T PRO* 1.3 71.4 - - - +
1177T ARG* 1.3 70.8 + - + +
1178T TRP 3.1 0.9 - - - -
1179T MET* 3.0 34.3 + - - +
1184T LEU* 4.0 18.0 - - + +
1213T TYR* 5.4 0.2 - - - -
1218T ASN* 4.3 33.9 - - + +
1221T VAL* 4.2 16.9 - - + +
1222T LEU* 4.0 21.1 - - + -
1225T VAL* 5.7 1.2 - - - +
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Residues in contact with ARG1177 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1175T PRO* 3.2 3.2 - - + -
1176T VAL* 1.3 82.9 - - + +
1178T TRP* 1.3 79.8 + - + +
1179T MET 5.1 0.6 - - - +
1196T TRP* 5.1 0.9 + - - -
1200T VAL* 3.9 15.9 - - - +
1211T GLN* 3.3 35.7 + - - +
1212T PRO* 2.8 35.3 + - + -
1213T TYR* 3.0 46.5 + - + +
1214T GLN* 4.4 0.8 - - - +
1216T LEU 2.7 22.8 + - - -
1217T SER* 3.5 1.6 - - - +
1218T ASN* 2.9 37.8 + - - +
1221T VAL* 3.7 11.3 - - + +
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Residues in contact with TRP1178 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088T LYS* 4.5 16.4 - - - -
1134T ARG 5.6 2.6 - - - +
1135T ASP* 6.2 1.1 - - - -
1136T LEU 3.2 28.7 - - - +
1137T ALA* 3.2 15.5 - - + +
1139T ARG* 4.0 13.2 - - - +
1175T PRO* 3.4 29.1 + - + +
1176T VAL 3.1 0.8 - - - -
1177T ARG* 1.3 101.3 - - + +
1179T MET* 1.3 60.8 + - + +
1180T SER 4.0 0.2 + - - -
1196T TRP* 3.6 10.2 - - - -
1197T SER* 2.8 30.4 + - - +
1200T VAL* 3.7 24.8 - - + +
1204T GLU* 2.8 43.1 + - - -
1211T GLN* 5.7 2.9 - - - -
1212T PRO* 3.9 21.1 - - + -
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Residues in contact with MET1179 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134T ARG 5.4 4.0 - - - +
1174T LEU* 3.8 39.5 - - + +
1175T PRO 3.7 9.4 - - - +
1176T VAL* 3.0 19.8 + - + +
1177T ARG 3.5 0.7 - - - -
1178T TRP* 1.3 80.3 - - - +
1180T SER* 1.3 63.9 + - - +
1181T PRO 4.0 0.3 - - - -
1183T SER* 3.5 33.2 - - - +
1184T LEU* 3.2 36.5 - - + +
1189T PHE* 4.4 14.8 - - + -
1196T TRP* 3.4 11.1 + - - -
1225T VAL* 4.1 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