Contacts of the helix formed by residues 1175 - 1179 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1135E ASP* 4.3 6.3 - - - +
1139E ARG* 3.5 28.0 - - - +
1173E LEU 3.3 4.9 - - - +
1174E LEU* 1.3 93.1 - - + +
1176E VAL* 1.3 65.2 + - + +
1177E ARG* 3.3 2.0 - - + +
1178E TRP* 3.4 35.9 + - + +
1179E MET* 3.7 10.2 + - - +
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Residues in contact with VAL1176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1174E LEU 4.1 8.1 - - - +
1175E PRO* 1.3 69.7 - - + +
1177E ARG* 1.3 74.3 + - + +
1178E TRP 2.9 11.1 + - - -
1179E MET* 2.9 32.8 + - - +
1184E LEU* 4.2 14.5 - - + +
1218E ASN* 4.1 35.9 - - + +
1221E VAL* 4.2 18.1 - - + +
1222E LEU* 4.7 16.4 - - + +
1225E VAL* 5.9 1.0 - - - +
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Residues in contact with ARG1177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1175E PRO* 3.3 2.3 - - + -
1176E VAL* 1.3 82.9 - - + +
1178E TRP* 1.3 79.4 + - + +
1179E MET 3.5 1.3 - - - +
1196E TRP* 5.0 1.2 + - - -
1200E VAL* 4.1 13.0 - - - +
1211E GLN* 3.5 33.7 + - - +
1212E PRO* 3.0 32.1 + - + -
1213E TYR* 2.9 55.5 + - + -
1216E LEU 2.8 23.0 + - - -
1217E SER* 4.0 1.2 - - - +
1218E ASN* 3.1 30.8 + - - +
1221E VAL* 3.6 16.7 - - + +
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Residues in contact with TRP1178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088E LYS* 5.1 10.5 - - - -
1135E ASP 6.3 1.6 - - - -
1136E LEU 3.6 22.2 - - - +
1137E ALA* 3.7 12.4 - - + +
1139E ARG* 4.2 15.5 - - - +
1175E PRO* 3.4 30.4 + - + +
1176E VAL 3.0 1.0 - - - -
1177E ARG* 1.3 98.2 - - + +
1179E MET* 1.3 62.2 + - - +
1196E TRP* 3.6 9.2 - - - -
1197E SER* 2.8 30.4 + - - +
1200E VAL* 3.3 33.0 - - + +
1201E VAL* 4.6 1.3 - - + +
1204E GLU* 2.9 41.9 + - - -
1211E GLN* 5.5 3.1 - - + -
1212E PRO* 3.6 22.9 - - + -
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Residues in contact with MET1179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134E ARG 5.8 0.9 - - - +
1174E LEU* 4.1 25.8 - - + +
1175E PRO 3.7 11.0 - - - +
1176E VAL* 2.9 26.9 + - - +
1177E ARG 5.0 0.7 - - - -
1178E TRP* 1.3 79.5 - - - +
1180E SER* 1.3 64.0 + - - +
1181E PRO 3.9 0.5 - - - -
1183E SER* 3.6 33.0 - - - +
1184E LEU* 3.5 33.1 - - + +
1187E GLY* 5.8 0.2 - - - -
1189E PHE* 4.1 19.7 - - + -
1196E TRP* 3.4 11.8 + - - -
1225E VAL* 4.4 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