Contacts of the helix formed by residues 1180 - 1187 (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 SER1180 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1178E TRP 3.9 0.6 + - - -
1179E MET* 1.3 76.1 - - - +
1181E PRO* 1.3 73.9 - - - +
1182E GLU* 2.7 33.9 + - - +
1183E SER* 2.9 25.1 + - - -
1184E LEU* 3.0 13.3 + - - +
1193E SER* 3.8 18.3 + - - -
1196E TRP* 3.8 22.3 - - - -
1225E VAL* 4.6 0.2 - - - -
1256E ARG* 4.0 0.9 - - - -
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Residues in contact with PRO1181 (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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1179E MET 3.9 0.2 - - - -
1180E SER* 1.3 87.6 - - - +
1182E GLU* 1.3 64.0 + - - +
1184E LEU* 3.2 7.7 + - + +
1185E LYS* 3.0 29.6 + - - +
1196E TRP* 3.4 39.5 - - + -
1225E VAL* 3.8 24.7 - - + +
1226E MET* 3.9 7.2 - - + +
1251E TYR* 4.0 37.9 - - + +
1256E ARG* 4.0 4.0 - - - +
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Residues in contact with GLU1182 (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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1180E SER* 2.7 18.5 + - - +
1181E PRO* 1.3 74.7 - - - +
1183E SER* 1.3 55.6 + - - +
1185E LYS* 4.2 8.3 - - - -
1186E ASP* 3.0 35.9 + - - +
1187E GLY 3.8 2.1 + - - -
1188E VAL* 4.1 20.1 + - + +
1190E THR* 4.4 4.0 + - - +
1192E TYR* 4.4 0.9 - - - +
1193E SER* 4.0 10.0 + - - -
1251E TYR 4.3 1.2 - - - +
1253E PRO* 3.3 28.7 - - + +
1256E ARG* 2.8 39.1 + - - -
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Residues in contact with SER1183 (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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1179E MET* 3.6 14.6 - - - +
1180E SER* 2.9 30.0 + - - -
1182E GLU* 1.3 74.0 - - - +
1184E LEU* 1.3 63.1 + - - +
1187E GLY* 3.0 25.8 + - - -
1188E VAL 2.9 25.4 + - - +
1189E PHE* 3.4 30.3 - - - -
1193E SER* 3.7 7.4 - - - -
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Residues in contact with LEU1184 (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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1176E VAL* 4.2 18.8 - - + +
1179E MET* 3.5 40.8 - - + +
1180E SER 3.0 15.0 + - - +
1181E PRO 3.5 4.9 - - - +
1183E SER* 1.3 77.5 - - - +
1185E LYS* 1.3 61.7 + - - +
1187E GLY 5.0 0.2 + - - -
1221E VAL* 5.3 1.1 - - + -
1222E LEU* 3.8 46.8 - - + +
1225E VAL* 3.8 32.1 - - + -
1226E MET* 3.9 11.6 - - + +
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Residues in contact with LYS1185 (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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1181E PRO 3.0 16.4 + - - +
1182E GLU* 3.8 8.5 - - - +
1183E SER 3.1 0.2 - - - -
1184E LEU* 1.3 80.6 - - - +
1186E ASP* 1.3 78.2 + - - +
1226E MET* 3.4 29.6 - - + -
1251E TYR* 5.1 11.0 + - - +
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Residues in contact with ASP1186 (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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1167E ARG* 3.5 33.2 + - - +
1168E LYS 4.8 2.8 - - - +
1182E GLU* 3.0 19.0 + - - +
1185E LYS* 1.3 100.1 + - - +
1187E GLY* 1.3 62.8 + - - +
1188E VAL* 4.1 10.6 - - + +
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Residues in contact with GLY1187 (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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1166E PTR 3.4 1.9 - - - +
1167E ARG* 3.2 2.6 - - - -
1168E LYS* 2.8 41.3 + - - +
1179E MET* 5.8 0.4 - - - -
1183E SER 3.0 18.3 + - - -
1184E LEU 5.0 0.2 + - - -
1185E LYS 3.9 0.2 - - - -
1186E ASP* 1.3 79.0 - - - +
1188E VAL* 1.3 62.1 + - - +
1189E PHE* 3.6 11.7 - - - -
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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