Contacts of the helix formed by residues 1180 - 1187 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1178S TRP 3.8 2.0 + - - -
1179S MET* 1.3 77.9 - - - +
1181S PRO* 1.3 72.0 - - - +
1182S GLU* 3.0 25.8 - - - +
1183S SER* 2.6 28.3 + - - -
1184S LEU* 3.0 26.4 + - - +
1193S SER* 3.5 14.0 + - - -
1196S TRP* 3.9 22.3 - - - +
1197S SER* 5.5 0.2 + - - -
1225S VAL* 4.7 0.2 - - - -
1256S ARG* 4.3 0.4 - - - -
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Residues in contact with PRO1181 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1180S SER* 1.3 90.2 - - - +
1182S GLU* 1.3 63.3 + - - +
1184S LEU* 3.5 5.9 + - + +
1185S LYS* 3.0 29.7 + - - +
1196S TRP* 3.4 39.5 - - + -
1225S VAL* 3.8 21.8 - - + +
1226S MET* 3.9 9.0 - - + +
1251S TYR* 3.7 40.6 - - + +
1256S ARG* 3.9 2.5 - - - +
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Residues in contact with GLU1182 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1180S SER* 3.0 15.4 + - - +
1181S PRO* 1.3 79.5 - - - +
1183S SER* 1.3 62.5 + - - +
1185S LYS* 3.3 6.4 + - - +
1186S ASP* 3.0 29.3 + - - +
1187S GLY 4.0 0.5 + - - -
1188S VAL* 4.2 18.6 + - + +
1190S THR* 4.2 4.9 + - - +
1193S SER* 4.1 9.7 + - - -
1251S TYR 4.5 1.6 - - - +
1253S PRO* 3.2 28.1 - - + +
1256S ARG* 2.7 44.2 + - - -
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Residues in contact with SER1183 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1179S MET* 3.5 21.5 - - - +
1180S SER* 2.6 32.9 + - - -
1182S GLU* 1.3 74.1 - - - +
1184S LEU* 1.3 61.2 + - - +
1187S GLY* 2.8 27.7 + - - -
1188S VAL 3.0 24.7 + - - +
1189S PHE* 3.9 15.2 - - - -
1193S SER* 3.5 12.3 + - - -
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Residues in contact with LEU1184 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176S VAL* 4.2 13.7 - - + +
1179S MET* 3.5 41.5 - - + +
1180S SER 3.0 22.2 + - - +
1181S PRO 3.8 4.0 - - - +
1183S SER* 1.3 77.2 - - - +
1185S LYS* 1.3 63.4 + - - +
1187S GLY 4.7 0.5 + - - -
1221S VAL* 4.4 0.7 - - + +
1222S LEU* 3.7 55.6 - - + +
1225S VAL* 4.3 19.7 - - + -
1226S MET* 3.8 18.0 - - + +
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Residues in contact with LYS1185 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1181S PRO 3.0 18.5 + - - +
1182S GLU* 3.7 7.9 - - - +
1183S SER 3.1 0.4 - - - -
1184S LEU* 1.3 79.6 - - - +
1186S ASP* 1.3 85.1 + - - +
1226S MET* 4.2 22.0 - - + -
1251S TYR* 5.1 11.6 + - - +
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Residues in contact with ASP1186 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1167S ARG* 3.5 30.8 + - - +
1168S LYS 5.0 1.4 - - - +
1182S GLU 3.0 10.9 + - - +
1185S LYS* 1.3 117.0 - - - +
1187S GLY* 1.3 67.5 + - - +
1188S VAL* 3.2 8.1 + - + -
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Residues in contact with GLY1187 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1167S ARG* 3.2 4.2 - - - -
1168S LYS* 2.8 39.0 + - - -
1179S MET* 5.6 0.7 - - - -
1183S SER 2.8 17.1 + - - -
1184S LEU 4.6 0.6 + - - -
1185S LYS 3.9 0.2 - - - -
1186S ASP* 1.3 78.4 - - - +
1188S VAL* 1.3 59.2 + - - +
1189S PHE* 3.5 16.2 - - - -
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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