Contacts of the helix formed by residues 1217 - 1227 (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 SER1217 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1177S ARG* 3.5 2.2 - - - +
1215S GLY 4.4 0.2 + - - -
1216S LEU* 1.3 74.1 - - - +
1218S ASN* 1.3 58.7 + - - +
1219S GLU* 3.7 9.7 + - - +
1220S GLN* 2.6 57.4 + - - +
1221S VAL* 2.8 10.0 + - - +
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Residues in contact with ASN1218 (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 22.9 - - + +
1177S ARG* 2.9 31.1 + - - +
1217S SER* 1.3 69.7 - - - +
1219S GLU* 1.3 62.3 + - - +
1221S VAL* 3.4 4.5 + - - +
1222S LEU* 2.9 25.6 + - - +
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Residues in contact with GLU1219 (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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1217S SER* 2.9 10.4 + - - +
1218S ASN* 1.3 79.9 - - - +
1220S GLN* 1.3 64.5 + - + +
1222S LEU* 3.3 16.9 - - - +
1223S ARG* 3.4 33.2 + - - +
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Residues in contact with GLN1220 (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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1215S GLY 3.8 4.7 - - - +
1216S LEU* 3.3 33.4 - - + +
1217S SER* 2.6 47.2 + - - +
1219S GLU* 1.3 69.6 - - + +
1221S VAL* 1.3 53.6 + - - +
1222S LEU 3.0 1.3 - - - -
1223S ARG* 2.6 42.1 + - - +
1224S PHE* 2.6 18.2 + - + +
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Residues in contact with VAL1221 (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* 4.4 12.3 - - + +
1177S ARG* 3.6 41.1 - - + +
1184S LEU* 5.0 0.7 - - + -
1213S TYR* 3.6 31.0 - - + -
1216S LEU* 3.7 15.7 - - + +
1217S SER 2.8 20.5 + - - +
1218S ASN 3.7 5.2 - - - +
1220S GLN* 1.3 71.0 - - - +
1222S LEU* 1.3 64.1 + - - +
1224S PHE* 3.9 9.0 - - - -
1225S VAL* 2.8 37.7 + - + +
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Residues in contact with LEU1222 (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* 4.6 15.7 - - + +
1184S LEU* 3.7 40.7 - - + +
1218S ASN 2.9 12.2 + - - +
1219S GLU* 3.3 15.9 - - - +
1221S VAL* 1.3 80.0 - - - +
1223S ARG* 1.3 61.3 + - + +
1226S MET* 3.1 50.7 + - + +
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Residues in contact with ARG1223 (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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1219S GLU* 3.4 38.3 + - - +
1220S GLN* 2.6 24.2 + - - +
1222S LEU* 1.3 77.4 - - + +
1224S PHE* 1.3 68.8 + - - +
1226S MET* 3.2 7.2 + - + +
1227S GLU* 2.4 50.3 + - - +
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Residues in contact with PHE1224 (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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1213S TYR* 4.3 10.5 - + - -
1216S LEU* 3.9 25.8 - - + -
1220S GLN* 2.6 18.3 + - + +
1221S VAL* 3.7 8.1 - - - +
1223S ARG* 1.3 75.6 - - - +
1225S VAL* 1.3 72.2 + - + +
1226S MET 3.2 0.2 + - - -
1227S GLU* 3.2 8.2 + - - +
1228S GLY 3.5 0.3 + - - -
1229S GLY* 3.0 51.9 + - - -
1230S LEU 3.5 19.7 - - - -
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Residues in contact with VAL1225 (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 5.7 1.8 - - - +
1179S MET 4.1 13.0 - - - +
1181S PRO* 3.8 18.3 - - + +
1184S LEU* 4.3 12.6 - - + -
1196S TRP* 3.7 29.9 - - + -
1213S TYR* 3.5 38.1 - - + +
1221S VAL* 2.8 31.1 + - + +
1224S PHE* 1.3 78.0 - - + +
1226S MET* 1.3 61.5 + - - +
1228S GLY* 3.4 11.3 + - - -
1229S GLY 3.9 11.0 + - - +
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Residues in contact with MET1226 (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* 3.9 22.4 - - - +
1184S LEU* 3.8 26.7 - - + +
1185S LYS* 4.1 19.1 - - + -
1222S LEU* 3.1 42.2 + - + +
1223S ARG* 3.2 8.3 + - + +
1224S PHE 3.1 1.0 - - - -
1225S VAL* 1.3 81.1 - - - +
1227S GLU* 1.3 63.5 + - + +
1228S GLY 3.3 0.9 - - - -
1251S TYR* 2.9 27.2 + - - +
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Residues in contact with GLU1227 (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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1223S ARG* 2.4 57.7 + - - +
1224S PHE* 3.2 3.5 + - - +
1226S MET* 1.3 82.6 - - + +
1228S GLY* 1.3 57.9 + - - +
1229S GLY 3.6 1.3 - - - -
1251S TYR* 4.6 2.2 - - - -
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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