Contacts of the helix formed by residues 1221 - 1232 (chain A) in PDB entry 5A31
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 ASP1221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1216A LYS* 2.7 48.4 + - + +
1219A THR* 3.8 3.7 - - + -
1220A MET* 1.3 75.5 - - - +
1222A MET* 1.3 63.1 + - - +
1223A SER* 2.7 41.3 + - - -
1224A ILE* 3.9 6.8 - - + +
1225A THR* 3.0 31.3 + - - -
1260A VAL* 4.0 5.9 - - - +
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Residues in contact with MET1222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220A MET 3.6 4.4 + - - +
1221A ASP* 1.3 78.2 + - - +
1223A SER* 1.3 60.5 + - - +
1225A THR* 4.1 4.9 - - + -
1226A ARG* 3.1 46.8 + - - +
1261A TYR* 4.3 16.2 - - - +
542C THR* 4.5 21.8 - - + -
146R SER* 6.3 3.4 - - - -
152R PRO* 4.2 26.7 - - + +
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Residues in contact with SER1223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1216A LYS* 5.6 0.2 - - - -
1221A ASP* 2.7 24.7 + - - -
1222A MET* 1.3 73.8 - - - +
1224A ILE* 1.3 68.7 + - - +
1226A ARG* 3.9 15.5 + - - +
1227A LEU* 3.4 19.9 + - - +
98R GLU 5.1 4.9 - - - +
99R LEU* 6.0 1.2 - - - +
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Residues in contact with ILE1224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193A ILE* 5.8 5.8 - - + -
1212A VAL* 3.5 37.9 - - + -
1213A SER* 4.3 2.2 - - - +
1216A LYS* 3.7 38.1 - - + +
1221A ASP* 3.5 11.1 + - + +
1223A SER* 1.3 81.7 - - - +
1225A THR* 1.3 65.5 + - - +
1227A LEU* 3.0 15.3 + - + +
1228A LEU* 2.9 29.8 + - + +
1260A VAL* 3.5 31.0 - - + -
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Residues in contact with THR1225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221A ASP 3.0 22.2 + - - -
1222A MET* 3.8 11.9 - - - -
1224A ILE* 1.3 78.8 - - - +
1226A ARG* 1.3 52.1 + - - +
1228A LEU* 3.3 6.8 + - - +
1229A SER* 2.6 47.7 + - - +
1235A LEU* 5.4 1.1 - - + -
1257A ILE* 4.3 6.1 - - + +
1260A VAL* 3.7 6.5 - - - +
1261A TYR* 2.7 45.5 + - + +
152R PRO* 3.9 21.1 - - + -
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Residues in contact with ARG1226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1222A MET* 3.1 39.7 + - - +
1223A SER* 3.9 14.3 + - - +
1225A THR* 1.3 81.2 - - - +
1227A LEU* 1.3 62.1 + - - +
1229A SER* 3.4 8.3 + - - -
1230A ILE 3.2 17.3 + - - -
97R ASN 5.1 3.0 + - - -
98R GLU* 3.4 60.1 + - - +
146R SER* 5.9 1.2 + - - -
152R PRO* 3.9 28.6 + - + +
153R VAL 4.6 1.6 - - - -
154R SER* 4.8 8.3 - - - -
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Residues in contact with LEU1227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193A ILE* 4.3 21.3 - - + -
1197A LEU* 3.7 23.1 - - + -
1209A LEU* 4.4 18.4 - - + -
1212A VAL* 4.5 20.2 - - + -
1223A SER 3.4 10.5 + - - +
1224A ILE* 3.0 15.7 + - + +
1226A ARG* 1.3 77.5 - - - +
1228A LEU* 1.3 65.0 + - + +
1230A ILE* 3.0 23.1 - - - +
1231A HIS* 3.1 13.5 + - + -
95R LEU* 3.7 20.6 - - + -
98R GLU* 4.8 7.9 - - + +
99R LEU* 3.9 13.0 - - + -
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Residues in contact with LEU1228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1209A LEU* 3.9 34.8 - - + -
1212A VAL* 5.5 0.9 - - + -
1213A SER* 3.6 21.1 - - - +
1224A ILE* 2.9 22.8 + - + +
1225A THR* 3.6 5.8 - - - +
1227A LEU* 1.3 74.8 - - + +
1229A SER* 1.3 59.6 + - - +
1231A HIS* 2.8 25.3 + - - +
1232A ILE* 3.2 13.0 + - - +
1253A ALA* 4.3 10.9 - - + +
1256A GLY* 3.5 31.4 - - - +
1257A ILE* 3.6 24.7 - - + +
1260A VAL* 3.9 13.0 - - + -
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Residues in contact with SER1229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1225A THR* 2.6 32.8 + - - +
1226A ARG* 3.5 9.0 - - - -
1228A LEU* 1.3 75.8 - - - +
1230A ILE* 1.3 64.9 + - - +
1231A HIS 3.2 0.2 + - - -
1232A ILE* 2.9 22.5 - - - +
1235A LEU* 3.1 38.7 - - - +
1236A LEU* 3.9 7.4 + - - +
1257A ILE* 4.8 0.2 - - - +
152R PRO* 3.9 8.5 - - - +
153R VAL* 4.1 13.9 - - - -
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Residues in contact with ILE1230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1226A ARG 3.2 5.6 + - - +
1227A LEU* 3.0 25.6 - - - +
1229A SER* 1.3 77.9 - - - +
1231A HIS* 1.3 75.6 + - + +
1232A ILE 3.6 0.2 + - - -
1233A PRO* 5.4 0.3 - - - +
1236A LEU* 4.2 13.9 - - + +
1243A LEU* 4.3 13.1 - - + +
1245A VAL* 4.8 2.3 - - - +
91R TYR* 3.5 32.5 - - + +
94R LEU* 3.4 53.4 - - + -
95R LEU* 4.3 10.5 - - + +
98R GLU* 3.9 17.9 - - + +
153R VAL* 4.1 7.5 - - + +
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Residues in contact with HIS1231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197A LEU* 4.2 20.5 - - + +
1205A SER* 5.0 2.8 - - - -
1209A LEU* 3.8 13.4 - - + +
1227A LEU* 3.1 36.3 + - + -
1228A LEU 2.8 15.2 + - - +
1230A ILE* 1.3 83.5 - - + +
1232A ILE* 1.3 57.1 + - - +
1233A PRO* 5.1 0.2 - - - -
1245A VAL* 3.7 21.6 - - + +
1249A VAL* 3.7 25.8 - - + +
1250A GLN* 3.7 19.8 + - - +
1253A ALA* 3.8 16.4 - - + -
91R TYR* 3.0 34.2 + + - -
95R LEU* 4.8 1.3 - - + -
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Residues in contact with ILE1232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1228A LEU 3.2 7.7 + - - +
1229A SER 2.9 15.6 - - - +
1231A HIS* 1.3 76.6 - - - +
1233A PRO* 1.3 71.1 - - + +
1234A ALA 3.2 0.3 + - - -
1235A LEU* 3.6 47.1 + - + +
1236A LEU* 3.3 4.1 - - - +
1250A GLN* 4.2 3.4 - - + +
1253A ALA* 3.4 28.5 - - + -
1254A VAL* 3.8 23.3 - - + +
1257A ILE* 3.8 19.7 - - + -
1272A VAL* 5.2 1.6 - - + -
1273A LEU* 5.2 2.9 - - + -
1276A GLU* 4.1 16.4 - - - +
1294A TYR* 4.6 1.1 - - - +
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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