Contacts of the helix formed by residues 1154 - 1161 (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 ASP1154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1152A GLN 4.4 0.2 - - - -
1153A ILE* 1.3 76.6 - - - +
1155A SER* 1.3 67.6 + - - +
1156A ALA* 3.7 15.3 - - - +
1157A TRP* 3.1 35.8 + - - +
1158A ILE* 3.4 9.8 + - - +
1187A LYS* 5.0 5.2 - - - -
328O ILE* 5.1 3.2 - - - +
329O ARG* 3.3 35.5 + - - +
332O GLN* 4.2 7.8 + - - -
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Residues in contact with SER1155 (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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1154A ASP* 1.3 73.5 - - - +
1156A ALA* 1.3 65.2 + - - +
1158A ILE* 2.9 18.7 + - - +
1159A VAL* 3.0 13.3 + - - +
1187A LYS 3.5 26.5 + - - -
1188A LEU* 3.4 21.8 - - - +
1189A ALA* 3.4 21.8 + - - +
1192A ASN* 4.2 7.6 + - - -
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Residues in contact with ALA1156 (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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1154A ASP* 3.2 16.6 - - - +
1155A SER* 1.3 79.6 + - - +
1157A TRP* 1.3 56.7 + - - +
1159A VAL* 3.5 9.4 + - - +
1160A TYR* 2.9 28.7 + - - +
329O ARG* 4.1 29.2 - - + +
332O GLN* 4.0 11.1 - - + +
333O GLU* 4.4 15.2 - - + +
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Residues in contact with TRP1157 (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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1094A PRO* 4.1 26.7 - - + -
1095A VAL 4.1 7.9 + - - -
1096A PRO* 3.8 22.4 - - + +
1098A GLU 3.4 18.2 + - - -
1099A PRO 3.3 19.5 - - - -
1100A LEU* 4.2 6.7 - - + -
1147A ILE* 3.8 24.9 - - + -
1153A ILE* 3.5 40.2 - - + -
1154A ASP* 3.1 28.8 + - - +
1155A SER 3.0 0.8 - - - -
1156A ALA* 1.3 76.0 - - - +
1158A ILE* 1.3 64.9 + - + +
1160A TYR* 3.0 14.9 + + - +
1161A ASN* 2.7 39.5 + - - +
1175A PHE* 4.0 9.4 - + - -
332O GLN* 3.9 12.9 - - - +
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Residues in contact with ILE1158 (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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1153A ILE* 4.1 15.5 - - + +
1154A ASP 3.4 14.8 + - - +
1155A SER* 2.9 11.5 + - - +
1157A TRP* 1.3 94.0 - - + +
1159A VAL* 1.3 65.2 + - + +
1160A TYR 3.1 0.9 + - - -
1161A ASN* 3.2 12.7 + - - +
1172A TYR* 3.0 15.0 + - - +
1175A PHE* 4.5 4.7 - - + -
1176A LEU* 4.0 24.7 - - + -
1179A LEU* 4.2 14.1 - - + -
1184A HIS 4.0 20.6 - - - +
1185A LEU* 4.1 19.1 - - + -
1187A LYS 5.4 0.2 - - - -
1188A LEU* 3.9 22.7 - - + +
1196A TYR* 5.1 0.7 - - - +
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Residues in contact with VAL1159 (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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1155A SER* 3.0 16.8 + - - +
1156A ALA* 3.7 9.4 - - - +
1158A ILE* 1.3 75.8 - - - +
1160A TYR* 1.3 61.6 + - - +
1162A LYS* 3.1 29.6 + - + +
1172A TYR* 3.8 0.2 - - - -
1188A LEU* 4.2 9.0 - - + -
1192A ASN* 3.8 33.0 - - - +
1196A TYR* 3.7 24.5 - - - +
332O GLN 6.0 0.7 - - - +
333O GLU* 6.0 7.6 - - - +
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Residues in contact with TYR1160 (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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1097A THR* 3.3 19.7 + - - +
1098A GLU 3.6 8.7 - - - -
1099A PRO* 3.6 29.3 - - + +
1156A ALA 2.9 15.7 + - - +
1157A TRP* 3.0 13.8 + + - +
1159A VAL* 1.3 77.2 - - - +
1161A ASN* 1.3 59.5 + - - +
1162A LYS 3.6 5.2 + - - +
332O GLN* 3.3 44.9 - - + +
335O ASN* 3.8 30.7 - - + +
337O HIS* 2.4 37.5 + + - +
340O LEU* 3.9 20.0 - - + +
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Residues in contact with ASN1161 (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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1099A PRO* 2.4 43.3 + - - +
1100A LEU* 3.4 18.6 - - - +
1102A ILE* 5.3 4.1 - - + +
1157A TRP* 2.7 42.6 + - - +
1158A ILE 3.2 7.8 + - - +
1159A VAL 3.2 0.6 - - - -
1160A TYR* 1.3 75.0 - - - +
1162A LYS* 1.3 66.4 + - - +
1163A PRO* 3.4 5.9 - - - +
1172A TYR* 3.6 10.1 - - + -
1175A PHE* 3.9 22.9 - - + -
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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