Contacts of the helix formed by residues 1154 - 1162 (chain A) in PDB entry 2H7C
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 GLY1154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1122A TYR* 3.4 31.9 - - - -
1152A TYR 3.6 2.6 + - - -
1153A ASP* 1.3 73.5 + - - +
1155A LEU* 1.3 64.0 + - - +
1156A ALA 3.5 0.9 - - - -
1157A LEU* 3.5 4.0 + - - +
1158A ALA* 3.0 25.3 + - - +
1165A VAL* 3.9 20.6 - - - +
1167A THR* 5.5 0.2 - - - -
1476A PHE* 4.6 6.3 - - - -
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Residues in contact with LEU1155 (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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1038A VAL* 3.7 33.7 - - + +
1039A SER 4.8 1.6 - - - +
1040A LEU* 4.1 20.4 - - + -
1047A VAL* 3.4 39.9 - - + -
1049A ILE* 4.3 8.7 - - + -
1122A TYR* 3.4 8.2 - - + -
1153A ASP* 3.0 23.1 + - - +
1154A GLY* 1.3 76.5 - - - +
1156A ALA* 1.3 63.7 + - - +
1158A ALA* 3.6 3.5 - - - +
1159A ALA* 3.0 24.4 + - - +
1481A LEU* 4.0 20.4 - - + -
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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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1040A LEU* 4.4 6.7 - - + -
1153A ASP 4.7 0.6 + - - -
1154A GLY 3.5 0.4 - - - -
1155A LEU* 1.3 79.9 - - - +
1157A LEU* 1.3 58.2 + - - +
1160A HIS* 2.9 43.5 + - + +
1476A PHE 3.9 9.9 - - - +
1477A GLY* 3.6 28.3 - - - +
1480A PHE* 4.2 12.1 - - + -
1481A LEU* 4.0 16.7 - - + +
1497A MET* 4.3 2.0 - - - -
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Residues in contact with LEU1157 (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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1136A MET* 4.2 15.7 - - + -
1154A GLY* 3.5 9.0 + - - +
1155A LEU 3.4 0.2 - - - -
1156A ALA* 1.3 78.0 - - - +
1158A ALA* 1.3 65.1 + - - +
1160A HIS* 4.8 0.2 - - - -
1161A GLU* 3.1 32.5 + - + +
1163A VAL* 3.8 7.4 - - + +
1165A VAL* 3.8 21.8 - - + -
1218A PHE* 4.2 25.8 - - + -
1475A VAL* 4.1 21.5 - - + +
1476A PHE* 4.7 12.4 + - + -
1497A MET* 3.8 36.9 - - + +
1500A TRP* 5.5 2.5 - - + -
1501A ALA* 5.1 0.2 - - + -
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Residues in contact with ALA1158 (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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1047A VAL* 4.5 6.1 - - + -
1122A TYR* 3.7 22.9 - - + +
1124A PRO* 3.4 12.4 - - + +
1154A GLY 3.0 19.1 + - - +
1155A LEU 3.6 3.6 - - - +
1157A LEU* 1.3 76.7 - - - +
1159A ALA* 1.3 57.3 + - - +
1162A ASN* 2.9 31.5 + - - -
1163A VAL* 3.4 23.5 + - - +
1165A VAL* 3.9 5.1 - - + +
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Residues in contact with ALA1159 (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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1040A LEU* 3.8 24.7 - - + -
1043A PHE* 3.4 29.7 - - + -
1045A GLN 6.0 0.4 - - - +
1047A VAL* 3.9 17.2 - - + +
1124A PRO* 4.4 9.4 - - - +
1155A LEU 3.0 16.6 + - - +
1158A ALA* 1.3 79.2 - - - +
1160A HIS* 1.3 61.1 - - - +
1162A ASN* 3.9 13.0 + - - -
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Residues in contact with HIS1160 (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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1040A LEU* 3.9 13.4 - - + +
1043A PHE* 3.8 31.7 - + - -
1156A ALA* 2.9 38.1 + - + +
1157A LEU 4.4 0.9 - - - +
1159A ALA* 1.3 74.8 - - - +
1161A GLU* 1.3 72.6 + - + +
1162A ASN* 5.4 1.3 - - - +
1480A PHE* 3.7 42.2 - + - +
1494A LYS* 5.2 6.9 - - + +
1497A MET* 3.8 23.6 - - + +
1498A LYS* 5.0 2.4 + - - -
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Residues in contact with GLU1161 (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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1157A LEU* 3.1 17.1 + - + +
1160A HIS* 1.3 88.3 - - + +
1162A ASN* 1.3 71.5 + - - +
1163A VAL* 3.4 4.6 + - + +
1494A LYS 4.6 1.6 - - - +
1497A MET* 3.5 22.6 - - + +
1498A LYS* 3.1 48.6 + - - +
1501A ALA* 3.3 22.2 - - + -
1505A ARG* 2.9 49.9 + - - -
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Residues in contact with ASN1162 (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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1124A PRO* 3.9 22.3 + - - +
1133A LEU* 3.8 20.6 - - + +
1134A PRO* 3.8 14.2 - - - +
1158A ALA 2.9 11.6 + - - -
1159A ALA 4.1 10.9 + - - -
1160A HIS 3.6 1.4 - - - +
1161A GLU* 1.3 80.8 - - - +
1163A VAL* 1.3 58.8 + - - +
1505A ARG* 4.5 2.0 + - - +
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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