Contacts of the helix formed by residues 1131 - 1140 (chain A) in PDB entry 5VZU
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 THR1131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1129A GLY 5.2 2.2 - - - +
1130A LYS* 1.3 75.1 - - - +
1132A PRO* 1.3 78.4 - - + +
1133A GLU* 3.4 15.7 + - - +
1134A GLU* 2.8 44.3 + - - +
1135A ILE* 2.9 20.8 + - - +
89B SER* 4.3 2.2 - - - -
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Residues in contact with PRO1132 (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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1131A THR* 1.3 90.6 - - + +
1133A GLU* 1.3 76.1 + - - +
1135A ILE* 3.4 3.0 + - + +
1136A ARG* 3.1 32.9 + - - +
89B SER* 3.7 35.4 - - - +
92B GLN* 3.7 39.0 - - + +
93B VAL* 3.9 6.3 - - + +
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Residues in contact with GLU1133 (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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1131A THR* 3.4 20.5 + - - +
1132A PRO* 1.3 91.0 - - - +
1134A GLU* 1.3 66.6 + - + +
1136A ARG* 3.2 23.7 + - - +
1137A LYS* 3.0 32.5 + - - +
1154A ARG* 5.6 3.3 + - - -
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Residues in contact with GLU1134 (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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1129A GLY 4.4 1.7 - - - +
1130A LYS* 3.3 25.5 - - + +
1131A THR* 2.8 50.9 + - - +
1133A GLU* 1.3 76.7 - - + +
1135A ILE* 1.3 58.1 + - - +
1137A LYS* 3.4 7.1 + - - +
1138A THR* 2.7 33.9 + - - -
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Residues in contact with ILE1135 (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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1127A ILE* 4.2 16.8 - - + +
1130A LYS* 3.8 25.1 - - + +
1131A THR 2.9 17.5 + - - +
1132A PRO 3.7 6.1 - - - +
1134A GLU* 1.3 77.6 - - - +
1136A ARG* 1.3 62.0 + - - +
1138A THR* 3.2 5.4 + - - -
1139A PHE* 3.0 48.7 + - + +
1141A ILE* 4.9 1.1 - - + +
67B LEU* 5.4 0.2 - - + -
86B ASP 5.4 0.2 - - - +
89B SER* 4.2 13.5 - - - -
90B LEU* 4.2 26.5 - - + -
93B VAL* 3.7 31.9 - - + -
97B PHE* 4.8 4.0 - - + -
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Residues in contact with ARG1136 (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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1132A PRO* 3.1 17.0 + - - +
1133A GLU* 3.5 38.8 + - - +
1135A ILE* 1.3 75.7 - - - +
1137A LYS* 1.3 53.9 + - - +
1140A ASN* 2.8 32.7 + - - -
1141A ILE* 3.1 35.5 + - - +
1143A ASN* 3.1 45.7 + - - +
1145A PHE* 4.6 0.2 - - - -
1150A GLU* 4.0 7.3 + - - -
92B GLN 2.9 26.4 + - - -
93B VAL* 3.1 27.6 + - + +
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Residues in contact with LYS1137 (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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1133A GLU* 3.0 21.6 + - - +
1134A GLU* 3.9 7.0 - - + +
1136A ARG* 1.3 78.1 - - + +
1138A THR* 1.3 63.5 + - - +
1140A ASN* 3.6 16.4 + - - +
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Residues in contact with THR1138 (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 GLN* 2.6 34.1 + - - +
1126A MET* 4.5 7.6 - - + +
1130A LYS* 3.2 29.4 + - - +
1134A GLU 2.7 22.0 + - - -
1135A ILE* 3.5 5.8 - - - -
1136A ARG 3.2 0.2 - - - -
1137A LYS* 1.3 80.9 - - - +
1139A PHE* 1.3 80.9 + - + +
1140A ASN* 3.8 2.6 + - - +
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Residues in contact with PHE1139 (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 GLN* 3.7 22.6 - - - +
1101A PHE* 4.0 21.1 - + - -
1123A VAL* 4.4 6.7 - - + -
1126A MET* 3.8 39.3 - - + -
1127A ILE* 3.8 26.7 - - + -
1135A ILE* 3.0 37.7 + - + +
1138A THR* 1.3 90.3 - - + +
1140A ASN* 1.3 69.9 + - - +
1141A ILE* 3.3 20.8 + - + +
66B SER* 4.6 14.2 - - - -
67B LEU* 3.8 24.1 + - + +
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Residues in contact with ASN1140 (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 ARG 2.8 14.7 + - - -
1137A LYS* 3.6 12.0 + - - +
1138A THR 3.5 4.7 - - - +
1139A PHE* 1.3 74.8 - - - +
1141A ILE* 1.3 59.1 + - - +
1142A LYS* 4.1 1.7 + - - +
66B SER* 5.7 2.8 - - - -
68B LEU* 5.8 1.2 - - - +
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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