Contacts of the helix formed by residues 985 - 993 (chain A) in PDB entry 3AVR
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 SER 985 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A EDO 3.7 32.5 - - - -
981A LEU 3.5 2.6 + - - -
982A GLY* 3.1 18.2 + - - -
984A PHE* 1.3 81.0 - - - +
986A THR* 1.3 65.2 + - - +
987A LYS* 3.7 9.0 + - - +
988A THR* 3.1 17.3 + - - -
989A LEU* 3.0 21.0 + - - +
1159A ILE* 4.5 0.7 - - - -
1235A ASN* 3.9 1.6 - - - +
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Residues in contact with THR 986 (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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5A EDO 4.0 12.5 + - - +
9A EDO 5.0 1.6 + - - -
985A SER* 1.3 72.2 - - - +
987A LYS* 1.3 63.7 + - - +
989A LEU* 3.3 3.6 + - - +
990A VAL* 3.0 24.5 + - + +
1036A ALA* 3.3 34.5 - - + +
1039A GLN* 2.6 29.4 + - - +
1040A ALA* 6.0 0.9 - - + -
1136A MET* 3.6 14.1 - - + +
1235A ASN* 3.1 21.7 + - - +
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Residues in contact with LYS 987 (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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985A SER* 3.2 8.9 - - - +
986A THR* 1.3 80.3 - - - +
988A THR* 1.3 64.7 + - - +
990A VAL* 3.6 4.5 + - - +
991A GLU* 3.2 51.8 + - - +
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Residues in contact with THR 988 (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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982A GLY 2.9 24.1 + - - +
983A LEU* 3.4 30.1 - - + +
985A SER* 3.1 10.0 + - - -
987A LYS* 1.3 82.1 - - - +
989A LEU* 1.3 63.9 - - - +
991A GLU* 3.4 13.7 + - - +
992A ALA* 3.1 20.2 + - + +
1099A GLN* 3.7 12.3 - - - +
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Residues in contact with LEU 989 (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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983A LEU 3.8 17.3 - - - +
984A PHE* 3.3 30.3 - - + +
985A SER 3.0 15.9 + - - +
986A THR* 3.8 5.4 - - - +
988A THR* 1.3 74.5 - - - +
990A VAL* 1.3 64.2 + - - +
992A ALA* 3.2 3.6 + - - +
993A ASN* 3.1 22.5 + - - +
1032A ILE* 3.7 17.4 - - + +
1090A LEU* 4.9 3.1 - - + -
1096A TRP* 3.6 32.3 - - + -
1099A GLN* 4.2 7.9 - - + +
1134A LEU* 3.5 37.0 - - + -
1136A MET* 5.1 1.3 - - - -
1235A ASN* 4.0 7.0 - - - +
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Residues in contact with VAL 990 (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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986A THR* 3.0 21.7 + - + +
987A LYS* 3.9 5.4 - - - +
989A LEU* 1.3 76.0 - - - +
991A GLU* 1.3 66.1 + - + +
994A ASN* 3.1 46.0 + - - +
1032A ILE* 3.8 25.8 - - + +
1033A ALA* 4.4 5.6 - - + -
1036A ALA* 3.3 31.2 - - + -
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Residues in contact with GLU 991 (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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987A LYS* 3.2 49.4 + - + +
988A THR* 3.7 12.0 + - - +
990A VAL* 1.3 80.9 - - + +
992A ALA* 1.3 62.2 + - - +
994A ASN* 4.9 0.9 + - - +
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Residues in contact with ALA 992 (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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988A THR* 3.1 14.1 + - + +
989A LEU* 3.5 8.5 - - - +
990A VAL 3.2 0.4 - - - -
991A GLU* 1.3 79.6 - - - +
993A ASN* 1.3 81.8 + - - +
994A ASN 4.0 0.4 - - - -
1095A LYS 4.5 4.0 - - - +
1096A TRP* 3.9 11.2 - - + -
1099A GLN* 4.9 8.7 - - - +
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Residues in contact with ASN 993 (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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989A LEU 3.1 3.8 + - - +
990A VAL 3.6 1.6 - - - -
992A ALA* 1.3 86.9 - - - +
994A ASN* 1.3 61.6 + - - +
995A GLU 3.0 4.8 + - - -
996A HIS* 3.0 13.0 + - + +
1032A ILE* 2.9 22.9 - - - +
1095A LYS* 2.9 56.4 + - + +
1096A TRP* 3.2 38.3 - - + -
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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