Contacts of the helix formed by residues 953 - 962 (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 PHE 953 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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949A ARG 3.3 6.2 + - - +
950A ASP* 3.3 20.5 + - - +
951A ALA 3.3 0.9 - - - +
952A PHE* 1.3 76.0 - - - +
954A PRO* 1.3 78.7 - - + +
955A PRO* 3.6 36.6 - - + -
956A LEU* 3.0 26.2 + - + +
957A HIS 4.3 0.2 + - - -
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Residues in contact with PRO 954 (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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952A PHE 3.3 10.3 - - - +
953A PHE* 1.3 88.5 - - + +
955A PRO* 1.3 68.0 - - + +
956A LEU 2.9 6.3 + - - -
957A HIS* 3.1 22.5 + - + +
958A GLN* 3.9 6.0 + - - +
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Residues in contact with PRO 955 (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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953A PHE* 3.5 39.0 - - + -
954A PRO* 1.3 96.4 - - + +
956A LEU* 1.3 56.7 + - - +
957A HIS 3.3 0.2 - - - -
958A GLN* 3.1 32.6 - - + +
959A PHE* 3.0 28.9 + - - +
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Residues in contact with LEU 956 (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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943A ILE* 2.9 47.8 - - + -
945A LEU* 4.4 10.8 - - + -
950A ASP 3.8 13.5 - - - +
951A ALA* 3.3 30.1 - - - +
953A PHE* 3.0 21.2 + - + +
954A PRO 2.9 0.2 + - - -
955A PRO* 1.3 77.9 - - - +
957A HIS* 1.3 63.0 + - - +
959A PHE* 3.2 7.3 + - + +
960A CYS* 3.1 22.9 + - - -
970A ILE* 4.2 12.6 - - + -
973A LEU* 6.4 0.4 - - + -
1107A PRO* 5.7 0.2 - - + -
1109A PHE* 3.9 18.8 - - + -
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Residues in contact with HIS 957 (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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953A PHE 4.3 0.4 + - - -
954A PRO* 3.1 13.1 + - + +
956A LEU* 1.3 80.2 - - - +
958A GLN* 1.3 61.4 + - - +
960A CYS* 3.3 1.7 + - - +
961A THR* 3.2 36.9 + - + +
1109A PHE* 3.5 52.5 + + + +
1219A TRP* 5.4 0.4 - + - -
1243A PRO* 4.7 11.8 - - + +
1244A LEU 6.3 0.4 - - - -
1245A THR* 6.3 0.4 - - - +
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Residues in contact with GLN 958 (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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954A PRO* 4.4 3.6 - - - +
955A PRO* 3.1 46.1 - - + +
957A HIS* 1.3 76.6 - - - +
959A PHE* 1.3 65.0 + - - +
961A THR* 3.4 9.3 + - - +
962A ASN* 3.0 24.9 + - - +
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Residues in contact with PHE 959 (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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941A PRO* 3.8 21.8 - - + -
942A SER 4.3 13.5 - - - -
943A ILE* 3.7 24.9 - - + -
955A PRO 3.0 17.5 + - - +
956A LEU* 3.2 8.3 + - - +
958A GLN* 1.3 79.8 - - - +
960A CYS* 1.3 61.3 + - - +
962A ASN* 3.4 8.6 - - - +
965A ASN* 3.1 40.8 + - - +
968A THR* 3.7 23.1 - - + -
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Residues in contact with CYS 960 (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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943A ILE* 4.0 8.3 - - - -
956A LEU 3.1 17.4 + - - +
957A HIS 3.8 6.7 - - - +
958A GLN 3.3 0.2 - - - -
959A PHE* 1.3 77.4 - - - +
961A THR* 1.3 61.1 + - - +
962A ASN 4.2 0.5 - - - +
965A ASN 4.2 3.5 - - - +
968A THR* 3.8 34.3 + - - -
970A ILE* 4.1 11.2 - - - -
1109A PHE* 3.9 19.7 - - + -
1219A TRP* 3.1 42.7 + - + +
1221A ASN* 3.4 10.7 + - - -
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Residues in contact with THR 961 (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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8A EDO 3.1 28.5 + - - -
957A HIS* 3.2 37.4 + - + +
958A GLN* 3.4 9.9 + - - -
960A CYS* 1.3 76.2 - - - +
962A ASN* 1.3 67.4 + - - +
963A PRO* 3.1 7.2 - - - +
1219A TRP* 3.9 10.3 - - + -
1221A ASN* 3.5 7.6 + - - -
1243A PRO* 3.8 27.6 - - + -
1245A THR* 5.1 6.1 - - + +
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Residues in contact with ASN 962 (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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958A GLN 3.0 14.7 + - - +
959A PHE* 3.4 17.4 - - - +
960A CYS 3.3 0.6 - - - -
961A THR* 1.3 73.8 + - - +
963A PRO* 1.3 73.4 - - - +
964A ASN* 2.9 33.0 + - - +
965A ASN* 3.0 27.2 + - - +
1221A ASN* 2.9 15.2 + - - -
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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