Contacts of the strand formed by residues 1208 - 1212 (chain A) in PDB entry 3AVS
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 TYR1208 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938A PRO* 3.5 34.9 - - + +
939A PRO 3.5 26.9 - - - -
940A THR* 4.2 6.1 - - - +
941A PRO* 4.0 21.1 - - + -
964A ASN 4.6 4.0 + - - -
966A PRO* 3.7 30.6 - - + +
967A VAL* 4.3 8.5 - - + -
1166A TRP 3.7 1.1 - - - +
1167A PHE* 3.4 4.3 - - - -
1168A VAL* 2.8 66.4 + - + +
1170A PRO* 3.9 17.3 - - + +
1206A PRO* 4.9 4.0 - - + -
1207A VAL* 1.3 73.1 - - - +
1209A ARG* 1.3 58.5 + - - +
1210A PHE* 4.3 2.5 - - + -
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Residues in contact with ARG1209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937A ASN* 6.2 0.4 - - - +
938A PRO 4.8 3.8 + - - +
940A THR* 4.0 5.4 + - - -
1008A ALA* 5.1 4.2 - - - +
1009A ASP* 2.8 40.0 + - - +
1165A GLU* 2.8 34.1 + - + +
1166A TRP 3.3 6.7 - - - +
1167A PHE* 3.4 27.1 - - + -
1197A LEU* 3.7 14.5 - - - +
1207A VAL* 3.7 9.4 + - + +
1208A TYR* 1.3 76.0 - - - +
1210A PHE* 1.3 66.9 + - - +
1515A EDO 4.9 2.4 + - - -
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Residues in contact with PHE1210 (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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940A THR* 3.4 29.2 - - + +
967A VAL* 3.9 23.3 - - + -
969A VAL* 4.1 19.5 - - + -
971A ARG* 4.4 2.2 - - - +
1165A GLU* 3.5 5.4 - - - +
1166A TRP* 2.9 65.7 + + + -
1168A VAL* 4.5 5.6 - - + -
1208A TYR 4.8 1.6 - - - -
1209A ARG* 1.3 80.5 - - - +
1211A ILE* 1.3 76.0 + - - +
1212A GLN* 4.3 2.9 - - + -
1218A VAL* 3.6 37.2 - - + -
1515A EDO 3.8 16.4 - - - +
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Residues in contact with ILE1211 (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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971A ARG* 2.8 31.1 + - - +
1163A ASP* 3.5 35.9 - - + +
1164A CYS 3.3 2.9 - - - +
1165A GLU* 3.8 37.7 - - + +
1210A PHE* 1.3 77.9 - - - +
1212A GLN* 1.3 64.5 + - - +
1213A ARG* 4.5 6.1 - - + +
1231A ILE* 4.5 10.5 - - + -
1515A EDO 5.1 0.4 + - - -
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Residues in contact with GLN1212 (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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969A VAL* 5.2 0.4 - - - -
971A ARG* 4.3 0.9 - - - +
1156A ASN* 3.1 31.1 + - - +
1158A ASN* 3.0 22.1 + - + +
1163A ASP* 3.5 1.6 - - - -
1164A CYS* 2.8 37.3 + - - +
1166A TRP* 2.9 34.9 + - + +
1210A PHE* 4.1 3.0 + - + -
1211A ILE* 1.3 72.3 - - - +
1213A ARG* 1.3 61.0 + - - +
1216A ASP* 3.1 34.7 + - + +
1218A VAL* 3.6 19.0 - - + +
1236A ASN* 3.3 15.9 - - - +
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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