Contacts of the strand formed by residues 1225 - 1230 (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 VAL1225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1146A HIS 3.6 11.9 - - - +
1147A GLN* 3.6 28.0 - - + +
1168A VAL* 3.4 1.2 - - - -
1169A VAL* 2.8 43.8 + - + +
1170A PRO 4.6 4.3 - - - +
1174A TRP* 3.9 18.2 - - + +
1177A LEU* 3.3 33.0 - - + -
1188A PHE* 4.7 3.1 - - + -
1193A TRP* 4.0 17.7 - - + -
1223A GLY 3.9 1.8 - - - +
1224A THR* 1.3 71.0 - - - +
1226A HIS* 1.3 67.2 + - - +
1227A TRP* 4.2 7.4 - - + -
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Residues in contact with HIS1226 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1145A GLY* 3.4 0.3 - - - -
1146A HIS* 3.0 55.8 + + - -
1148A GLU* 2.8 22.0 - - + -
1166A TRP* 3.9 19.1 - + + -
1167A PHE 3.1 13.7 - - - +
1168A VAL* 3.9 13.7 - - + -
1220A ILE* 3.6 20.9 - - + +
1224A THR* 3.0 19.4 + - + -
1225A VAL* 1.3 77.6 - - - +
1227A TRP* 1.3 69.5 + - - +
1228A VAL* 4.5 2.5 - - + -
1501A OGA 3.3 4.8 + - - -
1503A NI 2.2 35.3 - - + +
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Residues in contact with TRP1227 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1143A THR 3.3 15.5 - - - +
1144A PRO* 3.7 0.7 - - + -
1145A GLY* 3.5 17.7 - - - +
1146A HIS* 5.1 0.7 - - - -
1166A TRP* 4.6 0.2 - - - +
1167A PHE* 2.9 68.7 + + + +
1168A VAL 4.9 0.2 - - - -
1169A VAL* 3.6 31.6 - - + -
1177A LEU* 4.4 2.5 - - + -
1194A TRP* 3.6 42.3 - + + +
1195A PRO* 3.5 44.3 + - + +
1197A LEU* 4.1 11.6 - - + +
1200A LEU* 3.8 12.8 - - + -
1207A VAL* 4.9 2.2 - - + -
1225A VAL* 4.2 15.9 - - + -
1226A HIS* 1.3 86.6 - - - +
1228A VAL* 1.3 66.9 - - - +
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Residues in contact with VAL1228 (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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1137A LYS* 4.2 9.6 - - - +
1141A SER 4.5 0.2 - - - -
1142A ARG* 3.2 4.3 - - - -
1143A THR* 2.8 32.4 + - - -
1164A CYS* 4.3 2.5 - - + -
1165A GLU 3.5 11.9 - - - +
1166A TRP* 3.6 48.7 - - + +
1194A TRP* 3.5 8.1 - - - -
1226A HIS* 4.5 2.7 - - + -
1227A TRP* 1.3 83.7 - - - +
1229A GLN* 1.3 68.7 + - - +
1501A OGA 3.8 42.2 - - - +
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Residues in contact with GLN1229 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1006A GLN 5.2 1.6 - - - +
1008A ALA* 3.1 22.5 + - - +
1009A ASP* 4.4 0.2 - - - +
1137A LYS* 5.3 0.4 - - - +
1140A GLY* 4.9 5.7 - - - +
1141A SER 3.2 6.5 - - - +
1142A ARG* 2.9 43.7 + - + +
1164A CYS* 3.5 1.7 - - - -
1165A GLU* 2.8 69.6 + - + +
1167A PHE* 3.9 8.8 - - + -
1194A TRP* 3.9 6.7 - - + -
1228A VAL* 1.3 81.0 - - - +
1230A ALA* 1.3 63.9 - - - +
1231A ILE* 4.1 11.8 - - + +
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Residues in contact with ALA1230 (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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1137A LYS* 3.8 29.4 - - + +
1138A VAL 3.5 21.5 - - - +
1140A GLY* 2.9 24.0 + - - -
1141A SER 3.0 11.0 + - - +
1163A ASP 3.9 4.7 - - - -
1164A CYS* 4.3 4.7 - - - -
1229A GLN* 1.3 74.9 - - - +
1231A ILE* 1.3 63.9 + - - +
1232A GLY 3.5 13.5 - - - +
1234A CYS* 4.3 4.5 - - - -
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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