Contacts of the strand formed by residues 1004 - 1012 (chain F) in PDB entry 1AWV
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 PRO1004 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1002F VAL 4.3 1.8 - - - +
1003F ASN* 1.4 89.4 - - - +
1005F THR* 1.3 59.4 + - - +
1006F VAL 4.2 0.2 - - - -
1023F GLU* 3.4 4.9 - - - +
1024F LEU* 2.8 63.1 + - + +
1026F ALA* 4.0 20.0 - - + -
1033F ALA* 6.2 0.2 - - + -
1034F GLU* 6.0 1.3 - - - +
1037F ARG* 4.3 7.9 - - - -
1163F GLN* 3.8 17.9 - - - +
1165F GLU* 3.4 9.2 - - - +
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Residues in contact with THR1005 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003F ASN 4.3 4.2 + - - -
1004F PRO* 1.3 75.8 + - - +
1006F VAL* 1.3 68.2 - - - +
1021F SER* 4.3 9.0 - - - -
1022F PHE 3.1 11.7 - - - +
1023F GLU* 5.0 1.9 - - - +
1133F LYS* 3.6 32.5 + - + +
1163F GLN* 3.3 2.6 - - - +
1164F LEU* 2.8 37.1 + - + -
1165F GLU* 2.7 37.2 + - - +
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Residues in contact with VAL1006 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005F THR* 1.3 78.9 - - - +
1007F PHE* 1.3 61.6 + - - +
1021F SER* 3.0 7.3 - - - -
1022F PHE* 2.7 39.9 + - + -
1024F LEU* 3.9 31.9 - - + -
1036F PHE* 3.9 18.2 - - + -
1037F ARG* 3.5 37.5 - - + +
1040F SER* 4.3 7.4 - - - +
1162F GLY 3.3 9.6 - - - +
1163F GLN* 3.9 12.6 - - + +
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Residues in contact with PHE1007 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006F VAL* 1.3 76.6 - - - +
1008F PHE* 1.3 78.7 + - - +
1009F ASP* 2.9 29.4 - - - -
1019F ARG* 3.5 33.0 - - + -
1020F VAL 3.0 15.3 - - - +
1021F SER* 3.7 11.7 - - - +
1022F PHE* 4.1 2.2 - - - -
1040F SER* 3.4 1.6 + - - -
1160F ASP* 5.3 2.5 - - - -
1161F CYS* 4.0 7.6 - - - -
1162F GLY* 2.7 69.6 + - - -
1163F GLN 4.2 0.9 - - - -
1164F LEU* 3.5 38.1 - - + -
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Residues in contact with PHE1008 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007F PHE* 1.3 89.6 - - - +
1009F ASP* 1.3 60.3 + - - +
1010F ILE* 3.6 9.8 + - + -
1019F ARG* 3.3 2.6 - - - +
1020F VAL* 2.7 47.7 + - + +
1022F PHE* 3.4 20.4 - + - -
1036F PHE* 3.3 32.1 - + - -
1040F SER* 3.6 19.5 - - - -
1048F TYR* 3.8 24.2 - + - -
1053F PHE* 4.4 8.1 - + - -
1112F PHE* 3.5 26.0 - + - -
1114F ILE* 5.1 0.2 - - + -
1158F ILE* 3.8 21.5 - - + -
1160F ASP 3.5 3.6 - - - -
1161F CYS* 3.4 11.7 - - + -
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Residues in contact with ASP1009 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007F PHE* 2.9 28.6 - - - -
1008F PHE* 1.3 70.7 - - - +
1010F ILE* 1.3 57.5 - - - +
1018F GLY 3.9 4.8 - - - +
1019F ARG* 3.5 32.8 + - - +
1158F ILE 3.5 0.9 - - - -
1159F ALA* 2.7 36.9 + - + +
1160F ASP* 2.5 44.8 + - + +
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Residues in contact with ILE1010 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008F PHE* 3.8 22.2 - - + -
1009F ASP* 1.3 74.3 - - - +
1011F ALA* 1.3 71.5 + - - +
1012F VAL* 5.0 0.4 - - + -
1016F PRO* 3.9 2.6 - - - +
1017F LEU* 3.0 35.5 + - + -
1018F GLY 3.0 20.1 + - - +
1020F VAL* 4.0 15.5 - - + -
1053F PHE* 4.1 13.7 - - + -
1138F ILE* 4.4 5.4 - - + -
1142F MET* 3.4 33.4 - - + -
1156F ILE* 4.1 12.3 - - + -
1157F THR 3.6 11.0 - - - +
1158F ILE* 4.1 14.6 - - + -
1159F ALA* 4.6 0.9 - - - -
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Residues in contact with ALA1011 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010F ILE* 1.3 77.7 - - - +
1012F VAL* 1.3 63.9 + - - +
1013F ASP 3.6 1.4 + - - -
1014F GLY* 4.1 21.1 - - - +
1015F GLU 3.5 11.4 - - - +
1016F PRO* 4.7 2.5 - - + -
1017F LEU 4.5 0.4 - - - +
1156F ILE* 3.7 2.8 - - - -
1157F THR* 2.9 40.1 + - - +
1159F ALA* 3.6 24.0 - - + +
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Residues in contact with VAL1012 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010F ILE* 5.0 2.5 - - + -
1011F ALA* 1.3 75.5 - - - +
1013F ASP* 1.3 74.2 + - - +
1014F GLY 3.5 0.2 - - - -
1015F GLU* 2.9 24.5 + - + +
1017F LEU* 3.9 38.3 - - + +
1142F MET* 5.0 0.7 - - + -
1145F PHE* 4.1 34.5 - - + -
1154F LYS* 4.6 6.7 - - + -
1155F LYS 3.4 9.2 - - - +
1156F ILE* 4.2 17.9 - - + -
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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