Contacts of the strand formed by residues 1005 - 1012 (chain C) 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 THR1005 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1003C ASN 3.7 7.4 + - - -
1004C PRO* 1.3 75.5 + - - +
1006C VAL* 1.3 64.1 + - - +
1021C SER* 4.4 5.8 - - - -
1022C PHE 3.3 13.1 + - - +
1023C GLU* 4.9 2.1 - - - +
1133C LYS* 3.4 38.1 - - + +
1163C GLN* 3.2 7.6 - - - +
1164C LEU* 2.8 42.6 + - + -
1165C GLU* 2.7 33.6 + - + +
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Residues in contact with VAL1006 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005C THR* 1.3 80.3 - - - +
1007C PHE* 1.3 63.7 + - - +
1008C PHE* 5.7 0.2 - - + -
1021C SER* 3.3 6.3 - - - -
1022C PHE* 2.8 34.9 + - + +
1024C LEU* 4.0 18.8 - - + -
1036C PHE* 3.6 33.9 - - + -
1037C ARG* 3.9 28.9 - - + +
1040C SER* 4.0 17.7 - - - +
1162C GLY 3.1 13.9 - - - +
1163C GLN* 4.1 7.2 - - + +
1164C LEU 4.7 0.2 - - - +
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Residues in contact with PHE1007 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006C VAL* 1.3 77.0 - - - +
1008C PHE* 1.3 81.6 + - - +
1009C ASP* 3.1 26.2 - - - -
1019C ARG* 3.4 37.9 - - - -
1020C VAL 3.2 13.0 - - - +
1021C SER* 3.8 9.2 - - - -
1022C PHE* 4.3 2.9 - - - -
1040C SER* 4.9 0.7 - - - -
1160C ASP* 4.0 8.5 - - - -
1161C CYS* 3.0 26.8 - - - +
1162C GLY* 2.9 49.1 + - - -
1163C GLN 5.1 0.2 - - - -
1164C LEU* 3.4 38.8 - - + -
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Residues in contact with PHE1008 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007C PHE* 1.3 92.1 - - - +
1009C ASP* 1.3 59.6 + - - +
1010C ILE* 3.7 11.0 - - + -
1019C ARG* 3.3 3.5 - - - +
1020C VAL* 2.9 43.3 + - + +
1022C PHE* 3.6 23.8 - + - -
1036C PHE* 3.5 23.6 - + - -
1040C SER* 3.7 18.6 - - - -
1048C TYR* 4.0 12.6 - + + -
1053C PHE* 4.4 8.5 - + - -
1112C PHE* 3.4 31.9 - + - -
1158C ILE* 3.5 28.9 - - + -
1160C ASP 3.4 3.6 - - - -
1161C CYS* 3.5 14.8 - - + -
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Residues in contact with ASP1009 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007C PHE* 3.1 24.9 - - - -
1008C PHE* 1.3 69.7 - - - +
1010C ILE* 1.3 59.4 + - - +
1018C GLY 3.8 4.4 - - - +
1019C ARG* 3.3 36.1 + - - +
1158C ILE* 3.4 0.9 - - - +
1159C ALA* 2.5 42.7 + - + +
1160C ASP* 2.6 35.7 + - + +
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Residues in contact with ILE1010 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008C PHE* 3.8 22.4 - - + -
1009C ASP* 1.3 74.4 - - - +
1011C ALA* 1.3 66.2 + - - +
1016C PRO* 3.6 3.8 - - - +
1017C LEU* 2.8 29.7 + - + -
1018C GLY 2.8 22.6 + - - +
1020C VAL* 4.0 13.0 - - + -
1053C PHE* 4.0 23.6 - - + -
1138C ILE* 4.2 7.2 - - + -
1142C MET* 3.4 42.6 - - + -
1156C ILE* 3.5 15.0 - - + -
1157C THR 3.2 10.1 - - - +
1158C ILE* 4.1 3.1 - - + -
1159C ALA* 4.8 0.4 - - - -
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Residues in contact with ALA1011 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010C ILE* 1.3 73.7 - - - +
1012C VAL* 1.3 64.1 + - - +
1013C ASP 3.8 0.4 + - - -
1014C GLY* 3.4 20.6 - - - +
1015C GLU 3.1 13.5 - - - +
1016C PRO* 4.4 2.0 - - + -
1155C LYS 3.4 1.2 - - - +
1156C ILE* 3.3 6.2 - - - +
1157C THR* 2.8 42.0 + - - +
1159C ALA* 4.1 19.3 - - + -
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Residues in contact with VAL1012 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010C ILE* 5.2 0.9 - - + -
1011C ALA* 1.3 72.3 - - - +
1013C ASP* 1.3 60.2 + - + +
1014C GLY 2.7 13.3 + - - -
1015C GLU* 2.9 34.6 + - + +
1017C LEU* 3.8 29.8 - - + -
1145C PHE* 3.7 23.6 - - + -
1154C LYS* 3.6 44.0 - - + -
1155C LYS 3.3 2.7 - - - -
1156C ILE* 4.0 9.6 - - + -
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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