Contacts of the helix formed by residues 1052 - 1062 (chain B) in PDB entry 6A5T
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 VAL1052 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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667A ILE* 4.6 21.1 - - + -
671A ILE* 5.0 11.7 - - + -
806A LEU* 3.7 29.2 - - + +
761B HIS* 5.2 3.4 - - + -
1027B ILE* 4.1 27.8 - - + -
1030B LEU* 4.7 10.3 - - + +
1051B THR* 1.3 77.7 - - - +
1053B ASP* 1.3 67.0 + - - +
1054B ALA 3.7 0.2 - - - -
1055B VAL* 3.7 7.8 - - - +
1056B SER* 2.8 32.2 + - - +
1067B ARG* 5.6 1.1 - - - +
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Residues in contact with ASP1053 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671A ILE* 6.0 0.3 - - - +
722B THR* 5.2 4.2 + - - +
723B ALA* 4.7 16.6 - - + +
1051B THR* 3.2 7.2 + - + +
1052B VAL* 1.3 76.9 - - - +
1054B ALA* 1.3 59.4 + - - +
1055B VAL 3.0 1.6 - - - -
1056B SER* 2.3 33.5 + - - -
1057B ASN* 2.8 19.7 + - - +
1067B ARG* 3.6 23.7 + - - -
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Residues in contact with ALA1054 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050B LEU* 4.8 14.1 - - + -
1051B THR* 2.8 22.6 + - + +
1053B ASP* 1.3 70.2 - - - +
1055B VAL* 1.3 62.8 + - - +
1057B ASN* 3.4 12.0 + - - +
1058B LEU* 3.0 33.8 + - + +
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Residues in contact with VAL1055 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758B PHE* 6.3 0.2 - - + -
1027B ILE* 5.7 4.9 - - + +
1030B LEU* 3.5 32.5 - - + -
1031B LEU* 4.5 20.9 - - + +
1034B VAL* 4.1 14.7 - - + +
1050B LEU* 3.9 27.1 - - + -
1051B THR* 3.9 17.7 + - - +
1052B VAL* 3.7 9.1 + - - +
1053B ASP 2.8 0.6 + - - -
1054B ALA* 1.3 77.9 - - - +
1056B SER* 1.3 63.3 + - - +
1058B LEU* 3.2 8.8 + - + +
1059B LEU* 2.9 20.1 + - - +
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Residues in contact with SER1056 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030B LEU* 4.4 6.8 - - - +
1052B VAL* 2.8 20.4 + - - +
1053B ASP* 2.3 25.3 + - - -
1055B VAL* 1.3 71.5 - - - +
1057B ASN* 1.3 62.1 + - - -
1059B LEU* 3.1 8.4 + - - +
1060B ARG 2.9 18.0 + - - -
1066B SER* 3.1 27.0 + - - -
1067B ARG* 2.8 36.1 + - - -
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Residues in contact with ASN1057 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053B ASP* 2.8 20.5 + - - +
1054B ALA* 3.8 12.9 - - - +
1056B SER* 1.3 74.2 - - - +
1058B LEU* 1.3 71.1 + - + +
1060B ARG* 2.9 27.0 + - - +
1061B ASP* 3.0 24.9 + - - +
1066B SER* 5.4 1.1 - - - -
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Residues in contact with LEU1058 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034B VAL* 4.4 15.0 - - + -
1038B ARG* 3.3 37.7 + - - +
1040B TYR* 4.5 11.4 - - - +
1050B LEU* 6.5 1.1 - - + -
1054B ALA* 3.0 21.5 + - + +
1055B VAL* 3.7 7.6 - - + +
1057B ASN* 1.3 78.8 - - + +
1059B LEU* 1.3 60.2 + - - +
1061B ASP* 3.7 9.8 + - - +
1062B ASN* 2.8 24.6 - - - +
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Residues in contact with LEU1059 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030B LEU* 4.0 26.5 - - + -
1033B LYS* 4.6 17.0 - - + +
1034B VAL* 3.9 20.8 - - + +
1037B ILE* 4.5 18.8 - - + -
1055B VAL 2.9 13.3 + - - +
1056B SER* 3.3 10.8 - - - +
1057B ASN 2.9 0.4 - - - -
1058B LEU* 1.3 77.8 - - - +
1060B ARG* 1.3 64.5 + - - +
1062B ASN* 3.0 18.5 + - - +
1063B GLY 3.8 1.9 + - - -
1064B TYR* 3.8 23.3 + - + +
1065B GLN 3.5 23.8 - - - +
1066B SER* 4.3 4.9 - - - +
1068B GLY* 4.3 4.0 - - - +
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Residues in contact with ARG1060 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056B SER 2.9 6.0 + - - +
1057B ASN* 2.9 18.0 + - - +
1059B LEU* 1.3 77.3 - - - +
1061B ASP* 1.3 64.7 + - - +
1063B GLY* 2.8 20.6 + - - -
1064B TYR 3.2 21.3 - - - +
1066B SER* 3.5 32.4 + - - +
199C LYS 5.8 2.4 + - - -
200C GLU* 4.4 25.1 - - - +
202C PRO* 5.0 4.5 - - + -
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Residues in contact with ASP1061 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038B ARG* 4.2 11.2 + - - +
1057B ASN* 3.0 25.0 + - - +
1058B LEU* 3.8 16.0 - - - +
1059B LEU 3.2 0.2 - - - -
1060B ARG* 1.3 84.4 + - - +
1062B ASN* 1.3 58.8 + - - +
1063B GLY 3.2 2.3 + - - -
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Residues in contact with ASN1062 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034B VAL* 5.5 2.3 - - - +
1037B ILE* 3.7 33.5 - - + +
1038B ARG* 3.8 30.4 - - - +
1058B LEU 2.8 21.5 - - - +
1059B LEU* 3.0 10.7 + - - +
1061B ASP* 1.3 79.2 + - - +
1063B GLY* 1.3 63.2 + - - +
1064B TYR* 3.7 14.0 - - + -
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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