Contacts of the helix formed by residues 1056 - 1066 (chain B) in PDB entry 2B7A
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 SER1056 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020B TRP* 5.7 0.2 - - - -
1045B TYR* 4.7 0.2 - - - -
1049B THR* 5.6 2.0 - - - -
1051B ILE* 6.2 6.1 - - - +
1052B GLU 3.5 5.4 + - - -
1053B LYS* 3.6 11.5 + - - -
1054B SER 3.5 1.0 - - - -
1055B LYS* 1.3 80.1 - - - +
1057B PRO* 1.4 69.5 - - - +
1058B PRO* 3.4 10.3 - - - +
1059B ALA* 3.3 21.5 + - - +
1060B GLU* 2.8 27.4 + - - +
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Residues in contact with PRO1057 (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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1019B PHE* 4.0 18.8 - - + +
1020B TRP* 3.6 29.2 - - + -
1042B VAL* 3.7 18.8 - - + -
1045B TYR* 4.1 18.6 - - + -
1046B GLU* 4.3 9.4 - - + -
1049B THR* 6.1 0.2 - - - +
1055B LYS 3.8 0.2 - - - -
1056B SER* 1.4 86.6 - - - +
1058B PRO* 1.4 69.4 - - + +
1060B GLU* 4.0 0.2 - - - +
1061B PHE* 2.9 33.1 + - + -
1088B LEU* 3.9 17.0 - - + -
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Residues in contact with PRO1058 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019B PHE* 3.6 30.9 - - + -
1020B TRP* 3.7 24.0 - - + -
1056B SER* 3.4 13.5 - - - +
1057B PRO* 1.4 97.7 - - + +
1059B ALA* 1.3 54.2 + - - +
1061B PHE* 4.0 0.3 - - - +
1062B MET* 3.0 39.2 + - + +
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Residues in contact with ALA1059 (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 LYS 4.0 7.6 - - - +
1054B SER* 3.7 20.6 - - - +
1056B SER* 3.2 20.3 + - - +
1058B PRO* 1.3 78.1 - - - +
1060B GLU* 1.3 59.1 + - - +
1062B MET* 4.0 4.1 - - - +
1063B ARG* 3.2 26.3 + - - +
1067B ASN* 5.8 0.9 + - - -
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Residues in contact with GLU1060 (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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1045B TYR* 3.3 21.4 + - - +
1054B SER 3.8 5.2 - - - +
1055B LYS* 3.4 35.7 - - - +
1056B SER 2.8 20.6 + - - +
1059B ALA* 1.3 71.0 - - - +
1061B PHE* 1.3 66.5 + - - +
1063B ARG* 3.4 24.4 + - - +
1064B MET* 3.3 30.0 + - - +
1088B LEU* 3.7 17.0 - - + -
1089B PRO* 3.7 23.6 - - + +
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Residues in contact with PHE1061 (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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1019B PHE* 3.5 55.4 - + + -
1038B TRP* 5.8 3.8 - + - -
1042B VAL* 6.0 1.6 - - + -
1057B PRO* 2.9 23.3 + - + +
1060B GLU* 1.3 76.0 - - - +
1062B MET* 1.3 58.4 + - - +
1064B MET* 3.4 7.5 + - - +
1065B ILE* 3.0 36.6 + - + +
1078B LEU* 3.8 10.8 - - + -
1081B LEU* 3.7 22.4 - - + -
1082B LEU* 4.1 28.9 - - + -
1087B ARG* 4.6 6.1 - - + -
1088B LEU* 3.7 44.0 - - + -
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Residues in contact with MET1062 (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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1019B PHE* 3.9 15.7 - - + -
1058B PRO* 3.0 26.9 + - + +
1059B ALA* 4.1 4.9 - - - +
1061B PHE* 1.3 75.0 - - - +
1063B ARG* 1.3 57.7 + - - +
1065B ILE* 4.5 8.5 - - + -
1066B GLY 2.8 45.8 + - - +
1067B ASN* 3.3 28.7 + - - +
1069B LYS* 5.2 4.3 - - + +
1070B GLN 5.1 2.5 - - - +
1074B ILE* 3.8 48.9 - - + -
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Residues in contact with ARG1063 (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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1054B SER* 5.6 4.5 + - - -
1055B LYS* 5.5 6.5 - - - +
1059B ALA 3.2 18.1 + - - +
1060B GLU* 3.5 28.4 + - - +
1061B PHE 3.1 0.2 - - - -
1062B MET* 1.3 76.9 - - - +
1064B MET* 1.3 59.3 + - - +
1066B GLY* 3.4 12.3 + - - -
1067B ASN* 4.6 13.4 + - - +
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Residues in contact with MET1064 (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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1060B GLU* 3.4 17.9 - - - +
1061B PHE* 3.6 13.5 - - - +
1063B ARG* 1.3 76.4 - - + +
1065B ILE* 1.3 62.2 + - - +
1081B LEU* 3.8 40.8 - - + +
1086B GLY* 4.3 2.9 - - - -
1087B ARG 3.7 37.5 - - - +
1088B LEU* 5.1 2.5 - - - -
1089B PRO* 5.4 5.2 - - - -
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Residues in contact with ILE1065 (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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1019B PHE* 4.9 5.2 - - + -
1061B PHE* 3.0 26.7 + - + +
1062B MET* 4.2 12.8 - - - +
1063B ARG 4.1 0.2 - - - -
1064B MET* 1.3 79.2 - - - +
1066B GLY* 1.3 65.4 + - - +
1069B LYS* 4.5 9.4 - - + -
1074B ILE* 4.4 6.5 - - + +
1077B HIS* 3.7 33.4 - - + +
1078B LEU* 3.9 36.8 - - + +
1081B LEU* 3.8 20.6 - - + -
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Residues in contact with GLY1066 (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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1062B MET* 2.8 16.0 + - - +
1063B ARG 3.4 9.3 + - - -
1065B ILE* 1.3 81.3 - - - +
1067B ASN* 1.3 62.3 + - - -
1068B ASP* 3.1 11.2 + - - -
1069B LYS* 3.3 22.3 + - - +
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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