Contacts of the helix formed by residues 1001 - 1011 (chain B) in PDB entry 6KJV
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 ASN1001 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255B LEU 5.6 0.8 + - - -
256B ALA 4.2 10.9 + - - -
257B PHE* 1.3 83.9 - - - +
334B LYS* 5.5 9.7 - - - +
1002B ILE* 1.3 61.5 + - + +
1003B PHE* 3.0 33.8 + - + +
1004B GLU* 3.1 21.4 + - - +
1005B MET* 2.9 27.9 + - - +
1157B TRP* 4.6 11.2 - - - -
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Residues in contact with ILE1002 (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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1001B ASN* 1.3 74.3 - - + +
1003B PHE* 1.3 84.2 + - + +
1005B MET* 4.1 12.1 - - - -
1006B LEU* 2.9 55.7 + - + +
1070B VAL* 4.5 11.7 - - + -
1096B ALA* 3.4 45.4 - - + +
1099B ILE* 4.2 25.8 - - + -
1100B ASN 4.3 4.0 - - - +
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Residues in contact with PHE1003 (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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1001B ASN* 3.0 24.7 + - + +
1002B ILE* 1.3 88.1 - - + +
1004B GLU* 1.3 65.6 + - - +
1007B ARG* 2.9 29.3 + - - +
1066B PHE* 3.5 35.3 - + + -
1067B ASN* 4.1 32.1 - - - -
1070B VAL* 3.9 33.0 - - + -
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Residues in contact with GLU1004 (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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256B ALA 4.2 12.1 - - - +
257B PHE* 3.7 26.2 - - + -
1001B ASN* 3.1 24.3 + - - +
1003B PHE* 1.3 82.6 - - - +
1005B MET* 1.3 64.3 + - - +
1007B ARG* 3.3 9.7 + - - +
1008B ILE* 2.9 29.6 + - + +
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Residues in contact with MET1005 (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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257B PHE* 3.7 15.3 - - + -
1001B ASN 2.9 17.4 + - - +
1002B ILE* 3.6 10.8 - - - +
1004B GLU* 1.3 76.1 - - - +
1006B LEU* 1.3 57.4 + - - +
1008B ILE* 3.1 6.6 + - - +
1009B ASP* 3.0 29.1 + - - -
1096B ALA* 3.9 17.0 - - - +
1097B ALA* 4.1 14.6 - - + +
1100B ASN* 3.7 26.9 - - + +
1148B VAL* 4.4 5.6 - - + -
1151B THR* 4.2 11.0 - - - +
1157B TRP* 3.6 20.2 - - + -
1160B TYR* 3.2 48.2 - - + +
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Residues in contact with LEU1006 (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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1002B ILE* 2.9 38.3 + - + +
1005B MET* 1.3 70.2 - - - +
1007B ARG* 1.3 61.7 + - - +
1009B ASP* 4.3 1.3 - - - +
1010B GLU* 2.8 38.3 + - + +
1028B ILE* 4.5 1.3 - - - -
1066B PHE* 3.6 21.3 - - + -
1070B VAL* 4.0 11.2 - - + -
1099B ILE* 5.3 2.0 - - + -
1100B ASN* 3.4 24.9 - - - +
1103B PHE* 3.6 47.1 - - + -
1144B ARG* 3.6 19.1 - - - +
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Residues in contact with ARG1007 (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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1003B PHE 2.9 18.6 + - - +
1004B GLU* 3.3 13.9 + - - +
1006B LEU* 1.3 76.2 - - - +
1008B ILE* 1.3 65.3 + - + +
1011B GLY* 3.5 18.6 + - - +
1028B ILE* 4.2 17.9 - - + -
1063B GLU* 6.1 0.9 - - - +
1066B PHE* 4.4 3.7 - - + -
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Residues in contact with ILE1008 (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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257B PHE* 4.8 10.3 - - + -
1004B GLU* 2.9 21.4 + - + +
1005B MET* 3.4 7.6 - - - +
1006B LEU 3.1 0.2 - - - -
1007B ARG* 1.3 82.8 - - + +
1009B ASP* 1.3 66.7 + - - +
1010B GLU 3.7 0.2 + - - -
1011B GLY* 4.1 3.5 + - - -
1147B ARG* 5.6 4.5 - - - +
1160B TYR* 4.2 25.4 - - + +
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Residues in contact with ASP1009 (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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1005B MET 3.0 10.2 + - - +
1006B LEU* 3.3 2.4 + - - +
1008B ILE* 1.3 82.7 - - - +
1010B GLU* 1.3 59.6 + - - +
1011B GLY 3.8 0.2 + - - -
1100B ASN* 3.1 19.8 + - - +
1144B ARG* 3.5 33.6 + - + +
1147B ARG* 3.1 36.9 + - - +
1160B TYR* 2.5 36.3 + - - -
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Residues in contact with GLU1010 (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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1006B LEU* 2.8 25.7 + - + +
1009B ASP* 1.3 72.6 - - - +
1011B GLY* 1.3 62.6 + - - +
1013B ARG* 6.0 1.4 - - - +
1028B ILE* 4.0 13.7 - - + -
1029B GLY* 3.7 19.6 + - - +
1031B LEU* 5.8 1.9 - - - +
1103B PHE* 3.7 30.8 - - + +
1104B GLN* 4.2 9.9 - - - +
1144B ARG* 2.8 39.7 + - - +
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Residues in contact with GLY1011 (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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1006B LEU 4.1 0.4 + - - -
1007B ARG* 3.5 20.0 + - - -
1008B ILE 4.1 2.8 + - - -
1009B ASP 3.6 2.0 - - - -
1010B GLU* 1.3 82.2 - - - +
1012B LEU* 1.3 61.7 + - - +
1013B ARG* 5.7 1.3 - - - -
1027B GLY 3.5 1.2 - - - +
1028B ILE* 3.4 26.8 - - - +
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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