Contacts of the helix formed by residues 1006 - 1019 (chain B) in PDB entry 5IY8
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 VAL1006 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1003B ASN 5.2 0.4 + - - -
1004B ASP* 3.1 16.3 - - + +
1005B ALA* 1.3 79.4 - - - +
1007B ASN* 1.3 54.5 + - - +
1008B VAL* 2.8 19.0 + - - +
1009B GLN* 3.0 20.9 + - + +
1010B LYS* 3.2 29.6 + - + +
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Residues in contact with ASN1007 (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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828A LEU 4.6 1.7 - - - +
829A ALA* 4.6 7.0 + - - +
713B PHE* 4.0 22.4 - - + -
716B HIS* 3.0 39.6 + - - -
982B ILE* 4.8 6.4 - - - +
985B LEU* 5.5 0.2 - - - +
1003B ASN* 5.5 3.1 - - - +
1005B ALA* 2.6 18.3 + - + +
1006B VAL* 1.3 73.0 - - - +
1008B VAL* 1.3 85.3 + - - +
1010B LYS* 4.8 0.4 - - - +
1011B ILE* 3.0 43.4 - - + +
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Residues in contact with VAL1008 (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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689A ILE* 3.9 28.0 - - + -
693A ILE* 4.4 9.0 - - + -
828A LEU* 4.0 37.5 - - + +
829A ALA* 5.6 2.9 - - - -
982B ILE* 5.3 10.5 - - + -
985B LEU* 4.7 3.6 - - + +
1006B VAL 2.8 7.8 + - - +
1007B ASN* 1.3 89.4 + - - +
1009B GLN* 1.3 73.9 + - + +
1011B ILE* 4.0 1.2 - - - +
1012B SER* 3.0 31.2 + - - +
1023B ARG* 6.1 0.7 - - - +
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Residues in contact with GLN1009 (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 VAL* 3.0 12.5 + - + +
1008B VAL* 1.3 84.6 - - + +
1010B LYS* 1.3 62.6 + - - +
1012B SER* 3.1 11.1 + - - -
1013B ASN* 2.9 33.3 + - + +
1022B LEU* 5.3 1.0 - - - +
1023B ARG* 4.5 15.4 + - - +
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Residues in contact with LYS1010 (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 ALA* 3.6 25.9 - - + +
1006B VAL* 3.2 27.4 + - + +
1007B ASN* 4.9 0.7 - - - -
1009B GLN* 1.3 78.8 - - - +
1011B ILE* 1.3 64.4 + - + +
1013B ASN* 3.4 7.8 + - - +
1014B LEU* 3.1 43.8 + - + +
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Residues in contact with ILE1011 (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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713B PHE* 4.9 2.7 - - + -
982B ILE* 4.5 11.9 - - + -
985B LEU* 3.5 39.7 - - + +
986B GLN* 3.0 41.1 - - + +
989B VAL* 3.8 11.9 - - + -
1007B ASN* 3.0 35.1 + - + +
1008B VAL 4.0 1.1 - - - +
1009B GLN 3.2 0.4 - - - -
1010B LYS* 1.3 79.2 - - + +
1012B SER* 1.3 62.8 + - - +
1014B LEU* 3.1 11.2 + - + +
1015B LEU* 3.0 22.6 + - + +
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Residues in contact with SER1012 (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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689A ILE* 5.0 0.9 - - - +
985B LEU* 4.0 11.1 - - - +
1008B VAL* 3.0 24.3 + - - +
1009B GLN* 3.1 12.7 + - - -
1011B ILE* 1.3 76.7 - - - +
1013B ASN* 1.3 62.4 + - - +
1015B LEU* 3.8 0.6 + - - -
1016B SER* 3.1 18.0 + - - -
1022B LEU* 3.2 49.5 + - - +
1023B ARG* 4.2 12.2 + - - +
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Residues in contact with ASN1013 (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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1009B GLN* 2.9 20.7 + - + +
1010B LYS* 3.8 8.1 + - - +
1012B SER* 1.3 76.9 - - - +
1014B LEU* 1.3 66.6 + - - +
1016B SER* 2.7 23.3 + - - -
1017B ASP* 3.2 14.1 + - - +
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Residues in contact with LEU1014 (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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989B VAL* 4.4 22.4 - - + -
993B LYS* 6.0 6.1 - - + -
1010B LYS* 3.1 35.4 + - + +
1011B ILE* 3.1 10.8 + - + +
1013B ASN* 1.3 82.3 - - + +
1015B LEU* 1.3 62.4 + - - +
1017B ASP* 3.3 14.0 + - + +
1018B TYR* 3.2 26.6 + - + +
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Residues in contact with LEU1015 (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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985B LEU* 3.7 30.3 - - + +
988B LYS* 3.9 39.3 - - + +
989B VAL* 3.6 27.2 - - + +
992B ASN* 5.7 0.4 - - + -
1011B ILE* 3.0 11.2 + - + +
1012B SER 4.1 3.8 - - - +
1014B LEU* 1.3 77.3 - - - +
1016B SER* 1.3 59.6 + - - +
1018B TYR* 3.4 11.5 + - + +
1019B GLY 3.3 14.6 + - - -
1020B TYR* 3.7 26.6 + - + -
1021B HIS 4.1 11.0 - - - +
1022B LEU 4.0 9.9 - - - +
1024B GLY* 4.1 2.2 - - - -
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Residues in contact with SER1016 (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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1012B SER 3.1 9.0 + - - -
1013B ASN* 2.7 27.0 + - - -
1015B LEU* 1.3 74.0 - - - +
1017B ASP* 1.3 63.9 + - - +
1018B TYR 3.1 1.3 - - - -
1019B GLY* 3.0 14.9 + - - -
1020B TYR 3.7 14.3 + - - +
1022B LEU* 3.6 27.0 - - - +
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Residues in contact with ASP1017 (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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1013B ASN* 3.2 17.2 + - - +
1014B LEU* 3.3 16.0 + - + +
1016B SER* 1.3 77.0 + - - +
1018B TYR* 1.3 73.6 + - - +
1019B GLY* 3.5 0.5 + - - -
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Residues in contact with TYR1018 (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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989B VAL* 4.4 9.6 - - + -
992B ASN* 2.7 37.2 + - + +
993B LYS* 3.2 56.7 + - + +
1014B LEU* 3.2 15.0 + - + +
1015B LEU* 3.5 14.4 - - + +
1016B SER 3.1 0.6 - - - -
1017B ASP* 1.3 89.2 - - - +
1019B GLY* 1.3 55.8 + - - +
1020B TYR* 4.6 7.9 - - + -
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Residues in contact with GLY1019 (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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1015B LEU 3.3 0.8 + - - -
1016B SER 3.0 13.6 + - - -
1017B ASP 3.3 0.4 - - - -
1018B TYR* 1.3 80.0 - - - +
1020B TYR* 1.3 76.1 + - - +
204C PRO* 4.8 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