Contacts of the helix formed by residues 999 - 1013 (chain B) in PDB entry 1Q6S
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 GLU 999 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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997B LYS* 2.8 13.8 + - + +
998B LEU* 1.3 75.0 - - - +
1000B PHE* 1.3 65.5 + - + +
1001B MET 3.1 2.0 - - - -
1002B GLU* 3.0 34.8 + - + +
1003B MET* 3.3 8.7 + - + +
1240B ASP* 2.7 31.0 - - - +
1241B PRO* 3.5 16.8 - - - +
1242B SER* 2.9 32.9 + - - +
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Residues in contact with PHE1000 (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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997B LYS* 3.6 22.7 - - + -
998B LEU* 3.1 1.5 - - - -
999B GLU* 1.3 80.4 - - + +
1001B MET* 1.3 59.6 + - - +
1003B MET* 3.7 22.6 - - + +
1004B GLU* 2.9 47.2 + - + +
1241B PRO* 4.8 12.1 - - + -
1275B ILE* 4.3 2.7 - - + -
1278B ALA* 3.1 50.0 - - + -
1279B LYS* 3.6 26.5 - - + -
1282B MET* 3.4 24.7 - - + -
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Residues in contact with MET1001 (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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998B LEU* 3.1 26.5 + - + +
999B GLU 3.1 0.2 - - - -
1000B PHE* 1.3 78.1 - - - +
1002B GLU* 1.3 61.7 + - - +
1004B GLU* 3.8 8.5 - - - +
1005B LYS* 3.0 30.3 + - - +
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Residues in contact with GLU1002 (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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998B LEU 2.9 24.1 - - - +
999B GLU* 3.0 21.5 + - + +
1001B MET* 1.3 79.8 - - - +
1003B MET* 1.3 55.8 + - + +
1005B LYS* 3.0 35.4 + - - +
1006B GLU* 2.6 38.8 + - - +
1242B SER* 6.0 2.2 - - - -
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Residues in contact with MET1003 (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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999B GLU* 3.6 15.0 - - + +
1000B PHE* 3.4 32.1 + - + +
1002B GLU* 1.3 75.5 - - + +
1004B GLU* 1.3 52.9 + - - +
1006B GLU* 3.1 13.1 + - - +
1007B PHE* 2.6 36.4 + - - +
1235B MET* 3.3 30.7 - - + -
1241B PRO* 3.3 11.4 - - + -
1242B SER* 3.2 44.0 - - - +
1275B ILE* 4.2 25.1 - - + +
1278B ALA* 5.0 1.8 - - - -
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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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1000B PHE* 2.9 29.2 + - - +
1001B MET* 3.8 8.4 + - - +
1003B MET* 1.3 76.9 - - - +
1005B LYS* 1.3 57.7 + - - +
1007B PHE* 3.1 8.6 + - - +
1008B GLU* 2.8 45.4 + - - +
1275B ILE* 3.9 22.0 - - + -
1279B LYS* 3.7 27.4 - - - +
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Residues in contact with LYS1005 (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 MET 3.0 15.1 + - - +
1002B GLU* 3.0 54.5 + - - +
1004B GLU* 1.3 76.1 - - - +
1006B GLU* 1.3 57.3 + - - +
1008B GLU* 3.0 18.4 + - - +
1009B GLN* 2.7 36.1 + - - +
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Residues in contact with GLU1006 (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 GLU 2.6 22.9 + - - +
1003B MET* 3.1 12.8 - - - +
1005B LYS* 1.3 77.2 - - + +
1007B PHE* 1.3 62.1 + - - +
1009B GLN* 3.1 30.4 + - - +
1010B ILE* 3.3 27.9 + - + +
1271B TYR* 6.3 2.9 - - + -
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Residues in contact with PHE1007 (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 MET 2.6 15.2 + - - +
1004B GLU* 3.1 11.0 + - - +
1006B GLU* 1.3 73.2 - - - +
1008B GLU* 1.3 74.0 + - + +
1010B ILE* 2.9 13.1 + - - +
1011B ASP* 2.9 41.9 + - - +
1016B TRP* 3.6 22.0 - + - -
1268B ARG* 3.4 40.6 - - + -
1271B TYR* 3.7 30.1 - + + -
1272B LEU* 4.0 21.1 - - + -
1275B ILE* 3.9 18.4 - - + -
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Residues in contact with GLU1008 (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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1004B GLU* 2.8 41.1 + - - +
1005B LYS* 3.4 16.9 - - - +
1007B PHE* 1.3 83.3 - - + +
1009B GLN* 1.3 51.3 + - - +
1011B ASP* 3.2 11.0 + - + +
1012B LYS* 2.6 43.5 + - + +
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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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1005B LYS 2.7 15.5 + - - +
1006B GLU* 3.1 28.8 + - - +
1007B PHE 3.0 0.2 - - - -
1008B GLU* 1.3 74.1 - - - +
1010B ILE* 1.3 92.2 + - - +
1012B LYS* 3.1 23.8 + - + +
1013B SER* 3.3 14.1 + - - -
1015B SER* 5.2 0.5 + - - -
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Residues in contact with ILE1010 (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 GLU* 3.3 30.3 - - + +
1007B PHE* 2.9 8.4 + - - +
1009B GLN* 1.3 92.1 + - - +
1011B ASP* 1.3 58.3 + - - +
1013B SER* 3.6 2.9 + - - -
1014B GLY* 2.9 21.8 + - - -
1015B SER* 3.1 18.4 + - - +
1016B TRP* 3.4 46.2 + - + -
1019B ILE* 3.8 26.0 - - + -
1271B TYR* 4.4 13.0 - - + -
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Residues in contact with ASP1011 (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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616A LYS* 5.6 0.2 - - - +
1007B PHE* 2.9 24.0 + - - +
1008B GLU* 3.3 12.6 - - - +
1010B ILE* 1.3 75.5 - - - +
1012B LYS* 1.3 66.9 + - - +
1014B GLY* 2.9 14.5 + - - +
1016B TRP* 3.0 13.5 + - - +
1268B ARG* 2.7 47.5 + - - -
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Residues in contact with LYS1012 (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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616A LYS* 3.7 19.6 - - - +
1008B GLU* 2.6 30.6 + - + +
1009B GLN* 3.3 11.9 - - - +
1011B ASP* 1.3 75.5 - - - +
1013B SER* 1.3 58.4 + - - +
1014B GLY 3.4 1.2 + - - -
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Residues in contact with SER1013 (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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616A LYS* 4.5 28.0 - - - +
1009B GLN* 3.3 19.2 + - - -
1010B ILE 3.8 1.0 + - - -
1012B LYS* 1.3 76.3 - - - +
1014B GLY* 1.3 67.4 + - - +
1015B SER* 2.7 24.6 + - - -
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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