Contacts of the helix formed by residues 906 - 915 (chain A) in PDB entry 1QU2
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 CYS 906 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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886A CYS* 3.3 10.6 - - + -
889A CYS* 3.9 6.5 - - - -
891A ASN* 5.5 2.5 - - + +
893A SER* 3.8 20.0 - - - -
895A ASP 4.4 0.2 - - - -
896A LEU* 3.5 6.8 - - - +
905A LEU* 1.3 75.9 - - - +
907A PRO* 1.3 72.7 - - + +
908A ARG* 3.1 17.0 - - - -
909A CYS 3.1 14.2 + - - -
910A GLN* 2.8 26.4 + - - +
1001A ZN 2.4 35.4 - - - -
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Residues in contact with PRO 907 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893A SER* 3.8 9.4 - - - +
895A ASP* 3.4 31.0 - - + +
906A CYS* 1.3 87.4 - - + +
908A ARG* 1.3 62.1 + - - +
910A GLN* 3.3 16.8 + - + +
911A GLN* 3.2 22.7 + - - +
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Residues in contact with ARG 908 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726A ASP* 2.4 60.4 + - - -
730A ILE* 3.7 17.1 - - + +
731A GLU* 3.1 35.0 + - - +
850A HIS* 6.0 2.3 + - - -
851A GLN* 3.3 5.6 - - - +
889A CYS* 3.8 20.0 - - - +
891A ASN* 4.1 6.1 + - - +
906A CYS* 3.1 13.9 - - - -
907A PRO* 1.3 82.4 - - - +
909A CYS* 1.3 61.5 + - - +
911A GLN* 3.3 7.1 + - - +
912A VAL* 3.3 21.9 + - + +
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Residues in contact with CYS 909 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730A ILE* 3.7 10.8 - - - -
886A CYS* 4.2 2.9 - - - -
888A ARG* 3.4 36.8 - - + +
889A CYS* 3.6 14.8 - - - -
905A LEU* 4.4 5.4 - - + -
906A CYS* 3.1 8.2 + - - +
908A ARG* 1.3 76.9 - - - +
910A GLN* 1.3 65.3 + - - +
912A VAL* 4.4 6.5 - - - +
913A VAL* 3.0 31.2 + - - +
1001A ZN 2.3 35.2 - - - -
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Residues in contact with GLN 910 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895A ASP 3.9 4.2 - - - +
897A GLY* 3.0 24.0 + - - +
898A ALA 5.2 2.2 + - - -
899A VAL* 3.6 21.2 - - + +
905A LEU* 3.0 27.4 - - + +
906A CYS 2.8 21.3 + - - +
907A PRO* 3.3 15.4 + - - +
909A CYS* 1.3 76.5 - - - +
911A GLN* 1.3 57.9 + - - +
913A VAL* 3.8 1.0 - - - +
914A LYS* 2.9 57.1 + - - +
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Residues in contact with GLN 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732A GLN* 3.7 13.2 - - - +
907A PRO 3.2 8.9 + - - +
908A ARG* 3.5 12.3 - - - +
909A CYS 3.2 0.4 - - - -
910A GLN* 1.3 77.8 - - - +
912A VAL* 1.3 66.7 + - + +
914A LYS* 3.5 10.5 + - - +
915A SER* 3.2 21.7 + - - -
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Residues in contact with VAL 912 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A THR 5.1 1.1 - - - +
730A ILE 3.4 28.0 - - - +
731A GLU* 4.2 11.0 - - - +
732A GLN* 3.8 38.6 - - + +
888A ARG* 3.8 19.7 - - - +
908A ARG* 3.3 17.8 + - + +
909A CYS* 3.4 6.7 + - - +
911A GLN* 1.3 76.4 - - + +
913A VAL* 1.3 62.7 + - - +
915A SER* 2.6 21.5 + - - +
916A LEU* 3.3 15.8 - - + +
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Residues in contact with VAL 913 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A THR* 4.4 10.1 - - + -
888A ARG* 3.9 30.3 - - - +
899A VAL* 3.8 26.7 - - + +
902A LEU* 4.3 16.2 - - + -
905A LEU* 4.3 9.6 - - + -
909A CYS 3.0 18.6 + - - +
910A GLN* 3.8 4.3 - - - +
912A VAL* 1.3 73.5 - - - +
914A LYS* 1.3 60.7 + - - +
916A LEU* 2.8 38.2 + - + +
917A VAL* 3.6 5.6 + - + +
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Residues in contact with LYS 914 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898A ALA 5.2 2.0 + - - -
899A VAL* 3.7 25.6 - - + +
910A GLN* 2.9 53.1 + - - +
911A GLN* 3.7 8.3 - - + +
912A VAL 3.4 0.2 - - - -
913A VAL* 1.3 76.4 - - - +
915A SER* 1.3 58.4 + - - +
916A LEU 3.1 0.2 - - - -
917A VAL* 2.9 25.8 - - - +
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Residues in contact with SER 915 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732A GLN* 3.4 32.2 + - - +
911A GLN 3.2 11.0 + - - -
912A VAL 2.6 19.4 + - - -
913A VAL 3.1 0.8 - - - -
914A LYS* 1.3 76.2 - - - +
916A LEU* 1.3 66.0 + - - +
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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