Contacts of the helix formed by residues 767 - 774 (chain B) in PDB entry 2QEP
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 ARG 767 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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763B PHE* 3.1 13.7 + - - +
764B VAL* 3.1 52.9 + - - +
766B GLN* 1.3 79.5 - - - +
768B GLU* 1.3 68.4 + - - +
769B GLU* 4.2 7.9 - - + +
770B ASN* 3.0 25.3 + - - +
771B VAL* 3.4 8.7 + - - +
786B ARG* 5.4 1.8 - - - +
799B ASP* 5.9 0.6 + - - -
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Residues in contact with GLU 768 (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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766B GLN 3.7 1.6 + - - -
767B ARG* 1.3 73.1 - - - +
769B GLU* 1.3 61.0 + - - +
770B ASN 3.3 0.5 + - - -
771B VAL* 3.6 19.9 + - - +
772B PRO* 4.1 4.0 - - - +
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Residues in contact with GLU 769 (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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767B ARG* 3.0 5.9 + - + +
768B GLU* 1.3 78.5 - - - +
770B ASN* 1.3 69.2 + - - +
772B PRO* 4.0 9.7 - - - +
773B LYS* 4.1 15.5 + - - +
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Residues in contact with ASN 770 (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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764B VAL* 2.8 28.5 + - - +
765B ALA 3.6 14.4 - - - +
767B ARG* 3.0 19.5 + - - +
769B GLU* 1.3 80.9 - - - +
771B VAL* 1.3 60.7 + - - +
772B PRO* 3.3 3.4 - - - -
773B LYS* 2.8 48.4 + - - +
774B ASN* 3.1 12.4 + - - -
798B SER* 4.0 2.4 + - - -
800B TYR* 3.6 34.8 - - + +
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Residues in contact with VAL 771 (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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766B GLN* 4.5 13.7 - - + +
767B ARG 3.4 13.1 + - - +
768B GLU* 3.9 12.1 - - - +
769B GLU 3.6 0.2 - - - -
770B ASN* 1.3 75.6 - - - +
772B PRO* 1.3 66.8 - - + +
774B ASN* 3.2 32.7 + - - +
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Residues in contact with PRO 772 (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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768B GLU 4.1 5.6 - - - +
769B GLU 4.0 12.3 - - - +
770B ASN 3.4 4.0 - - - -
771B VAL* 1.3 95.8 - - + +
773B LYS* 1.3 59.7 + - + +
774B ASN 3.2 6.5 - - - +
823B LEU* 3.5 18.1 - - + +
825B ALA* 4.1 16.4 - - + +
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Residues in contact with LYS 773 (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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769B GLU* 4.1 14.3 + - - +
770B ASN* 2.8 38.2 + - - +
772B PRO* 1.3 75.1 - - + +
774B ASN* 1.3 63.6 + - - +
796B SER* 4.3 18.6 + - - -
798B SER* 3.3 34.4 + - - -
800B TYR* 4.0 26.6 - - + +
801B ILE* 5.9 0.9 - - - -
802B ASN* 4.1 4.9 + - - +
820B GLN* 2.8 22.4 + - - -
823B LEU* 4.5 1.1 - - - -
825B ALA* 5.6 2.9 - - + +
826B THR* 3.8 24.4 - - + +
829B ASP* 4.6 8.1 - - - +
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Residues in contact with ASN 774 (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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765B ALA 3.0 26.1 + - - -
766B GLN* 5.0 1.0 - - - +
770B ASN 3.1 14.6 + - - -
771B VAL* 3.2 19.4 + - - +
772B PRO* 3.2 1.8 - - - +
773B LYS* 1.3 80.7 - - - +
775B ARG* 1.3 64.4 + - - +
776B SER 4.5 6.5 - - - +
777B LEU* 6.1 0.2 - - - -
780B LEU* 3.4 25.2 - - + +
800B TYR* 2.4 31.7 + - - -
802B ASN* 3.6 5.7 - - - +
820B GLN* 3.6 4.0 - - - +
823B LEU* 3.8 10.8 - - - +
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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