Contacts of the helix formed by residues 756 - 764 (chain A) in PDB entry 4HPF
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 SER 756 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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720A VAL* 4.8 3.2 + - - +
722A GLY 3.6 26.8 + - - +
723A ASP* 4.1 4.7 - - - +
755A GLY* 1.3 70.1 - - - -
757A LEU* 1.3 59.7 + - - +
758A ASP* 3.5 11.4 + - - +
759A TYR* 3.3 20.3 + - - +
760A LEU* 2.8 30.2 + - - +
778A GLY 3.7 4.7 + - - +
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Residues in contact with LEU 757 (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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697A LEU* 4.1 14.8 - - + -
701A THR* 3.9 28.3 - - + +
755A GLY 3.2 6.2 + - - -
756A SER* 1.3 72.3 + - - +
758A ASP* 1.3 64.6 + - - +
760A LEU* 3.0 6.9 + - + +
761A GLN* 2.6 51.2 + - + +
775A ILE* 5.3 7.0 - - + -
777A PRO* 4.1 23.3 - - + +
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Residues in contact with ASP 758 (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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723A ASP* 5.3 0.2 - - - -
724A ALA* 4.6 18.8 - - + +
756A SER* 3.7 9.1 + - - +
757A LEU* 1.3 85.0 + - - +
759A TYR* 1.3 60.4 + - - +
761A GLN* 3.6 13.7 + - - +
762A ARG* 3.4 24.0 + - - +
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Residues in contact with TYR 759 (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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720A VAL* 4.1 23.6 - - + -
721A PHE 3.8 16.2 - - - -
722A GLY* 3.7 13.7 - - - -
723A ASP 3.6 35.4 - - - +
726A SER* 4.0 10.1 - - - -
727A ALA 2.8 23.7 + - - -
728A PRO* 4.1 4.5 - - + -
729A MET* 2.8 48.7 + - + +
731A LEU* 5.4 0.2 - - + -
756A SER* 3.1 13.5 + - - +
758A ASP* 1.3 78.5 - - - +
760A LEU* 1.3 68.3 + - + +
762A ARG* 3.3 26.3 + - + +
763A GLU* 3.8 13.9 + - + +
803A PRO* 4.1 3.0 - - + +
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Residues in contact with LEU 760 (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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697A LEU* 6.0 0.2 - - + -
720A VAL* 3.5 27.8 - - + -
731A LEU* 3.7 25.4 - - + -
753A PHE* 4.0 20.2 - - + -
755A GLY* 4.0 22.2 - - - +
756A SER 2.8 19.1 + - - +
757A LEU* 3.0 5.6 + - + +
759A TYR* 1.3 78.3 - - + +
761A GLN* 1.3 62.9 + - - +
762A ARG 3.1 2.5 - - - -
763A GLU* 3.1 15.8 + - + +
764A TRP* 3.2 12.5 + - - +
767A LEU* 5.9 1.4 - - + +
775A ILE* 3.7 41.8 - - + +
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Residues in contact with GLN 761 (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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697A LEU* 3.5 28.4 - - + +
757A LEU* 2.6 30.4 + - + +
758A ASP* 3.6 13.6 + - - +
760A LEU* 1.3 74.2 - - - +
762A ARG* 1.3 80.3 + - - +
763A GLU 3.2 0.2 - - - -
764A TRP* 3.4 14.8 + - - +
765A ARG* 4.5 2.1 + - - +
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Residues in contact with ARG 762 (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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723A ASP 2.6 29.9 + - - -
724A ALA* 2.9 21.6 + - - +
726A SER 2.8 23.6 + - - -
728A PRO* 4.8 14.7 - - + +
758A ASP 3.4 18.0 + - - +
759A TYR* 3.3 20.7 + - + +
760A LEU 3.1 1.2 - - - -
761A GLN* 1.3 94.5 - - - +
763A GLU* 1.3 59.5 + - + +
765A ARG* 4.6 5.0 + - - +
766A PHE* 4.5 11.8 - - - -
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Residues in contact with GLU 763 (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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728A PRO* 3.3 18.0 - - - +
729A MET 2.8 45.4 + - - +
730A GLY* 4.0 2.8 - - - -
731A LEU* 3.4 36.0 + - + +
732A ARG 4.9 0.9 + - - -
759A TYR* 3.9 18.4 + - + +
760A LEU* 3.1 10.8 + - + +
762A ARG* 1.3 76.7 - - + +
764A TRP* 1.3 59.1 + - - +
765A ARG 3.2 2.5 - - - -
766A PHE* 2.9 38.6 + - - +
767A LEU* 3.5 14.6 + - + +
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Residues in contact with TRP 764 (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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695A THR* 3.2 24.3 + - - -
696A SER* 4.9 0.4 - - - -
697A LEU* 3.4 36.8 - - + +
700A VAL* 3.4 42.8 - - + -
760A LEU 3.2 9.2 + - - +
761A GLN* 3.4 18.9 + - - +
763A GLU* 1.3 78.6 - - - +
765A ARG* 1.3 64.0 + - - +
767A LEU* 3.0 34.7 + - + +
768A TRP* 3.1 39.3 + + - +
770A PHE 5.8 1.6 - - - -
773A ILE* 3.8 27.6 - - + -
775A ILE* 3.8 18.2 - - + -
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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