Contacts of the helix formed by residues 725 - 731 (chain A) in PDB entry 5IJ7
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 ASP 725 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689A HIS* 3.2 8.0 - - - -
690A SER 3.2 17.4 + - - +
691A VAL* 3.6 13.2 - - - +
693A PRO* 3.8 15.3 - - + +
695A CYS 4.4 0.8 + - - -
696A TYR* 5.7 0.4 - - - +
697A ALA* 6.0 0.2 - - - +
724A PHE* 1.3 78.6 - - - +
726A TYR* 1.3 64.7 + - - +
727A ARG* 2.8 50.6 + - - +
728A TYR* 3.4 37.2 + - + +
729A SER* 4.3 2.1 + - - -
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Residues in contact with TYR 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A TYR* 5.3 1.4 + - - -
664A SER* 4.0 16.4 - - - -
665A PHE* 4.6 11.5 - + - -
667A PHE* 3.5 28.5 - + + -
685A ARG 4.2 5.5 + - - -
687A ALA 2.6 24.9 + - - -
688A ASN* 3.8 4.3 - - - -
689A HIS* 2.9 44.1 + - + +
724A PHE* 3.5 41.3 - + - -
725A ASP* 1.3 71.0 - - - +
727A ARG* 1.4 63.2 + - + +
729A SER* 3.1 16.6 + - - -
730A GLN* 3.1 32.0 + - - +
9001A 6BN 4.1 10.4 - - - +
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Residues in contact with ARG 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A HIS* 4.0 10.1 - - + +
691A VAL* 3.6 29.0 + - - +
725A ASP* 2.8 37.3 + - - +
726A TYR* 1.4 75.7 - - + +
728A TYR* 1.3 68.7 + - + +
730A GLN* 3.6 18.1 + - - +
731A ALA* 2.8 37.8 + - + +
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Residues in contact with TYR 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A ALA 6.2 0.4 - - - +
725A ASP* 3.4 44.9 - - + +
726A TYR 3.2 1.2 - - - -
727A ARG* 1.3 92.5 + - + +
729A SER* 1.3 60.6 + - - +
730A GLN 3.7 0.2 + - - -
731A ALA* 3.7 14.8 + - + +
732A ASP* 3.8 9.2 - - - +
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Residues in contact with SER 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A PHE* 3.4 34.0 - - - -
668A ASN* 3.5 31.5 + - - +
697A ALA* 3.8 24.4 - - - +
708A ILE* 5.4 3.4 - - - +
724A PHE* 4.2 8.2 - - - -
725A ASP 4.3 0.7 + - - -
726A TYR 3.1 6.0 + - - -
728A TYR* 1.3 79.3 - - - +
730A GLN* 1.3 59.9 + - - +
732A ASP* 3.7 5.1 - - - +
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Residues in contact with GLN 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A SER* 4.2 18.8 + - - -
666A LEU 4.9 4.9 - - - +
667A PHE* 4.4 12.9 - - + +
668A ASN* 3.1 16.5 + - - +
726A TYR* 3.1 37.0 + - - +
727A ARG* 3.6 21.0 + - - +
729A SER* 1.3 76.7 - - - +
731A ALA* 1.3 57.5 + - - +
732A ASP 2.9 10.7 + - - +
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Residues in contact with ALA 731 (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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727A ARG* 2.8 19.2 + - + +
728A TYR* 3.7 10.3 + - + +
729A SER 3.5 0.8 - - - -
730A GLN* 1.3 70.9 - - - +
732A ASP* 1.3 71.2 + - - +
733A ALA* 4.1 1.6 - - - -
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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