Contacts of the helix formed by residues 720 - 728 (chain A) in PDB entry 1ILE
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 VAL 720 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648A ASN* 5.4 0.4 - - - +
649A VAL* 3.3 30.7 - - + -
652A PHE* 4.8 19.7 - - + -
714A ASP 2.9 24.2 + - - +
715A LEU* 3.7 25.8 - - + -
716A SER 4.2 1.5 + - - +
718A TRP 3.1 1.0 + - - -
719A TYR* 1.3 69.0 - - + +
721A ARG* 1.3 65.1 + - - +
722A ARG 3.5 2.9 + - - -
723A ASN* 3.3 33.9 - - + +
724A ARG* 4.0 13.0 + - + +
743A LEU* 3.8 7.9 - - + -
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Residues in contact with ARG 721 (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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676A MET* 5.6 1.4 - - - +
716A SER* 4.3 18.3 - - - +
717A GLN 4.0 16.4 + - - +
718A TRP* 2.7 24.0 + - + +
720A VAL* 1.3 78.3 - - + +
722A ARG* 1.3 63.6 + - - +
724A ARG* 4.2 26.6 - - - +
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Residues in contact with ARG 722 (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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676A MET* 2.9 65.2 - - + +
677A ASP* 3.1 12.5 + - - -
718A TRP 4.7 0.2 - - - +
719A TYR* 2.8 69.7 + - - +
720A VAL 3.5 0.4 + - - -
721A ARG* 1.3 77.1 - - - +
723A ASN* 1.3 69.3 + - - +
724A ARG* 3.1 5.3 - - - +
725A ARG* 2.9 39.2 + - - +
726A ARG* 3.4 32.3 + - - +
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Residues in contact with ASN 723 (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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652A PHE* 2.7 30.8 - - - -
719A TYR* 3.0 23.6 + - - +
720A VAL* 3.3 26.3 - - + +
722A ARG* 1.3 80.0 - - - +
724A ARG* 1.3 64.4 + - - +
725A ARG 3.0 0.2 + - - -
726A ARG 4.8 0.2 - - - +
727A PHE* 2.9 59.9 + - - +
743A LEU* 3.2 38.0 - - - +
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Residues in contact with ARG 724 (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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652A PHE* 3.6 28.5 - - + -
720A VAL* 4.0 14.6 + - + +
721A ARG* 4.2 29.7 - - - +
722A ARG* 3.1 3.4 - - - +
723A ASN* 1.3 78.7 - - - +
725A ARG* 1.3 66.6 + - - +
728A TRP* 3.0 50.1 + - + +
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Residues in contact with ARG 725 (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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722A ARG* 2.9 25.2 + - - +
724A ARG* 1.3 85.0 - - - +
726A ARG* 1.3 82.9 + - - +
727A PHE 3.0 0.7 + - - -
728A TRP* 3.4 6.6 + - - -
729A LYS* 3.7 30.0 - - - +
730A ASN* 3.3 25.7 + - - +
736A ARG* 5.8 0.8 - - - +
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Residues in contact with ARG 726 (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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674A PRO* 2.9 39.8 - - - +
675A GLU* 4.4 6.1 + - - +
676A MET* 5.3 2.4 - - - +
677A ASP* 3.1 30.7 + - - +
722A ARG* 3.4 27.9 + - - +
723A ASN 3.4 1.4 + - - +
725A ARG* 1.3 93.5 - - - +
727A PHE* 1.3 70.4 + - + +
730A ASN* 3.1 37.5 + - - +
731A GLU* 4.8 0.3 - - - +
735A ASP 4.4 1.8 + - - -
736A ARG* 3.3 50.2 - - + +
739A ALA* 3.8 19.0 - - + +
740A TYR* 4.5 2.1 - - - -
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Residues in contact with PHE 727 (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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652A PHE* 4.0 11.7 - + + -
653A PHE* 4.6 3.8 - + - -
656A TYR* 3.7 15.0 - - + -
660A ASP* 3.3 20.3 - - - +
719A TYR* 4.7 1.6 - + - -
723A ASN* 2.9 62.5 + - - +
726A ARG* 1.3 82.8 - - + +
728A TRP* 1.3 57.4 + - - +
729A LYS* 2.8 14.9 + - - -
739A ALA* 3.0 50.0 - - + -
740A TYR* 3.3 51.7 + + - +
743A LEU* 3.9 14.4 - - + -
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Residues in contact with TRP 728 (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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652A PHE* 4.3 5.8 - + - -
656A TYR* 3.0 49.1 + + - -
660A ASP* 5.1 1.6 - - - +
724A ARG* 3.0 56.7 + - + +
725A ARG* 3.4 0.6 + - - -
727A PHE* 1.3 75.1 - - - +
729A LYS* 1.3 78.4 + - + +
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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