Contacts of the helix formed by residues 761 - 769 (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 LEU 761 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A PHE* 4.0 20.6 - - + -
13A LEU* 5.5 0.7 - - + -
612A ASP* 2.9 15.0 + - + +
642A TYR* 5.0 8.1 - - + +
643A PHE* 4.7 28.7 - - + +
646A LEU* 4.0 22.9 - - + -
647A TRP* 4.0 29.8 - - + -
754A ALA* 6.2 0.2 - - + -
758A THR* 4.1 11.4 - - - +
760A PHE* 1.3 77.6 - - - +
762A ALA* 1.3 65.3 + - - +
764A VAL* 2.8 24.9 + - + +
765A LEU* 2.8 23.1 + - + +
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Residues in contact with ALA 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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751A ALA* 3.2 31.3 - - - +
754A ALA* 3.8 6.0 - - + +
755A ALA* 3.5 23.3 - - + +
758A THR* 3.2 16.9 + - - +
759A PRO 4.8 1.8 - - - -
761A LEU* 1.3 78.9 - - - +
763A GLU* 1.3 57.1 + - - +
765A LEU* 3.5 7.2 + - - +
766A TRP* 2.8 30.7 + - - +
781A VAL* 3.4 5.4 - - + +
782A HIS* 5.2 0.2 - - - +
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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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17A VAL* 3.4 25.1 - - + -
20A PHE* 3.3 21.0 - - + -
21A TRP* 2.7 19.1 + - - -
759A PRO 3.6 14.7 + - - +
760A PHE 2.7 18.5 + - - +
762A ALA* 1.3 71.5 - - - +
764A VAL* 1.3 52.2 + - - +
766A TRP* 3.6 0.3 - - - -
767A GLN* 2.7 50.9 + - + +
780A SER* 2.7 25.1 + - - -
781A VAL* 3.1 30.8 + - + +
782A HIS* 4.6 1.1 - - + -
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Residues in contact with VAL 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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13A LEU* 4.3 29.6 - - + -
17A VAL* 3.8 19.5 - - + -
647A TRP* 3.9 20.9 - - + -
650A TYR* 4.6 4.0 + - - +
760A PHE* 2.8 19.3 + - + +
761A LEU* 2.8 20.4 + - + +
763A GLU* 1.3 69.0 - - - +
765A LEU* 1.3 95.8 + - + +
767A GLN* 3.0 17.4 + - - +
768A ASN* 3.2 13.9 + - - +
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Residues in contact with LEU 765 (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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646A LEU* 4.3 24.7 - - + -
647A TRP* 4.2 7.9 - - + -
650A TYR* 3.9 47.3 - - + -
747A LEU* 4.7 11.4 - - + +
750A VAL* 5.8 0.4 - - + -
751A ALA* 3.7 24.5 - - + +
761A LEU* 2.8 20.1 + - + +
762A ALA* 3.7 4.9 - - - +
764A VAL* 1.3 100.8 - - + +
766A TRP* 1.3 57.2 + - - +
769A LEU* 3.1 42.0 + - + +
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Residues in contact with TRP 766 (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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748A VAL* 5.4 4.0 - - + -
751A ALA* 4.6 6.7 - - + +
752A THR* 4.0 17.7 - - + -
762A ALA 2.8 7.3 + - - +
763A GLU* 3.8 0.9 - - - +
765A LEU* 1.3 73.6 - - - +
767A GLN* 1.3 83.5 + - - +
768A ASN 3.1 2.2 + - - -
770A VAL* 3.3 55.9 - - + +
771A ARG* 3.4 8.0 + - + +
777A ALA* 4.4 4.0 - - + -
778A LYS* 3.1 41.1 + - + -
779A GLU 3.8 1.4 + - - -
780A SER* 3.5 17.8 - - - +
781A VAL* 3.3 44.2 - - + -
784A ALA* 4.0 23.1 - - + -
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Residues in contact with GLN 767 (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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20A PHE* 4.2 15.6 - - + -
763A GLU* 2.7 36.5 + - + +
764A VAL* 3.0 8.5 + - - +
766A TRP* 1.3 81.7 - - - +
768A ASN* 1.3 57.0 - - + +
771A ARG* 2.7 61.3 + - - +
772A SER* 4.6 0.5 + - - -
779A GLU 3.1 20.6 + - - +
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Residues in contact with ASN 768 (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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2A PHE* 3.6 11.9 - - - +
3A LYS* 3.4 51.1 + - + +
4A GLU 4.7 3.8 + - - -
5A VAL* 5.8 0.6 - - - +
650A TYR* 3.2 28.3 + - - +
654A VAL* 4.8 2.2 - - - +
764A VAL 3.2 7.6 + - - +
766A TRP 3.1 0.6 - - - -
767A GLN* 1.3 76.7 - - - +
769A LEU* 1.3 59.0 + - - +
770A VAL 2.5 17.8 + - - -
771A ARG 3.2 1.4 + - - -
772A SER* 2.8 39.2 + - - -
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Residues in contact with LEU 769 (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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2A PHE* 3.5 15.1 - - + -
650A TYR* 3.4 36.6 - - + -
653A PHE* 3.7 15.5 - - + -
654A VAL* 3.6 20.0 - - + -
744A TYR* 2.5 47.2 + - + -
747A LEU* 3.5 41.3 - - + +
748A VAL* 4.7 4.7 - - + +
751A ALA* 6.0 0.4 - - + -
765A LEU* 3.1 23.2 + - + +
768A ASN* 1.3 77.1 - - - +
770A VAL* 1.3 54.9 + - + +
773A VAL* 3.7 0.9 - - - +
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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