Contacts of the helix formed by residues 700 - 714 (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 PRO 700 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A TYR* 3.8 16.8 - - + -
66A LEU* 3.6 28.0 - - + -
67A PHE* 4.1 8.9 - - + -
579A ILE* 4.5 2.9 - - + -
619A TYR* 3.9 13.4 - - + +
624A PRO* 3.7 28.9 - - + -
695A LEU* 4.4 2.7 - - + -
698A TYR 3.1 13.5 - - - +
699A ASP* 1.3 83.1 - - - +
701A THR* 1.3 61.6 + - + +
703A SER* 2.8 20.5 + - - +
704A ALA* 3.3 16.1 + - - +
757A PHE* 3.8 2.1 - - - -
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Residues in contact with THR 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR* 5.3 1.3 - - - +
618A ILE 4.7 0.7 - - - +
619A TYR* 2.8 25.8 - - - +
622A ALA 3.2 26.5 - - - +
623A PRO* 3.6 23.5 - - + +
624A PRO* 4.0 10.9 - - + +
699A ASP* 3.0 8.4 + - - -
700A PRO* 1.3 80.7 - - + +
702A THR* 1.3 76.8 + - - +
703A SER 3.0 1.3 - - - -
704A ALA* 3.5 0.7 + - - +
705A ARG* 3.0 40.1 + - - +
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Residues in contact with THR 702 (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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694A ALA* 3.8 9.2 - - - +
699A ASP* 2.6 36.2 + - - +
701A THR* 1.3 84.8 + - - +
703A SER* 1.3 57.2 + - - +
705A ARG* 3.7 16.2 - - - +
706A ALA* 2.9 31.0 + - - +
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Residues in contact with SER 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A VAL* 3.6 22.0 - - - +
694A ALA* 3.3 18.4 - - - +
695A LEU* 3.3 18.6 - - - +
699A ASP 3.1 16.5 + - - -
700A PRO 2.8 16.1 + - - -
702A THR* 1.3 76.3 + - - +
704A ALA* 1.3 74.0 + - - +
706A ALA* 3.2 11.0 + - - +
707A LEU* 3.2 8.7 + - - +
757A PHE* 3.2 18.7 - - - -
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Residues in contact with ALA 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A TRP* 3.2 24.9 - - + -
619A TYR* 3.8 17.7 - - + -
620A VAL* 5.0 1.8 - - + +
700A PRO 3.3 11.5 + - - +
701A THR 4.1 1.8 - - - +
703A SER* 1.3 80.0 + - - +
705A ARG* 1.3 62.7 + - - +
707A LEU* 3.1 15.4 + - - +
708A ARG 3.1 11.3 + - - -
757A PHE* 3.3 32.1 - - + -
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Residues in contact with ARG 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A VAL* 2.7 48.5 + - + +
621A SER 3.0 18.8 + - - -
622A ALA* 3.5 10.4 - - - +
623A PRO* 4.7 6.1 - - - +
701A THR* 3.0 34.7 + - - +
702A THR* 3.7 14.8 - - - +
704A ALA* 1.3 71.8 - - - +
706A ALA* 1.3 61.1 + - - +
707A LEU 3.0 2.1 + - - -
708A ARG* 3.3 12.8 + - + +
709A ASP* 2.8 36.3 + - - +
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Residues in contact with ALA 706 (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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683A ARG* 4.5 5.9 + - - +
687A LEU* 3.4 16.2 - - + +
690A ARG* 4.2 29.8 - - + +
691A VAL* 4.4 5.2 - - + +
702A THR 2.9 19.4 + - - +
703A SER* 3.2 5.6 + - - +
705A ARG* 1.3 75.2 - - - +
707A LEU* 1.3 61.0 + - - +
709A ASP* 3.7 12.6 + - - +
710A PHE* 3.4 12.0 + - - +
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Residues in contact with LEU 707 (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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616A TRP* 4.2 6.5 - - + -
642A TYR* 2.9 33.9 - - + +
687A LEU* 3.9 22.2 - - + +
691A VAL* 4.3 5.6 - - + +
703A SER 3.2 9.9 + - - +
704A ALA* 3.1 14.8 + - - +
705A ARG 3.0 0.4 - - - -
706A ALA* 1.3 75.7 - - - +
708A ARG* 1.3 67.0 + - - +
710A PHE* 3.2 13.9 + - + +
711A VAL* 3.2 15.3 + - + -
750A VAL* 4.3 16.6 - - + +
753A LEU* 3.9 31.0 - - + -
754A ALA* 5.1 7.9 - - + +
757A PHE* 5.9 5.2 - - + -
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Residues in contact with ARG 708 (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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616A TRP* 3.7 13.7 - - + +
620A VAL* 5.0 9.4 - - + +
641A ASP* 2.7 43.4 + - - -
642A TYR* 3.1 36.3 - - + -
704A ALA 3.1 5.2 + - - +
705A ARG* 3.3 19.1 - - - +
707A LEU* 1.3 78.5 - - - +
709A ASP* 1.3 96.3 + - - +
711A VAL* 3.1 2.3 + - - -
712A VAL* 2.8 57.0 + - + +
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Residues in contact with ASP 709 (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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683A ARG* 5.5 4.3 - - - +
705A ARG* 2.8 27.8 + - - +
706A ALA* 3.7 11.0 - - - +
708A ARG* 1.3 107.7 + - - +
710A PHE* 1.3 65.2 + - - +
712A VAL 3.1 19.4 + - - +
713A GLU* 3.3 8.7 - - - +
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Residues in contact with PHE 710 (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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680A LEU* 4.7 10.3 - - + -
683A ARG* 3.8 38.3 - - + +
684A MET* 3.9 27.6 - - + -
687A LEU* 3.7 32.8 - - + -
706A ALA 3.4 2.4 + - - +
707A LEU* 3.2 9.7 + - + +
709A ASP* 1.3 77.1 - - - +
711A VAL* 1.3 56.1 + - + +
712A VAL 3.0 1.2 + - - -
713A GLU* 3.0 27.5 + - - +
714A ASP* 2.8 56.1 + - + +
746A ALA* 4.3 9.6 - - + -
749A LEU* 5.7 0.7 - - + -
750A VAL* 3.6 31.0 - - + -
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Residues in contact with VAL 711 (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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642A TYR* 4.0 18.2 - - + -
645A THR* 3.7 6.6 - - + +
646A LEU* 3.4 39.9 - - + -
649A VAL* 4.9 3.6 - - + -
707A LEU* 3.2 10.9 + - + +
708A ARG 3.1 7.4 + - - +
710A PHE* 1.3 78.7 - - + +
712A VAL* 1.3 56.7 + - + +
713A GLU 3.3 0.4 - - - -
714A ASP* 3.8 9.6 - - + +
715A LEU* 3.0 27.0 + - - +
750A VAL* 3.5 43.1 - - + -
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Residues in contact with VAL 712 (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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641A ASP* 4.2 15.3 - - - +
642A TYR* 4.9 5.2 - - - -
645A THR* 3.9 21.3 - - + +
708A ARG* 2.8 52.2 + - + +
709A ASP 3.3 4.3 - - - +
710A PHE 3.0 0.4 + - - -
711A VAL* 1.3 75.4 - - + +
713A GLU* 1.3 62.0 + - - +
715A LEU 3.4 7.0 - - - +
716A SER* 4.6 13.5 - - - +
717A GLN* 4.1 8.4 - - - +
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Residues in contact with GLU 713 (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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679A TRP* 4.3 11.7 - - - -
680A LEU* 5.8 0.2 - - - +
683A ARG* 3.3 27.9 + - - -
709A ASP 3.3 9.2 - - - +
710A PHE* 3.0 36.1 - - - +
712A VAL* 1.3 79.2 - - - +
714A ASP* 1.3 64.8 + - - +
715A LEU 3.0 3.0 + - - -
716A SER 3.7 1.8 - - - -
717A GLN* 3.5 17.5 - - + -
718A TRP* 3.3 21.7 - - - +
719A TYR 3.8 1.2 + - - -
806A LEU* 3.9 37.5 - - + +
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Residues in contact with ASP 714 (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* 5.6 0.9 - - - +
649A VAL* 3.7 26.0 - - - +
680A LEU* 4.2 13.0 - - - +
710A PHE* 2.8 38.7 + - + +
711A VAL* 3.7 12.6 - - - +
713A GLU* 1.3 79.5 - - - +
715A LEU* 1.3 68.9 + - - +
716A SER 3.1 5.0 - - - +
719A TYR* 3.7 7.1 + - - +
720A VAL* 2.9 27.0 + - - -
743A LEU* 4.3 12.3 - - - +
746A ALA* 4.2 11.4 - - - +
747A LEU* 5.6 3.2 - - - +
750A VAL* 5.8 1.9 - - - +
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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