Contacts of the helix formed by residues 488 - 496 (chain A) in PDB entry 2I6W
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 488 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA* 4.0 9.6 - - + +
13A TRP* 4.5 26.5 - - + +
15A ILE* 6.3 2.7 - - + -
16A ALA* 3.7 26.7 - - + +
370A ILE* 5.3 2.0 - - + +
371A ALA* 5.7 3.1 - - - -
374A VAL* 4.2 24.9 - - + -
484A VAL* 4.2 14.8 - - + +
487A ILE* 1.3 80.6 - - + +
489A THR* 1.3 55.9 + - - +
491A ALA* 3.3 13.7 - - - +
492A LEU* 2.2 82.7 + - + +
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Residues in contact with THR 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ILE* 4.9 11.5 - - + +
371A ALA* 4.0 21.0 - - + +
409A ALA* 4.8 16.7 - - + +
412A VAL* 4.1 20.6 - - + -
413A VAL* 5.3 0.9 - - + -
484A VAL* 3.7 11.3 + - - +
485A ALA* 3.7 18.6 - - - +
487A ILE 2.3 19.6 + - - -
488A LEU* 1.3 66.5 - - - +
490A PRO* 1.3 69.3 - - + +
492A LEU* 3.0 7.0 + - - -
493A CYS* 2.6 37.9 + - + +
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Residues in contact with PRO 490 (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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4A PHE 5.7 0.7 - - - +
5A PHE 5.6 0.7 - - - +
6A ILE* 3.5 24.7 - - + -
412A VAL* 4.1 3.4 - - + -
435A MET* 3.9 23.3 - - + -
485A ALA 3.0 18.6 - - - +
486A LEU* 3.0 22.7 - - - +
487A ILE* 3.1 14.1 - - - +
489A THR* 1.3 90.9 - - + +
491A ALA* 1.3 52.2 + - - +
493A CYS* 3.1 13.4 - - - -
494A ALA* 2.7 38.8 + - - +
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Residues in contact with ALA 491 (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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6A ILE* 4.3 0.2 - - - +
7A ASP* 3.9 31.1 - - + +
9A PRO* 4.7 8.7 - - + +
12A ALA* 4.0 9.6 - - + -
487A ILE* 5.0 0.4 - - - +
488A LEU* 3.1 28.0 - - - +
490A PRO* 1.3 81.2 - - - +
492A LEU* 1.3 53.2 - - + +
494A ALA* 3.8 3.0 - - - +
495A THR* 2.5 44.0 + - - +
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Residues in contact with LEU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PRO* 6.2 0.4 - - + -
13A TRP* 3.4 35.7 - - + +
367A ILE* 4.4 14.1 - - + +
370A ILE* 4.1 38.4 - - + -
371A ALA* 5.4 2.2 - - + +
488A LEU* 2.2 68.1 + - + +
489A THR* 3.6 4.3 - - - +
491A ALA* 1.3 66.8 - - + +
493A CYS* 1.3 53.0 + - - +
494A ALA 2.7 8.6 + - - -
495A THR* 2.7 7.3 + - - +
496A MET* 2.4 51.6 + - + +
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Residues in contact with CYS 493 (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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367A ILE* 3.4 31.6 - - + +
412A VAL* 3.7 26.2 - - - +
413A VAL* 4.9 9.6 - - + -
416A VAL* 4.8 8.9 - - + +
427A PRO 5.1 0.7 - - - +
431A THR* 3.5 17.1 + - - +
489A THR* 2.6 31.0 + - - +
490A PRO* 3.1 23.3 - - - -
492A LEU* 1.3 72.4 - - - +
494A ALA* 1.3 55.7 + - - -
496A MET 3.7 12.1 - - - +
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Residues in contact with ALA 494 (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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6A ILE* 3.3 19.7 - - + -
427A PRO* 4.1 15.6 - - - +
428A LYS* 5.0 5.0 - - - +
431A THR* 3.2 28.3 - - + +
490A PRO 2.7 19.5 + - - +
491A ALA* 3.8 2.9 - - - +
492A LEU 2.7 4.4 + - - -
493A CYS* 1.3 74.4 - - - +
495A THR* 1.3 62.3 + - + +
496A MET 3.2 5.4 + - - +
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Residues in contact with THR 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASP 5.3 4.7 - - - +
9A PRO* 3.7 43.6 - - + +
13A TRP* 5.4 0.9 + - - -
491A ALA* 2.5 28.5 + - - +
492A LEU* 2.7 17.6 + - - +
494A ALA* 1.3 77.8 - - + +
496A MET* 1.3 64.1 + - - +
497A LEU 4.1 0.7 + - - -
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Residues in contact with MET 496 (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 TRP* 5.5 4.7 - - + -
363A ARG 4.4 4.7 - - - +
366A LEU* 4.6 11.0 - - + -
367A ILE* 4.2 25.4 - - + +
370A ILE* 4.1 27.1 - - + -
427A PRO* 6.0 1.7 - - - +
492A LEU* 2.4 44.7 + - + +
493A CYS* 3.7 12.3 - - - +
494A ALA 3.2 2.7 - - - +
495A THR* 1.3 80.0 - - - +
497A LEU* 1.3 99.5 + - + +
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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