Contacts of the helix formed by residues 478 - 491 (chain A) in PDB entry 2I91
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 HIS 478 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A MET* 3.7 14.5 + - + -
6A ASP 3.0 16.8 + - - -
7A GLN* 3.7 15.9 - - - +
9A GLN 2.6 29.7 + - - -
11A LEU* 3.5 27.9 - - + +
15A GLN* 3.6 17.9 + - - -
23A TYR 3.5 24.7 + - - -
25A TRP* 6.1 1.4 - - + -
448A ALA* 4.2 0.2 - - - -
477A VAL* 1.3 74.4 - - - +
479A PRO* 1.3 66.7 - - + +
480A ALA* 4.2 1.8 - - + +
481A THR* 2.7 38.3 + - - +
482A ALA* 2.8 10.7 + - - +
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Residues in contact with PRO 479 (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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7A GLN* 4.6 11.2 - - + +
23A TYR 6.0 0.2 - - - +
25A TRP* 6.2 0.4 - - + -
447A CYS* 3.4 26.0 - - + +
448A ALA* 3.7 16.4 - - + +
451A MET* 3.6 13.5 - - + +
472A THR* 5.0 4.9 - - + -
477A VAL 3.6 3.8 - - - +
478A HIS* 1.3 88.8 - - + +
480A ALA* 1.3 57.6 + - - +
482A ALA* 3.0 4.0 + - + +
483A LEU* 2.9 26.3 + - - +
496A LEU* 5.5 2.2 - - + -
508A ILE* 3.5 43.5 - - + +
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Residues in contact with ALA 480 (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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11A LEU* 4.4 8.3 - - + -
25A TRP* 3.8 34.5 - - + -
478A HIS* 3.1 1.0 - - + -
479A PRO* 1.3 81.6 - - - +
481A THR* 1.3 63.1 + - - +
483A LEU* 3.4 5.0 + - - +
484A LYS* 3.2 30.5 + - - +
496A LEU* 5.6 0.7 - - - -
508A ILE 4.3 2.8 + - - +
510A ASP* 4.4 2.7 - - + +
516A MET* 4.1 28.1 - - + +
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Residues in contact with THR 481 (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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5A MET* 5.7 2.1 - - + +
11A LEU* 3.8 18.7 - - - +
477A VAL* 4.3 11.9 - - + -
478A HIS* 2.7 31.0 + - - +
480A ALA* 1.3 77.4 - - - +
482A ALA* 1.3 57.4 + - - +
484A LYS* 3.3 10.9 + - + +
485A GLN* 3.0 49.3 + - + +
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Residues in contact with ALA 482 (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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448A ALA* 3.8 24.2 - - + +
451A MET* 3.7 22.2 - - + +
452A LEU* 4.1 12.2 + - + +
455A GLN* 5.5 0.3 - - - +
477A VAL* 4.2 7.4 - - + +
478A HIS 2.8 10.6 + - - +
479A PRO* 3.0 9.8 + - + +
481A THR* 1.3 78.2 - - - +
483A LEU* 1.3 61.9 + - - +
485A GLN* 3.6 9.6 + - - +
486A TYR* 3.1 21.3 + - - +
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Residues in contact with LEU 483 (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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451A MET* 3.7 22.4 - - + +
464A PHE* 3.9 17.9 - - + -
479A PRO 2.9 11.2 + - - +
480A ALA* 3.7 9.0 - - - +
481A THR 3.2 0.2 - - - -
482A ALA* 1.3 76.2 - - - +
484A LYS* 1.3 61.1 + - - +
486A TYR* 2.9 6.1 + - + +
487A ARG* 2.8 58.6 + - - +
494A ALA* 3.9 22.0 - - + +
495A LYS 4.3 3.4 - - - +
496A LEU* 3.4 33.0 - - + +
516A MET* 3.8 14.4 - - + -
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Residues in contact with LYS 484 (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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480A ALA* 3.2 17.1 + - - +
481A THR* 3.3 12.1 + - + +
483A LEU* 1.3 77.3 - - - +
485A GLN* 1.3 64.7 + - + +
487A ARG* 3.0 22.0 + - - +
488A GLU* 3.0 35.8 + - - +
510A ASP* 5.3 7.6 - - - -
513A ASP* 3.9 19.9 + - - +
516A MET* 5.2 4.3 - - + -
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Residues in contact with GLN 485 (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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452A LEU* 4.2 21.8 - - - +
455A GLN* 3.7 12.8 + - - +
477A VAL* 4.7 13.8 - - - +
481A THR* 3.0 37.1 + - + +
482A ALA* 3.8 6.0 - - - +
484A LYS* 1.3 76.4 - - + +
486A TYR* 1.3 56.8 + - - +
488A GLU* 4.0 12.8 - - - +
489A LYS* 3.0 31.7 + - - +
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Residues in contact with TYR 486 (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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451A MET* 3.8 11.2 - - + +
454A ALA* 3.6 20.2 - - + -
455A GLN* 3.7 26.4 + - + -
459A THR 2.7 22.3 + - - -
460A ALA* 3.4 3.8 - - - -
461A ALA* 3.2 20.9 + - - +
464A PHE* 3.8 16.4 - + - -
482A ALA 3.1 14.8 + - - +
483A LEU* 2.9 16.2 + - + +
485A GLN* 1.3 74.9 - - - +
487A ARG* 1.3 68.9 + - - +
489A LYS* 3.1 2.1 + - - -
490A MET* 2.8 52.7 + - + +
492A ILE* 4.2 6.7 - - + +
494A ALA* 3.6 32.1 - - + -
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Residues in contact with ARG 487 (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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483A LEU* 2.8 55.0 + - - +
484A LYS* 3.0 18.4 + - - +
486A TYR* 1.3 73.7 - - - +
488A GLU* 1.3 56.7 + - + +
491A GLY* 2.6 37.9 + - - -
492A ILE 3.3 24.1 + - - +
493A PRO* 4.2 8.9 + - + +
494A ALA* 3.4 29.0 + - + +
513A ASP* 2.9 42.5 + - - -
514A ARG* 6.1 0.4 - - - +
515A GLY* 3.9 12.1 - - - -
516A MET* 3.7 3.0 - - - +
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Residues in contact with GLU 488 (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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484A LYS* 3.0 21.6 + - - +
485A GLN* 4.0 14.8 + - - +
487A ARG* 1.3 78.2 - - + +
489A LYS* 1.3 65.6 + - - +
491A GLY* 3.6 5.9 + - - -
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Residues in contact with LYS 489 (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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455A GLN* 3.4 45.1 - - + +
485A GLN 3.0 20.5 + - - +
486A TYR 3.7 2.0 - - - +
488A GLU* 1.3 79.8 - - - +
490A MET* 1.3 64.3 + - - +
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Residues in contact with MET 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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455A GLN* 4.3 14.4 - - - +
458A ASN* 3.4 53.6 - - - +
459A THR 3.7 13.0 - - - +
460A ALA* 4.1 9.9 - - + +
486A TYR* 2.8 56.6 + - + +
489A LYS* 1.3 77.9 - - + +
491A GLY* 1.3 61.9 + - - +
492A ILE* 3.7 16.2 - - + +
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Residues in contact with GLY 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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487A ARG 2.6 19.7 + - - -
488A GLU* 3.6 5.3 + - - -
489A LYS 3.4 3.2 - - - -
490A MET* 1.3 74.4 - - - +
492A ILE* 1.3 58.2 + - - +
493A PRO* 4.4 3.5 - - - +
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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