Contacts of the helix formed by residues 485 - 494 (chain A) in PDB entry 1H7B
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 THR 485 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483A ASN 4.0 1.6 + - - -
484A ILE* 1.3 90.9 - - - +
486A PRO* 1.3 79.2 - - - +
487A PHE* 3.5 18.7 + - + +
488A GLU* 2.9 34.7 + - + +
489A LYS* 3.7 0.6 - - - +
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Residues in contact with PRO 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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484A ILE 3.7 2.9 - - - +
485A THR* 1.3 88.5 - - - +
487A PHE* 1.3 70.2 + - + +
489A LYS* 3.3 5.7 + - + +
490A ILE* 2.9 35.5 + - - +
508A VAL* 3.8 24.5 - - + +
509A GLU 4.6 3.1 - - - +
510A LEU* 3.9 24.5 - - + -
523A VAL* 4.5 11.0 - - + -
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Residues in contact with PHE 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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485A THR* 3.2 15.9 - - + +
486A PRO* 1.3 85.3 - - + +
488A GLU* 1.3 60.2 + - - +
490A ILE* 3.8 1.3 - - + -
491A SER* 2.9 30.3 + - - -
522A ALA* 4.1 26.2 - - + -
523A VAL* 4.4 14.1 - - + -
526A TYR* 3.2 59.4 + + + +
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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 ILE* 3.2 30.0 - - + +
485A THR* 2.9 28.6 + - + +
487A PHE* 1.3 76.1 - - - +
489A LYS* 1.3 54.7 + - - +
491A SER* 2.9 9.3 + - - -
492A ARG* 2.6 56.7 + - - +
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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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477A HIS* 4.6 4.8 + - - +
478A VAL* 3.4 35.1 + - + +
479A SER 5.4 0.9 - - - -
480A VAL* 6.3 1.1 - - - +
484A ILE* 2.9 24.9 - - + +
485A THR 3.0 2.2 + - - +
486A PRO* 3.4 10.5 - - + +
488A GLU* 1.3 75.2 - - - +
490A ILE* 1.3 63.1 - - - +
492A ARG* 3.2 4.5 + - - +
493A GLU* 2.5 63.6 + - - +
507A TYR* 3.2 32.6 + - - +
508A VAL* 4.1 13.2 - - + +
509A GLU* 5.1 7.2 - - - +
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Residues in contact with ILE 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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486A PRO 2.9 20.7 + - - +
487A PHE* 3.7 4.5 - - + +
489A LYS* 1.3 75.5 - - - +
491A SER* 1.3 57.5 + - - +
493A GLU* 5.0 1.3 - - - -
494A ALA* 3.0 28.6 + - - +
506A SER* 5.7 2.2 - - - -
508A VAL* 4.0 5.1 - - + +
523A VAL* 3.8 25.8 - - + +
526A TYR* 3.5 31.6 - - + -
527A ALA* 3.7 31.0 - - + +
530A HIS* 4.4 7.4 - - + -
531A LEU* 3.8 21.0 - - + +
534A PHE* 4.0 16.6 - - + -
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Residues in contact with SER 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 PHE 2.9 19.8 + - - -
488A GLU* 2.9 12.1 + - - -
490A ILE* 1.3 77.9 - - - +
492A ARG* 1.3 64.0 + - - +
493A GLU 3.5 0.2 + - - -
494A ALA* 3.9 4.3 + - - +
495A PRO* 3.6 17.3 - - - +
526A TYR* 3.7 16.6 + - - -
530A HIS* 5.1 8.3 - - - -
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Residues in contact with ARG 492 (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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414A ASP* 6.1 0.4 - - - -
417A ARG* 5.9 0.7 + - - -
478A VAL* 3.6 25.9 - - + +
482A GLU* 2.9 35.0 + - - -
484A ILE* 3.2 18.3 - - - +
488A GLU* 2.6 42.9 + - - +
489A LYS 3.9 3.1 - - - +
491A SER* 1.3 72.9 - - - +
493A GLU* 1.3 61.1 + - - +
495A PRO* 3.8 7.7 - - - +
496A TYR* 3.8 15.3 - - - -
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Residues in contact with GLU 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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476A PHE* 3.9 15.0 - - + +
477A HIS* 3.2 13.5 - - - -
478A VAL* 2.7 32.3 + - + +
489A LYS* 2.5 51.6 + - - +
490A ILE 4.3 1.1 - - - +
492A ARG* 1.3 76.7 - - - +
494A ALA* 1.3 64.3 + - - +
495A PRO* 3.2 4.5 - - - -
496A TYR* 2.9 28.2 + - - +
497A HIS* 3.8 5.9 - - - -
506A SER* 2.6 46.9 + - - +
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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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490A ILE 3.0 19.8 + - - +
491A SER* 4.3 4.5 - - - +
493A GLU* 1.3 75.7 - - - +
495A PRO* 1.3 67.0 - - + +
497A HIS* 3.2 13.9 + - - +
498A PHE* 3.2 17.9 - - - -
530A HIS* 3.3 33.9 - - + +
531A LEU* 3.9 15.6 - - + +
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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