Contacts of the helix formed by residues 453 - 463 (chain A) in PDB entry 4U7D
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 CYS 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451A SER 3.6 2.8 + - - -
452A LYS* 1.3 74.7 - - - +
454A ARG* 1.3 69.5 + - - +
455A ARG* 3.6 16.4 - - - -
456A VAL* 3.1 33.2 + - + +
457A LEU* 3.2 12.5 + - - +
466A TRP* 5.0 2.0 - - - -
470A ALA 6.1 0.2 - - - -
471A CYS* 3.4 36.1 - - - -
475A CYS* 4.0 1.8 - - - -
477A ASN* 4.6 0.2 - - - -
478A CYS* 3.4 24.9 - - - -
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Residues in contact with ARG 454 (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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288A TYR* 3.8 17.4 + - + +
290A VAL* 3.7 27.5 + - - +
446A TYR* 3.2 55.8 + - - +
447A CYS 4.9 1.4 + - - -
449A ASN* 3.1 30.7 + - - +
450A ILE* 5.2 0.2 - - - +
452A LYS 3.4 0.6 + - - -
453A CYS* 1.3 75.5 - - - +
455A ARG* 1.3 61.6 + - - +
457A LEU* 3.4 9.9 + - - +
458A MET* 3.2 24.0 + - - +
475A CYS* 3.4 29.1 - - + -
476A ASP* 2.8 36.4 + - - +
477A ASN* 3.2 18.7 + - - +
480A LYS* 5.3 0.8 - - - +
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Residues in contact with ARG 455 (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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281A PHE* 3.6 17.0 - - + -
282A ASN* 3.0 23.4 + - - +
283A ARG 3.1 24.2 + - - -
284A PRO* 3.6 13.4 + - - +
286A LEU* 2.9 22.8 + - - +
288A TYR* 4.0 20.4 - - + -
453A CYS* 3.2 7.7 - - - -
454A ARG* 1.3 76.6 - - + +
456A VAL* 1.3 62.3 + - - +
458A MET* 3.4 3.2 + - - -
459A ALA* 3.0 25.6 + - - +
466A TRP* 3.8 23.3 + - + -
470A ALA 4.6 1.2 + - - -
471A CYS* 3.3 28.1 + - - +
474A MET* 2.7 41.2 + - - +
475A CYS* 4.7 0.4 - - - +
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Residues in contact with VAL 456 (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 LYS* 4.1 20.6 - - + -
453A CYS* 3.1 30.2 + - + +
455A ARG* 1.3 77.8 - - - +
457A LEU* 1.3 61.9 + - - +
459A ALA* 3.8 2.6 + - - +
460A GLN* 3.5 38.4 + - + +
466A TRP* 3.4 33.5 - - + +
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Residues in contact with LEU 457 (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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395A MET* 5.5 2.2 - - - +
445A SER 5.9 0.7 - - - +
446A TYR* 4.0 31.4 - - + +
449A ASN* 3.6 45.3 - - + +
452A LYS* 3.7 20.6 - - + +
453A CYS 3.2 13.4 + - - +
454A ARG* 3.6 13.9 - - - +
455A ARG 3.2 0.2 - - - -
456A VAL* 1.3 76.7 - - - +
458A MET* 1.3 63.3 + - - +
460A GLN* 3.4 32.2 - - - +
461A HIS* 3.6 9.5 + - - +
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Residues in contact with MET 458 (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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281A PHE* 3.9 23.6 - - + -
288A TYR* 4.3 26.5 - - + -
395A MET* 3.7 22.4 - - + +
398A TYR* 3.9 31.6 - - + -
399A TYR* 4.0 29.6 - - + -
446A TYR* 5.0 6.1 - - + +
454A ARG 3.2 14.2 + - - +
455A ARG* 3.7 7.9 - - - +
457A LEU* 1.3 75.0 - - - +
459A ALA* 1.3 56.1 + - - +
460A GLN 3.1 1.6 - - - -
461A HIS* 2.7 33.5 + - - +
462A PHE* 3.2 22.8 + - + -
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Residues in contact with ALA 459 (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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281A PHE* 3.7 21.2 - - + -
455A ARG 3.0 17.9 + - - +
456A VAL 4.0 3.6 - - - +
458A MET* 1.3 76.4 - - - +
460A GLN* 1.3 56.8 + - - +
462A PHE* 3.4 2.5 + - - +
463A ASP 2.8 6.9 + - - -
464A GLU* 2.8 40.4 + - + +
466A TRP* 3.6 31.4 - - + -
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Residues in contact with GLN 460 (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 LYS* 5.3 5.7 - - - +
456A VAL* 3.5 28.9 + - + +
457A LEU* 3.4 30.0 + - - +
458A MET 3.1 0.8 - - - -
459A ALA* 1.3 78.1 - - - +
461A HIS* 1.3 57.7 + - + +
463A ASP* 3.1 24.6 + - - +
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Residues in contact with HIS 461 (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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395A MET* 3.4 36.7 - - + +
396A GLU* 2.8 32.6 + - - +
442A GLU* 3.0 50.9 + - + +
457A LEU 3.6 7.3 + - - +
458A MET* 2.7 18.7 + - - +
460A GLN* 1.3 78.9 - - + +
462A PHE* 1.3 61.6 + - + +
463A ASP* 3.1 17.7 - - - +
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Residues in contact with PHE 462 (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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255A ALA 5.9 2.7 - - - -
281A PHE* 4.3 27.6 - + + -
395A MET* 5.3 3.1 - - + -
396A GLU* 5.0 22.0 - - + -
399A TYR* 4.0 35.2 - + + -
458A MET* 3.2 41.4 + - + -
459A ALA 3.4 3.1 + - - +
461A HIS* 1.3 81.9 - - + +
463A ASP* 1.3 73.7 + - - +
464A GLU* 3.3 16.8 + - + +
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Residues in contact with ASP 463 (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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459A ALA 2.8 6.6 + - - -
460A GLN* 3.1 17.4 - - - +
461A HIS* 3.1 16.5 - - - +
462A PHE* 1.3 81.5 - - - +
464A GLU* 1.3 59.3 + - - +
465A VAL* 4.2 1.7 + - - +
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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