Contacts of the strand formed by residues 461 - 465 (chain A) in PDB entry 4ZZH
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 GLN 461 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ARG* 3.3 37.6 - - - +
436A LEU* 3.3 26.3 - - + +
452A PRO* 3.2 41.3 + - - +
455A ILE* 3.5 18.8 + - + +
456A PRO 4.8 1.0 + - - -
459A VAL 3.6 7.3 + - - +
460A PRO* 1.3 80.7 - - - +
462A ILE* 1.3 63.8 + - - +
472A LEU* 6.0 1.0 - - - +
473A HIS 4.6 2.1 - - - +
474A PHE* 3.8 20.1 - - + -
475A ASP* 3.1 34.6 + - - +
476A VAL 3.6 1.7 + - - -
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Residues in contact with ILE 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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240A ILE* 5.4 0.4 - - + -
246A ALA* 4.5 12.3 - - + +
249A LEU* 3.6 33.0 - - + -
250A LEU* 6.4 0.9 - - + -
435A LEU* 3.6 20.0 - - + -
436A LEU 2.9 11.3 + - - +
437A ILE* 3.4 12.1 - - + -
438A VAL* 2.8 28.4 + - - +
461A GLN* 1.3 80.6 - - - +
463A LEU* 1.3 72.8 + - - +
464A ILE* 4.1 13.5 - - + -
474A PHE* 3.9 4.1 - - - -
476A VAL* 3.7 25.8 - - + +
478A LEU* 4.5 13.5 - - + -
489A LEU* 6.3 0.2 - - + -
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Residues in contact with LEU 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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438A VAL* 3.6 29.4 - - + -
462A ILE* 1.3 73.9 - - - +
464A ILE* 1.3 66.4 + - - +
465A ASN* 3.9 13.2 - - + +
467A GLU 3.8 21.8 - - - +
468A PRO* 4.3 0.4 - - + -
469A LEU* 3.8 35.7 - - + +
474A PHE* 3.7 29.6 - - + -
476A VAL 3.1 11.2 + - - +
477A GLU* 4.6 7.0 - - + +
478A LEU* 2.8 32.1 + - - +
479A LEU* 3.9 16.2 - - + -
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Residues in contact with ILE 464 (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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329A PHE* 6.2 0.4 - - + -
437A ILE* 4.3 15.7 - - + -
438A VAL 2.7 19.6 + - - +
439A ILE* 3.2 15.4 - - + -
440A GLY 3.0 23.2 + - - -
462A ILE* 4.1 11.4 - - + -
463A LEU* 1.3 78.1 - - - +
465A ASN* 1.3 64.0 + - - +
478A LEU* 3.2 9.6 - - + -
482A CYS* 3.9 12.2 - - - +
485A ILE* 3.8 32.3 - - + -
486A ILE* 3.8 24.5 - - + -
489A LEU* 4.0 19.5 - - + -
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Residues in contact with ASN 465 (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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440A GLY* 3.1 34.0 - - - +
441A SER 3.2 17.3 + - - +
442A SER* 3.8 7.5 + - - -
463A LEU* 3.9 15.4 - - + +
464A ILE* 1.3 77.0 - - - +
466A ARG* 1.3 67.1 + - - +
467A GLU* 3.0 46.5 + - - +
469A LEU* 4.1 4.8 - - - +
478A LEU 3.1 7.3 + - - -
479A LEU* 3.1 9.4 - - - +
480A GLY 3.0 22.1 + - - -
482A CYS* 4.2 6.5 - - - -
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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