Contacts of the strand formed by residues 454 - 462 (chain A) in PDB entry 4ZPK
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 ILE 454 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369A ILE* 4.2 32.5 - - + -
416A VAL* 5.2 7.2 - - + -
445A THR* 3.6 27.1 - - + -
446A PHE 3.7 4.5 - - - -
447A GLN* 4.4 3.2 - - + +
453A GLU* 1.3 99.0 - - + +
455A GLU* 1.3 65.8 + - - +
456A TYR 5.0 1.6 - - - +
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Residues in contact with GLU 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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367A HIS 4.8 0.2 - - - +
368A ASN* 5.2 6.6 - - - +
446A PHE* 2.9 35.6 + - + -
448A ASN* 3.8 20.6 + - + +
453A GLU 4.0 6.7 - - - +
454A ILE* 1.3 82.1 - - - +
456A TYR* 1.3 82.1 + - + +
251B ASP 4.7 0.2 - - - +
253B LYS* 5.3 2.7 - - - -
276B SER* 3.0 37.1 + - - -
278B TYR* 4.1 9.4 - - - +
279B GLU* 4.3 11.6 - - - +
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Residues in contact with TYR 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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366A ARG* 3.5 33.4 - - + -
367A HIS 3.0 19.5 - - - +
368A ASN* 4.7 3.4 - - + +
369A ILE* 6.5 0.4 - - - -
374A THR* 5.6 7.6 - - + +
445A THR* 5.1 2.0 - - - -
446A PHE* 3.0 40.3 + + + +
454A ILE* 5.0 2.1 - - - +
455A GLU* 1.3 91.0 - - + +
457A ILE* 1.3 60.2 + - - +
458A ILE* 3.4 36.2 - - + +
278B TYR* 3.3 57.2 + - + +
279B GLU* 4.7 6.3 - - + -
286B SER* 3.8 14.2 - - - -
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Residues in contact with ILE 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A SER 3.8 0.2 - - - +
366A ARG* 3.4 5.0 - - - -
367A HIS* 2.9 37.7 + - + +
368A ASN* 3.9 16.6 - - - +
369A ILE* 4.3 6.3 - - + +
412A PHE* 3.7 32.3 - - + +
415A VAL* 3.8 29.8 - - + -
416A VAL* 3.9 27.4 - - + -
443A SER* 3.8 8.1 - - - -
444A PHE 3.8 4.3 - - - +
445A THR* 4.7 5.2 - - + +
456A TYR* 1.3 73.4 - - - +
458A ILE* 1.3 63.2 + - - +
459A CYS* 3.6 23.8 + - - -
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Residues in contact with ILE 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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364A ILE* 3.8 23.1 - - + -
365A SER 3.8 3.4 - - - +
366A ARG* 4.5 7.2 - - + -
442A SER 3.5 2.1 - - - +
443A SER* 3.2 19.6 - - - -
444A PHE* 3.2 51.1 + - + +
446A PHE* 4.2 14.1 - - + -
456A TYR* 3.4 35.2 + - + +
457A ILE* 1.3 69.9 - - - +
459A CYS* 1.3 62.7 + - - +
460A THR* 4.7 2.7 - - + -
283B ALA* 6.2 0.9 - - + -
286B SER* 4.4 14.8 - - - +
287B GLU* 6.5 0.7 - - - -
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Residues in contact with CYS 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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364A ILE* 3.2 4.4 - - - +
365A SER* 2.9 44.9 + - - +
367A HIS* 3.5 27.8 - - - +
396A ILE* 6.2 0.2 - - - -
412A PHE* 4.1 10.8 - - - -
441A THR* 3.5 12.1 - - - +
442A SER 3.2 4.5 - - - +
443A SER* 3.6 17.7 - - - -
457A ILE* 3.6 11.2 - - - -
458A ILE* 1.3 77.2 - - - +
460A THR* 1.3 60.8 + - - +
461A ASN* 3.5 16.5 + - - +
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Residues in contact with THR 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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363A PHE 4.2 2.0 - - - -
364A ILE* 3.6 22.7 - - + +
440A ARG 3.7 2.9 - - - +
441A THR* 3.7 1.2 - - - -
442A SER* 2.8 41.7 + - - +
444A PHE* 5.1 7.4 - - + -
458A ILE* 4.7 7.4 - - + -
459A CYS* 1.3 70.5 - - - +
461A ASN* 1.3 61.4 + - - +
462A THR* 3.7 7.7 + - - -
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Residues in contact with ASN 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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362A GLU* 3.6 2.3 - - - -
363A PHE* 2.8 79.9 + - + +
365A SER* 2.8 28.3 + - - -
367A HIS* 5.4 0.3 + - - -
373A PHE* 5.6 0.8 - - - -
396A ILE* 5.6 6.3 - - - +
439A MET* 4.5 13.9 - - + -
440A ARG 4.1 2.5 - - - -
441A THR* 3.0 26.3 + - - +
459A CYS* 3.5 11.9 + - - +
460A THR* 1.3 71.1 - - - +
462A THR* 1.3 59.8 + - - +
463A ASN* 4.7 1.2 - - - +
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Residues in contact with THR 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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361A THR* 4.7 2.2 - - + +
362A GLU* 3.6 31.4 - - + +
439A MET* 3.3 7.1 - - - +
440A ARG* 2.8 45.7 + - - -
460A THR* 4.1 8.7 + - - -
461A ASN* 1.3 77.1 - - - +
463A ASN* 1.3 75.5 + - - +
464A VAL* 4.8 6.3 - - + -
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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