Contacts of the strand formed by residues 428 - 433 (chain B) in PDB entry 5CP2
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 VAL 428 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B MET* 3.7 23.1 - - - -
392B ALA* 4.0 25.1 - - + +
395B ILE* 4.0 22.4 - - + -
396B GLU 4.7 0.9 - - - +
414B ALA* 4.7 11.2 - - + -
418B TYR* 6.2 4.0 - - + -
427B ASP* 1.3 82.8 - - - +
429B ASP* 1.3 66.8 + - - +
430B VAL* 3.9 23.1 - - + -
487B ARG* 5.8 0.2 - - + -
488B ARG 3.1 7.0 + - - +
489B LEU* 3.4 15.5 - - + +
490B ASP* 2.9 25.8 + - - -
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Residues in contact with ASP 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B ALA* 3.4 1.1 - - - -
415B CYS* 2.6 46.0 + - + +
416B GLY* 4.1 12.7 - - - +
417B SER 5.2 0.5 + - - -
427B ASP* 2.9 19.7 - - - +
428B VAL* 1.3 76.5 - - - +
430B VAL* 1.3 59.3 + - - +
490B ASP* 3.1 34.3 - - - +
506B PHE* 3.7 24.5 - - + +
5P A 3.9 1.6 - - - +
6P C 3.1 27.3 + - - +
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Residues in contact with VAL 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B GLU* 4.4 19.3 - - + +
399B VAL* 4.3 19.7 - - + -
412B CYS* 4.3 11.4 - - + -
413B VAL 3.5 7.6 - - - +
414B ALA* 4.5 5.4 - - - -
428B VAL* 3.9 19.7 - - + -
429B ASP* 1.3 74.2 - - - +
431B ALA* 1.3 65.7 + - - +
432B ILE* 3.9 20.4 - - + -
489B LEU* 4.1 10.8 - - + -
490B ASP 2.8 13.5 + - - +
491B ILE* 3.3 12.6 - - + +
492B ILE* 3.0 25.7 + - - -
506B PHE* 4.4 0.6 - - - -
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Residues in contact with ALA 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411B LEU 3.5 1.4 - - - +
412B CYS* 3.4 3.8 - - - -
413B VAL* 2.9 39.7 + - + +
415B CYS* 4.0 16.1 - - - -
429B ASP 3.9 1.2 + - - -
430B VAL* 1.3 72.5 - - - +
432B ILE* 1.3 60.5 + - - +
492B ILE* 3.7 26.9 - - + -
494B VAL* 5.8 0.9 - - + -
499B PHE* 4.3 19.8 - - + -
502B ALA* 5.3 2.2 - - + +
503B LEU* 4.3 5.2 - - + -
506B PHE* 4.7 1.3 - - + -
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Residues in contact with ILE 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B VAL* 4.1 11.9 - - + -
403B ALA* 4.5 3.6 - - + -
410B LEU* 4.2 22.4 - - + -
411B LEU 3.2 7.2 - - - +
412B CYS* 3.7 25.8 - - - -
430B VAL* 3.9 9.6 - - + +
431B ALA* 1.3 79.4 - - - +
433B THR* 1.3 67.1 + - - +
443B ILE* 5.0 3.8 - - + -
447B LEU* 3.5 31.9 - - + -
491B ILE* 4.2 7.9 - - + -
492B ILE 2.7 16.7 + - - +
493B VAL* 3.4 17.8 - - + +
494B VAL* 2.9 29.2 + - - +
499B PHE* 4.9 0.2 - - - -
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Residues in contact with THR 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B LEU* 3.4 10.5 - - - +
411B LEU* 2.7 41.8 + - + -
432B ILE* 1.3 76.2 - - - +
434B HIS* 1.3 63.2 + - - +
440B HIS* 4.5 3.8 - - - -
494B VAL* 2.8 22.2 + - - -
495B PRO 3.5 0.3 - - - -
496B TYR* 3.2 31.7 + - + -
499B PHE* 3.5 46.2 - - + -
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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