Contacts of the strand formed by residues 500 - 504 (chain B) in PDB entry 4Z4Q
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 LYS 500 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B LYS 5.3 1.1 - - - +
427B ASN 3.6 2.6 + - - -
428B GLU* 3.4 21.7 - - + +
429B LEU 2.8 25.5 + - - -
498B TYR* 3.9 2.9 - - - +
499B ASP* 1.3 101.6 - - + +
501B ILE* 1.3 64.8 + - - +
502B ILE* 4.0 7.0 - - + -
534B HIS 3.5 3.1 - - - -
536B TYR* 3.5 41.0 + - + -
601B ARG* 3.9 27.3 - - - +
603B LEU* 5.0 4.8 - - + +
1004B ILE* 5.8 3.0 - - - +
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Residues in contact with ILE 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LEU* 3.5 26.5 - - + +
431B LEU* 3.6 31.2 - - + -
483B ILE* 4.0 26.0 - - + -
498B TYR* 4.1 15.5 - - + +
500B LYS* 1.3 77.5 - - - +
502B ILE* 1.3 57.9 + - - +
503B ILE* 5.4 0.4 - - + -
522B PHE* 4.1 15.0 - - + -
529B LEU* 4.9 12.1 - - + -
534B HIS* 2.7 18.3 + - + +
535B VAL* 3.5 17.8 - - + +
536B TYR* 2.7 35.4 + - - +
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Residues in contact with ILE 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B GLU* 3.4 27.1 - - + +
429B LEU 2.7 12.1 + - - +
430B TYR* 3.2 56.6 - - + +
431B LEU* 3.0 25.1 + - - -
500B LYS* 4.4 10.3 - - + -
501B ILE* 1.3 78.1 - - - +
503B ILE* 1.3 66.0 + - - +
504B MET 3.6 1.2 + - - -
536B TYR* 3.5 11.4 - - + +
538B ALA* 3.8 26.5 - - + +
601B ARG* 3.9 7.6 - - - +
603B LEU* 4.7 10.1 - - + -
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Residues in contact with ILE 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B LEU* 3.8 22.7 - - + +
455B LEU* 5.7 0.2 - - + -
501B ILE* 5.4 0.2 - - + -
502B ILE* 1.3 74.5 - - - +
504B MET* 1.3 60.7 + - - +
505B THR* 3.9 17.9 + - + +
515B GLN* 4.4 14.6 - - + +
518B LEU* 3.8 36.3 - - + -
519B LEU* 4.1 22.2 - - + -
522B PHE* 4.6 4.0 - - + -
535B VAL* 4.0 25.8 - - + -
536B TYR 2.9 13.1 + - - +
537B ILE* 3.6 16.6 - - + +
538B ALA 3.0 23.0 + - - +
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Residues in contact with MET 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B TYR* 4.1 27.4 - - + -
431B LEU 3.1 12.0 + - - +
432B VAL* 3.1 46.6 - - + -
433B GLU 3.1 22.7 + - - -
437B ALA 4.8 0.4 - - - +
441B ALA* 4.1 15.9 - - + -
502B ILE 3.6 0.2 + - - -
503B ILE* 1.3 74.8 - - - +
505B THR* 1.3 62.8 + - - +
538B ALA* 4.2 14.4 - - + +
540B PRO* 5.2 2.5 - - + -
583B LEU* 3.8 21.8 - - + +
591B LEU* 4.2 17.0 - - + -
595B THR* 3.5 25.6 - - - +
596B MET* 4.4 4.9 - - - -
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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