Contacts of the strand formed by residues 491 - 496 (chain B) in PDB entry 4YCV
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 ARG 491 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B TYR* 4.9 5.1 - - - -
468B ILE 4.1 0.4 - - - +
469B VAL* 3.2 10.1 - - - +
470B GLU 2.7 29.9 + - - +
471B HIS* 3.2 35.5 + - + +
475B MET* 3.7 16.0 + - - +
476B SER* 3.3 33.4 - - - +
479B ALA* 4.4 1.6 - - + -
489B THR* 3.4 16.1 + - - +
490B GLU* 1.3 75.6 - - - +
492B LEU* 1.3 64.6 + - - +
493B GLU* 2.9 22.0 + - - -
500B GLU* 5.3 0.8 + - - -
503B ASN* 3.5 26.3 + - - +
504B ALA 3.5 13.9 - - - +
505B TYR* 3.7 16.1 - - + +
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Residues in contact with LEU 492 (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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354B TYR* 4.2 6.1 - - + +
357B LEU* 3.8 19.3 - - + +
358B ILE* 3.5 38.6 - - + +
361B SER* 4.5 0.4 - - - +
467B PHE* 3.8 23.8 - - + -
468B ILE 3.5 5.4 - - - -
469B VAL* 4.4 4.9 - - + +
471B HIS* 4.6 0.2 - - - -
491B ARG* 1.3 79.9 - - - +
493B GLU* 1.3 63.6 + - - +
502B LEU* 3.4 33.4 - - + -
503B ASN* 3.2 14.4 - - - +
504B ALA* 2.8 45.5 + - + +
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Residues in contact with GLU 493 (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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458B GLU* 5.1 0.5 - - - +
467B PHE* 3.4 3.5 - - - -
468B ILE 2.9 36.2 + - - +
471B HIS* 3.7 15.7 + - - +
491B ARG* 2.9 31.5 + - - -
492B LEU* 1.3 75.3 - - - +
494B MET* 1.3 58.6 + - - +
495B PHE* 3.3 33.3 - - + -
500B GLU* 3.2 37.8 - - + +
502B LEU 3.5 14.4 - - - +
503B ASN* 3.8 4.7 - - - +
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Residues in contact with MET 494 (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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361B SER* 4.5 3.6 - - - -
365B PHE* 3.6 49.6 - - + -
398B TYR* 4.0 17.5 - - - -
465B PRO* 4.1 14.6 - - + -
466B PHE 3.6 14.6 - - - +
467B PHE* 3.6 40.1 - - + -
492B LEU* 4.4 1.0 - - - +
493B GLU* 1.3 72.7 - - - +
495B PHE* 1.3 64.2 + - - +
496B ILE* 4.1 7.9 - - + -
500B GLU* 3.9 1.9 - - - -
501B VAL* 3.0 35.1 + - + -
502B LEU* 2.9 28.0 + - + +
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Residues in contact with PHE 495 (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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458B GLU* 3.4 36.6 - - + -
465B PRO* 3.2 7.8 - - - +
466B PHE* 2.9 56.9 + + + +
468B ILE* 3.5 30.5 - - + -
493B GLU* 3.3 49.1 - - + -
494B MET* 1.3 75.5 - - - +
496B ILE* 1.3 63.4 + - - +
497B CYS 4.2 0.6 + - - -
498B GLY* 4.0 11.0 - - - +
499B LYS 3.2 25.1 - - - +
500B GLU* 3.9 17.9 - - + -
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Residues in contact with ILE 496 (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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365B PHE* 4.0 15.9 - - + -
392B ILE* 4.2 18.8 - - + -
394B PHE* 3.5 31.0 - - + -
465B PRO* 4.2 9.6 - - + -
494B MET* 4.1 9.4 - - + -
495B PHE* 1.3 76.2 - - - +
497B CYS* 1.3 72.3 + - - +
498B GLY 3.1 0.7 - - - -
499B LYS 2.9 17.6 + - - +
501B VAL* 3.6 28.6 - - + +
560B ILE* 5.2 3.4 - - + -
563B PHE* 3.3 45.3 - - + -
564B LEU* 5.7 0.7 - - + -
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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