Contacts of the strand formed by residues 491 - 496 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A TYR* 4.7 7.6 - - - -
469A VAL* 3.3 5.9 - - - +
470A GLU* 2.9 25.8 + - - +
471A HIS* 3.3 37.9 + - + +
475A MET* 3.9 14.5 + - - +
476A SER* 2.7 38.7 + - - -
479A ALA* 4.3 0.4 - - + -
489A THR* 3.2 19.6 + - - +
490A GLU* 1.3 74.3 - - - +
492A LEU* 1.3 67.1 + - - +
493A GLU* 2.8 30.9 + - - +
503A ASN* 3.4 25.4 + - - +
504A ALA 3.6 11.9 - - - +
505A TYR* 3.8 14.5 - - + +
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Residues in contact with LEU 492 (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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354A TYR* 3.6 43.1 - - + +
357A LEU* 3.8 13.7 - - + -
358A ILE* 3.6 12.1 - - + +
361A SER* 4.1 4.5 - - - +
467A PHE* 3.6 30.7 - - + -
468A ILE 3.6 4.7 - - - -
469A VAL* 4.3 10.3 - - + -
491A ARG* 1.3 76.1 - - - +
493A GLU* 1.3 60.6 + - - +
502A LEU* 3.6 27.1 - - + -
503A ASN* 3.6 3.6 - - - +
504A ALA* 2.7 50.0 + - + +
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Residues in contact with GLU 493 (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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458A GLU* 5.1 0.7 - - - +
467A PHE* 3.5 2.0 - - - -
468A ILE* 2.9 41.3 + - - +
471A HIS* 3.4 17.3 + - + -
491A ARG* 2.8 28.5 + - - +
492A LEU* 1.3 74.8 - - - +
494A MET* 1.3 60.1 + - - +
495A PHE* 3.3 38.1 - - + -
500A GLU* 2.8 33.1 - - + +
502A LEU 3.4 9.0 - - - +
503A ASN* 4.0 6.9 + - + -
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Residues in contact with MET 494 (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 SER* 4.6 2.5 - - - -
365A PHE* 3.5 47.8 - - + -
398A TYR* 4.2 5.8 - - - -
465A PRO* 3.7 17.7 - - + -
466A PHE 3.5 11.2 - - - +
467A PHE* 3.6 38.5 - - + -
492A LEU 4.2 0.8 - - - -
493A GLU* 1.3 71.2 - - - +
495A PHE* 1.3 63.1 + - - +
496A ILE* 3.6 28.9 - - + -
500A GLU* 3.9 1.6 - - - +
501A VAL* 2.9 34.1 + - + +
502A LEU* 2.6 27.0 + - + +
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Residues in contact with PHE 495 (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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458A GLU* 3.4 48.9 - - + +
465A PRO* 3.1 3.9 - - - +
466A PHE* 2.9 56.1 + - + -
468A ILE* 3.4 28.9 - - + -
493A GLU* 3.3 50.7 - - + -
494A MET* 1.3 74.9 - - - +
496A ILE* 1.3 62.1 + - - +
497A CYS 4.1 0.3 + - - -
498A GLY 4.4 0.4 - - - -
499A LYS* 3.3 28.7 - - - +
500A GLU* 3.5 17.9 - - + -
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Residues in contact with ILE 496 (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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365A PHE* 3.9 11.9 - - + -
392A ILE* 4.2 15.9 - - + -
394A PHE* 3.5 32.5 - - + -
465A PRO* 3.7 12.1 - - + -
494A MET* 3.6 26.5 - - + -
495A PHE* 1.3 71.6 - - - +
497A CYS* 1.3 82.8 + - + +
498A GLY 3.2 2.0 - - - -
499A LYS 2.9 19.6 + - - +
501A VAL* 3.8 19.3 - - + +
560A ILE* 5.5 3.8 - - + -
563A PHE* 3.4 32.3 - - + -
564A LEU* 6.2 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