Contacts of the strand formed by residues 499 - 506 (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 LYS 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A ASP* 5.8 0.9 - - - -
337A THR* 3.0 45.8 - - + +
338A HIS* 4.9 7.6 - - - -
458A GLU* 5.9 0.9 - - - +
495A PHE* 3.3 8.9 - - - -
496A ILE 2.9 33.9 + - - +
497A CYS 3.3 1.8 - - - +
498A GLY* 1.3 83.7 + - - +
500A GLU* 1.3 65.5 + - - +
501A VAL* 3.9 2.7 - - - +
559A ARG* 4.2 18.6 - - - +
563A PHE* 4.7 12.6 - - + -
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Residues in contact with GLU 500 (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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493A GLU* 2.8 42.1 - - + +
494A MET 4.0 1.3 - - - +
495A PHE* 3.5 19.8 - - + -
499A LYS* 1.3 78.9 - - + +
501A VAL* 1.3 64.8 - - - +
502A LEU 4.5 4.7 - - - +
503A ASN* 3.7 16.3 + - - +
556A GLY* 5.5 0.2 - - - -
559A ARG* 2.8 43.7 + - - +
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Residues in contact with VAL 501 (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* 3.5 25.4 - - + -
494A MET* 2.9 18.7 + - + +
496A ILE* 3.8 31.0 - - + -
499A LYS 3.9 4.5 - - - +
500A GLU* 1.3 82.1 - - - +
502A LEU* 1.3 63.6 + - + +
554A GLY 4.1 0.3 - - - +
555A LEU* 3.6 2.6 - - - -
556A GLY* 3.0 31.7 + - - -
559A ARG* 4.8 4.0 - - + +
560A ILE* 3.5 31.9 - - + -
563A PHE* 4.1 15.0 - - + -
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Residues in contact with LEU 502 (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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360A TRP* 4.5 3.1 - - + -
361A SER* 3.2 27.1 - - - +
365A PHE* 3.6 18.6 - - + -
492A LEU* 3.6 30.5 - - + -
493A GLU* 3.4 5.5 - - - +
494A MET* 2.6 45.2 + - + +
500A GLU* 4.5 2.0 - - - +
501A VAL* 1.3 82.0 - - + +
503A ASN* 1.3 62.3 + - - +
504A ALA* 3.8 2.7 - - + -
553A LEU* 3.8 24.7 - - + -
554A GLY 3.4 6.1 - - - +
555A LEU* 3.6 25.1 - - + -
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Residues in contact with ASN 503 (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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491A ARG* 3.4 35.9 + - - +
492A LEU 3.6 9.3 - - - +
493A GLU* 4.0 5.5 + - + -
500A GLU* 3.7 16.4 + - - +
501A VAL 4.4 0.2 + - - -
502A LEU* 1.3 76.0 - - - +
504A ALA* 1.3 69.6 + - - +
505A TYR* 3.9 17.1 - - - -
553A LEU* 3.6 0.9 - - - -
554A GLY* 2.9 31.7 + - - +
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Residues in contact with ALA 504 (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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357A LEU* 4.0 3.4 - - + -
491A ARG* 3.6 1.4 - - - +
492A LEU* 2.7 61.7 + - + +
502A LEU* 3.8 0.8 - - + +
503A ASN* 1.3 75.9 + - - +
505A TYR* 1.3 61.8 + - - +
552A GLY 3.2 17.5 - - - +
553A LEU* 3.5 28.7 - - + +
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Residues in contact with TYR 505 (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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308A GLU* 4.0 7.7 + - - -
312A LYS* 4.6 0.3 + - - -
348A TYR* 3.9 18.4 + + - -
354A TYR* 5.2 1.3 - - - -
357A LEU* 4.0 5.8 - - - +
478A LEU* 3.2 39.6 - - + +
479A ALA* 3.6 26.0 - - + -
490A GLU 3.3 16.4 - - - +
491A ARG* 3.8 12.8 - - + +
503A ASN* 3.9 18.8 - - - -
504A ALA* 1.3 79.3 - - - +
506A THR* 1.3 64.7 + - - +
507A GLU* 3.1 27.0 + - + -
552A GLY* 2.8 33.7 + - - +
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Residues in contact with THR 506 (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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352A ALA 4.7 0.2 - - - +
353A ASP* 3.6 13.0 - - + -
354A TYR* 3.2 33.4 - - + +
479A ALA* 3.2 4.2 - - - -
480A LYS* 2.7 42.7 + - - +
490A GLU* 2.9 46.2 + - + +
505A TYR* 1.3 71.7 - - - +
507A GLU* 1.3 57.1 + - - +
550A THR 3.8 8.5 - - - -
551A GLY* 4.0 2.0 - - - -
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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