Contacts of the strand formed by residues 500 - 504 (chain A) in PDB entry 4GFG
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 500 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A PRO* 3.3 0.7 - - - +
456A LEU* 2.7 55.4 + - + -
478A VAL* 3.9 22.7 - - + -
495A LEU* 4.8 4.3 - - + -
496A ALA 3.6 14.1 - - - +
497A ALA* 3.2 4.1 + - - +
499A ASN* 1.3 79.8 - - - +
501A LEU* 1.3 67.3 + - - +
502A LEU* 5.3 0.2 - - + -
508A ALA* 3.8 26.0 - - + -
509A LYS 3.5 11.0 - - - +
510A ILE* 5.0 3.1 - - + -
561A LEU* 3.7 24.0 - - + -
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Residues in contact with LEU 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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433A VAL* 4.9 4.5 - - + -
451A ALA* 3.5 15.6 - - + +
454A GLY 3.6 3.4 - - - +
455A PRO* 3.7 17.7 - - + -
498A ARG 3.9 11.9 - - - +
500A VAL* 1.3 84.7 - - - +
502A LEU* 1.3 64.3 + - - +
503A VAL 3.7 0.9 + - - -
508A ALA* 3.4 2.8 - - - -
509A LYS* 2.8 39.7 + - - +
511A SER* 3.5 23.3 - - - +
701A 0XF 3.1 66.2 - - + +
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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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451A ALA* 3.5 8.2 - - - -
453A LEU* 3.0 40.6 + - + +
454A GLY 3.0 12.0 + - - +
456A LEU* 3.9 26.9 - - + -
459A TYR* 3.4 50.7 - - + -
474A LEU* 3.9 27.6 - - + -
501A LEU* 1.3 74.6 - - - +
503A VAL* 1.3 60.2 + - - +
504A THR 3.6 18.6 - - - +
505A GLN* 4.9 1.8 - - - -
507A TYR 3.6 0.2 - - - -
508A ALA* 4.0 15.7 - - + -
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Residues in contact with VAL 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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450A MET 4.9 7.0 - - - +
451A ALA* 4.1 19.7 - - + +
452A GLU* 4.6 5.3 + - - +
453A LEU* 3.6 15.6 - - - +
501A LEU 3.7 0.2 + - - -
502A LEU* 1.3 74.6 - - - +
504A THR* 1.3 67.7 + - + +
507A TYR* 2.7 36.6 + - + +
509A LYS* 3.6 40.2 - - + -
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Residues in contact with THR 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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453A LEU* 3.6 13.2 - - - -
502A LEU* 3.6 13.3 - - - +
503A VAL* 1.3 91.3 - - + +
505A GLN* 1.3 60.3 + - - +
506A HIS* 2.9 25.7 + - - +
507A TYR* 3.1 29.6 + - + +
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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