Contacts of the strand formed by residues 497 - 502 (chain A) in PDB entry 2FGJ
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 497 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496A GLU* 1.3 70.8 - - - +
498A ILE* 1.3 59.4 + - - +
648A MET* 4.3 13.0 - - + +
649A HIS* 5.7 1.3 - - - -
652A CYS* 3.9 32.1 - - + -
657A VAL* 3.5 13.0 - - + +
659A ILE* 4.1 24.2 - - + -
669A ASN 4.9 3.8 - - - +
670A ALA* 3.5 19.3 - - + +
671A ASP* 2.7 48.9 + - - +
672A ARG 3.4 4.5 + - - -
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Residues in contact with ILE 498 (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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492A ILE* 3.8 24.5 - - + -
496A GLU* 4.3 6.5 - - + +
497A VAL* 1.3 75.4 - - - +
499A GLY* 1.3 66.5 + - - +
500A ILE* 4.7 3.6 - - + -
657A VAL 2.8 18.6 + - - +
658A ILE* 3.3 31.4 - - + +
659A ILE* 2.8 26.3 + - - +
670A ALA* 4.5 0.9 - - - -
672A ARG* 3.3 39.5 - - + +
674A ILE* 3.2 38.4 - - + -
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Residues in contact with GLY 499 (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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498A ILE* 1.3 75.3 - - - +
500A ILE* 1.3 59.2 + - - +
501A VAL 4.2 0.2 - - - -
659A ILE* 3.2 9.4 - - - -
667A VAL* 3.8 23.6 - - - -
670A ALA* 3.9 4.5 - - - +
672A ARG 2.9 10.4 + - - +
673A ILE* 3.3 7.3 - - - -
674A ILE* 2.7 32.1 + - - +
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Residues in contact with ILE 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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490A LEU* 6.2 0.2 - - + -
498A ILE* 4.7 3.4 - - + -
499A GLY* 1.3 78.5 - - - +
501A VAL* 1.3 63.6 + - - +
508A LYS* 3.8 22.5 - - + +
511A LEU* 4.5 22.0 - - + -
512A THR* 4.8 2.9 - - - +
658A ILE* 3.5 31.2 - - + -
659A ILE 2.7 10.9 + - - +
660A ILE* 3.4 16.0 - - + -
661A ALA 3.0 25.1 + - - -
667A VAL* 4.8 0.2 - - - +
674A ILE* 3.4 25.1 - - + +
676A MET* 3.6 32.3 - - + -
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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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500A ILE* 1.3 77.1 - - - +
502A GLY* 1.3 58.8 + - - +
508A LYS* 3.6 8.3 - - - -
661A ALA* 3.4 22.2 - - + +
664A LEU* 3.7 24.9 - - + -
667A VAL* 3.9 26.0 - - + -
673A ILE* 3.9 10.5 - - + -
674A ILE 2.9 16.6 + - - +
675A VAL* 3.4 21.9 - - + -
676A MET* 2.9 28.6 + - - +
698A TYR* 4.1 11.2 - - + -
701A LEU* 5.0 3.6 - - + -
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Residues in contact with GLY 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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501A VAL* 1.3 78.3 - - - +
503A ARG* 1.3 70.1 + - - -
504A SER 3.7 0.3 + - - -
506A SER* 3.5 4.9 - - - -
508A LYS* 2.9 14.3 + - - +
661A ALA 4.8 2.1 + - - +
662A ALA* 5.9 1.2 - - - -
675A VAL* 5.0 2.0 - - - -
676A MET 3.6 15.0 - - - -
697A LEU* 5.7 0.4 - - - -
701A LEU* 4.4 15.7 - - - +
637B ASP* 3.8 12.3 - - - +
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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