Contacts of the strand formed by residues 497 - 502 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495C GLY 4.7 0.2 - - - +
496C GLU* 1.3 71.8 - - - +
498C ILE* 1.3 62.1 + - - +
645C MET* 5.3 2.9 - - + -
648C MET* 3.8 33.0 - - + +
652C CYS* 4.0 27.1 - - + -
657C VAL* 3.4 10.3 - - + +
659C ILE* 4.3 17.5 - - + -
669C ASN 5.4 2.0 - - - +
670C ALA* 3.5 17.6 - - + +
671C ASP* 2.8 51.1 + - - +
672C ARG 3.5 1.2 + - - -
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Residues in contact with ILE 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492C ILE* 3.5 32.8 - - + -
496C GLU* 3.7 36.8 - - + +
497C VAL* 1.3 75.8 - - - +
499C GLY* 1.3 60.7 + - - +
500C ILE* 3.9 6.7 + - + -
657C VAL 2.7 13.3 + - - +
658C ILE* 3.3 10.3 - - + +
659C ILE* 2.7 33.5 + - - +
670C ALA* 4.4 1.1 - - - -
672C ARG* 3.5 32.8 - - + +
674C ILE* 3.6 30.1 - - + -
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Residues in contact with GLY 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498C ILE* 1.3 75.9 - - - +
500C ILE* 1.3 60.4 + - - +
659C ILE* 3.4 6.3 - - - -
667C VAL* 4.0 24.0 - - - -
670C ALA* 3.8 4.9 - - - +
672C ARG 2.8 13.1 + - - +
673C ILE* 3.3 6.9 - - - -
674C ILE* 2.7 32.0 + - - +
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Residues in contact with ILE 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490C LEU* 6.0 1.3 - - + -
498C ILE* 4.4 7.4 - - + -
499C GLY* 1.3 78.3 - - - +
501C VAL* 1.3 65.0 + - - +
508C LYS* 3.9 20.3 - - + +
511C LEU* 4.2 19.3 - - + -
512C THR* 4.0 17.3 - - + -
658C ILE* 3.2 33.9 - - + -
659C ILE 2.7 12.5 + - - +
660C ILE* 3.5 9.2 - - + -
661C ALA* 3.1 26.3 + - - +
667C VAL* 5.4 0.8 - - - +
674C ILE* 3.4 13.7 - - + +
676C MET* 3.8 26.5 - - + -
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Residues in contact with VAL 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500C ILE* 1.3 77.2 - - - +
502C GLY* 1.3 54.4 + - - +
508C LYS* 3.7 8.7 - - - -
661C ALA* 3.2 22.7 - - + +
662C ALA* 5.3 0.7 - - - +
664C LEU* 3.4 33.0 - - + -
667C VAL* 5.3 4.3 - - + -
673C ILE* 3.9 17.0 - - + -
674C ILE 2.8 14.7 + - - +
675C VAL* 3.8 24.0 - - + -
676C MET* 2.6 35.2 + - - +
698C TYR* 4.4 8.5 - - + -
701C LEU* 5.2 5.8 - - + -
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Residues in contact with GLY 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501C VAL* 1.3 85.6 - - - +
503C ARG* 1.3 63.6 + - - -
504C SER 3.8 0.3 + - - -
506C SER* 3.3 7.0 - - - -
508C LYS* 2.8 20.2 + - - +
661C ALA 5.3 1.2 - - - +
662C ALA* 5.8 1.7 - - - -
675C VAL* 4.9 3.8 - - - -
676C MET 3.4 15.5 - - - -
697C LEU* 5.9 0.7 - - - -
701C LEU* 4.9 9.2 - - - -
637D ASP* 4.1 9.6 - - - +
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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