Contacts of the strand formed by residues 626 - 630 (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 ILE 626 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468C ILE* 3.6 24.0 - - + -
515C ILE* 3.7 17.7 - - + -
528C ILE* 5.3 4.3 - - + -
544C GLN* 3.0 21.4 + - + +
545C VAL* 3.4 23.3 - - + +
546C GLY 2.9 26.2 + - - +
624C PRO* 3.3 6.9 - - - +
625C LYS* 1.3 80.5 - - - +
627C LEU* 1.3 64.9 + - - +
628C ILE* 4.1 11.2 - - + -
656C THR* 3.4 15.7 - - - +
658C ILE* 3.4 31.2 - - + -
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Residues in contact with LEU 627 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C GLY 3.4 12.3 - - - +
548C VAL* 4.3 3.4 - - + -
619C ALA* 3.7 30.7 - - + +
620C LEU* 3.6 30.5 - - + -
624C PRO* 4.5 8.7 - - + -
625C LYS 4.4 0.2 - - - -
626C ILE* 1.3 74.2 - - - +
628C ILE* 1.3 62.3 + - - +
629C PHE* 3.7 27.1 - - + -
651C ILE* 4.0 12.3 - - + -
655C ARG* 3.9 25.4 - - - +
656C THR 2.8 9.9 + - - +
657C VAL* 3.3 10.6 - - + +
658C ILE 2.9 24.6 + - - +
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Residues in contact with ILE 628 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512C THR* 3.9 50.5 - - + +
515C ILE* 4.3 3.4 - - + -
516C GLN* 4.3 0.2 - - - +
545C VAL* 3.7 24.7 - - + -
546C GLY 2.7 12.4 + - - +
547C VAL* 3.4 14.1 - - + -
548C VAL* 2.8 33.1 + - - +
626C ILE* 4.1 21.5 - - + -
627C LEU* 1.3 76.5 - - - +
629C PHE* 1.3 69.0 + - - +
630C ASP* 4.4 5.8 - - + +
658C ILE* 3.3 17.5 - - + +
660C ILE* 4.8 3.8 - - + -
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Residues in contact with PHE 629 (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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548C VAL* 3.7 13.5 - - + -
616C ILE* 3.7 35.9 - - + -
619C ALA* 5.4 0.4 - - + -
620C LEU* 5.5 0.4 - - + -
627C LEU* 3.7 34.8 - - + -
628C ILE* 1.3 80.4 - - - +
630C ASP* 1.3 59.8 + - - +
631C GLU 3.6 2.5 + - - -
632C ALA* 3.8 19.1 - - + +
633C THR* 4.9 6.1 - - + -
644C ILE* 4.1 24.2 - - + -
645C MET* 5.5 2.0 - - - -
648C MET* 4.1 13.9 - - + -
651C ILE* 5.2 5.6 - - + -
657C VAL* 5.1 2.9 - - + -
658C ILE 2.8 13.0 + - - +
659C ILE* 3.5 28.6 - - + -
660C ILE* 2.9 26.5 + - - +
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Residues in contact with ASP 630 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C SER* 2.8 27.3 + - - -
512C THR* 4.6 3.2 + - - +
547C VAL* 6.2 0.9 - - + -
548C VAL 2.7 15.3 + - - +
549C LEU* 3.6 19.6 - - + +
550C GLN* 3.4 18.5 + - - +
628C ILE* 3.8 7.3 + - + -
629C PHE* 1.3 70.0 - - - +
631C GLU* 1.3 76.2 + - - +
632C ALA 3.1 1.2 + - - +
660C ILE* 3.5 34.2 - - + +
802C ATP 5.6 1.2 + - - -
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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