Contacts of the strand formed by residues 463 - 467 (chain B) in PDB entry 1GXD
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 PHE 463 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B PRO* 5.4 1.3 - - + -
389B GLY* 3.9 7.0 - - - -
435B VAL 4.9 2.0 - - - -
436B THR* 3.4 38.8 - - + -
437B PRO* 3.3 25.4 - - + -
458B PHE 3.7 1.2 - - - +
460B LYS 2.8 40.0 + - - +
461B ASP* 2.9 11.7 - - - -
462B ARG* 1.3 123.1 - - + +
464B ILE* 1.3 65.9 + - - +
465B TRP* 3.8 25.2 - + + -
477B PRO* 4.3 17.3 - - + -
478B LEU 3.3 12.1 - - - +
479B LEU* 3.8 17.9 - - + -
480B VAL* 3.7 7.6 - - - +
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Residues in contact with ILE 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B PHE* 4.3 15.5 - - + -
458B PHE 3.2 2.9 - - - +
459B PHE* 3.4 50.7 - - + -
463B PHE* 1.3 78.1 - - - +
465B TRP* 1.3 64.6 + - - +
466B ARG* 4.0 5.0 + - - -
476B GLY* 4.2 1.4 - - - -
477B PRO* 4.2 0.9 - - - +
478B LEU* 2.7 47.7 + - + +
479B LEU 3.8 9.9 - - - +
480B VAL* 3.6 14.8 - - + -
483B PHE* 3.5 33.2 - - + -
484B TRP* 4.5 2.0 - - + -
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Residues in contact with TRP 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B PRO* 3.3 39.7 - - + -
438B GLU 4.6 0.2 - - - -
439B ILE* 3.6 46.9 - - + +
444B ILE* 4.5 2.0 - - + -
446B PHE* 4.2 12.6 - + - -
456B ILE 3.5 1.7 - - - +
457B PHE* 3.3 2.8 - - - -
458B PHE* 2.6 76.0 + - + +
460B LYS* 3.9 16.4 - - + -
463B PHE* 3.8 24.7 - - + -
464B ILE* 1.3 75.6 - - - +
466B ARG* 1.3 60.5 + - - +
474B PRO* 3.9 14.4 - - + -
476B GLY* 3.6 24.4 - - - -
477B PRO* 3.5 33.5 - - + +
629B LEU* 6.1 0.2 - - + -
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Residues in contact with ARG 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ASN* 5.1 14.1 + - - +
66B GLU* 5.1 10.5 + - - -
455B GLU* 3.8 24.2 + - + +
456B ILE 3.2 5.8 - - - +
457B PHE* 3.5 31.8 - - + -
464B ILE* 4.4 5.6 - - - -
465B TRP* 1.3 74.5 - - - +
467B THR* 1.3 60.5 + - - +
474B PRO* 4.1 0.4 - - - -
475B MET* 2.7 60.4 + - + +
476B GLY 4.2 4.8 - - - +
478B LEU* 4.0 27.1 - - - +
483B PHE* 4.0 17.6 - - - -
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Residues in contact with THR 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455B GLU* 3.6 4.6 - - - -
456B ILE* 2.8 55.9 + - + +
458B PHE* 4.1 15.9 - - + -
466B ARG* 1.3 76.6 - - - +
468B VAL* 1.3 62.5 + - - +
469B THR 3.5 20.3 + - - -
470B PRO* 4.2 4.7 - - + +
472B ASP* 3.6 9.5 + - - -
473B LYS 4.1 2.1 + - - -
474B PRO* 3.7 20.8 - - + +
475B MET* 5.5 2.5 - - - -
628B TRP* 5.0 6.2 + - + +
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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
------------------------------------------------------------
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