Contacts of the strand formed by residues 485 - 492 (chain B) in PDB entry 4GT4
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 GLY 485 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481B GLU* 3.2 5.3 - - - +
482B ASP* 2.7 46.1 + - - +
483B ARG 3.4 0.8 + - - -
484B PHE* 1.3 80.1 - - - +
486B LYS* 1.3 61.7 + - - -
508B THR 3.6 5.6 + - - -
509B LEU 4.8 0.2 - - - -
510B LYS* 4.0 15.3 - - - -
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Residues in contact with LYS 486 (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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478B GLU* 3.6 25.4 - - - +
480B GLY 3.5 8.3 - - - +
481B GLU* 4.5 7.4 - - + -
485B GLY* 1.3 77.4 - - - +
487B VAL* 1.3 62.7 + - - +
488B TYR* 3.9 18.2 - - + +
508B THR* 2.5 40.6 + - - +
509B LEU 5.7 0.2 - - - -
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Residues in contact with VAL 487 (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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478B GLU* 3.2 9.7 - - - +
479B LEU* 2.9 45.4 + - + -
480B GLY 3.1 7.9 + - - +
482B ASP* 4.0 26.0 - - + +
486B LYS* 1.3 78.3 - - - +
488B TYR* 1.3 61.4 + - - +
505B ALA* 5.6 2.0 - - + -
506B ILE 3.1 14.6 - - - +
507B LYS* 4.0 14.4 - - + -
634B LEU* 5.5 5.8 - - + -
636B LEU* 3.6 39.5 - - + -
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Residues in contact with TYR 488 (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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475B PHE* 3.9 25.8 - + + -
476B MET 3.6 16.2 - - - +
478B GLU* 3.5 38.5 + - + +
479B LEU* 4.5 5.2 - - - -
486B LYS* 3.8 16.0 - - + +
487B VAL* 1.3 76.2 - - - +
489B LYS* 1.3 70.3 + - - +
505B ALA* 3.6 3.6 - - - -
506B ILE* 2.9 34.6 + - + +
508B THR* 3.7 37.5 - - + -
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Residues in contact with LYS 489 (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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475B PHE* 3.8 0.5 - - - -
476B MET* 2.8 36.9 + - + +
477B GLU* 3.0 20.2 + - + +
479B LEU* 4.0 25.1 - - + +
488B TYR* 1.3 77.5 - - - +
490B GLY* 1.3 59.1 + - - +
504B VAL 3.7 4.9 - - - -
506B ILE* 4.8 0.4 - - - -
555B TYR* 6.0 5.4 - - + -
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Residues in contact with GLY 490 (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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474B ARG 3.1 13.7 - - - -
476B MET* 4.2 8.8 - - - -
489B LYS* 1.3 76.6 - - - +
491B HIS* 1.3 71.6 + - - -
503B ALA* 3.8 1.4 - - - +
504B VAL* 2.9 36.6 + - - +
506B ILE* 4.4 7.6 - - - -
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Residues in contact with HIS 491 (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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472B ALA 3.7 1.0 - - - +
473B VAL* 3.6 4.5 - - - +
474B ARG* 2.9 43.0 + - + +
476B MET* 3.3 32.0 - - + +
490B GLY* 1.3 80.8 + - - -
492B LEU* 1.3 60.2 + - - +
493B PHE* 4.1 13.2 + - + -
501B THR* 4.4 10.1 - - - -
502B GLN 3.2 32.3 - - - +
503B ALA* 4.0 13.6 + - + +
504B VAL* 4.5 4.2 - - - +
506B ILE* 5.4 0.2 - - - +
557B SER* 5.7 0.2 + - - -
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Residues in contact with LEU 492 (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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468B ILE* 3.7 26.5 - - + -
472B ALA* 3.3 21.1 - - + +
473B VAL* 3.7 20.0 - - + -
491B HIS* 1.3 72.7 - - - +
493B PHE* 1.3 74.1 + - - +
501B THR* 3.5 3.6 - - - -
502B GLN* 2.8 46.6 + - + +
504B VAL* 3.7 26.6 - - + +
540B LEU* 5.3 5.6 - - + -
552B ILE* 4.9 7.4 - - + -
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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