Contacts of the strand formed by residues 470 - 475 (chain D) in PDB entry 4JVG
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 THR 470 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462D ARG* 3.8 14.8 - - + +
464D GLY 3.5 15.7 - - - +
465D SER* 3.6 14.6 - - - -
467D SER 5.1 1.6 + - - -
469D GLY* 1.3 77.4 + - - -
471D VAL* 1.3 62.0 + - - +
472D TYR* 3.4 39.8 - - + +
482D VAL 3.2 9.4 - - - +
483D LYS* 4.3 0.4 - - - +
484D MET* 3.2 25.8 + - - +
486D ASN* 4.1 18.5 + - - +
597D LEU* 5.1 0.2 - - - -
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Residues in contact with VAL 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462D ARG* 3.8 2.8 - - - +
463D ILE* 2.9 39.5 + - + -
464D GLY* 2.8 35.0 + - - +
470D THR* 1.3 77.7 - - - +
472D TYR* 1.3 63.9 + - - +
481D ALA* 5.7 1.1 - - + -
482D VAL 2.9 10.8 - - - +
483D LYS* 3.9 27.1 - - + -
597D LEU* 4.7 11.2 - - + +
801D B96 4.2 31.9 - - + +
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Residues in contact with TYR 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A ARG* 3.8 27.4 - - - -
459D VAL* 3.6 23.6 - - + -
460D GLY 3.5 18.6 - - - +
461D GLN 3.3 7.6 - - - +
462D ARG* 4.0 18.0 + - + +
463D ILE* 3.7 5.7 - - - +
470D THR* 3.4 45.3 - - + +
471D VAL* 1.3 74.5 - - - +
473D LYS* 1.3 62.6 + - - +
474D GLY 3.2 0.2 + - - -
481D ALA* 3.7 3.3 - - - +
482D VAL* 2.9 31.5 + - - +
484D MET* 3.8 26.5 - - + -
486D ASN* 4.7 13.7 + - - +
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Residues in contact with LYS 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D GLY* 2.4 40.0 + - - -
461D GLN* 2.9 21.0 + - + +
463D ILE* 3.3 12.1 - - + +
472D TYR* 1.3 70.2 - - - +
474D GLY* 1.3 59.8 + - - +
475D LYS* 5.4 2.2 - - - -
479D ASP* 3.8 25.8 + - - -
480D VAL 3.9 2.9 - - - +
531D TRP* 3.6 50.1 - - + +
533D GLU* 4.7 6.1 + - - -
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Residues in contact with GLY 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457D ILE* 5.3 0.2 - - - -
458D THR 3.1 12.1 - - - -
460D GLY 4.1 1.3 - - - -
472D TYR 3.2 3.2 + - - -
473D LYS* 1.3 80.6 - - - +
475D LYS* 1.3 75.2 + - - +
479D ASP* 3.8 1.0 - - - -
480D VAL* 2.7 39.1 + - - +
482D VAL* 3.9 11.4 - - - -
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Residues in contact with LYS 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716A GLU* 6.0 1.8 - - - +
562C ARG* 4.1 13.9 - - - +
715C GLU* 5.1 11.0 + - - -
456D GLN 4.2 3.3 - - - +
457D ILE* 4.1 1.6 - - - +
458D THR* 2.7 45.0 + - + +
473D LYS* 5.4 2.2 - - - -
474D GLY* 1.3 79.8 - - - +
476D TRP* 1.3 61.0 + - - +
477D HIS 4.3 0.2 - - - -
478D GLY* 3.2 14.8 - - - +
479D ASP* 2.7 37.1 + - - +
480D VAL* 3.6 1.5 - - - +
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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