Contacts of the strand formed by residues 466 - 473 (chain B) in PDB entry 4WQN
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 HIS 466 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B SER* 2.6 26.4 + - - -
461B VAL 4.1 0.3 + - - -
464B SER* 2.7 51.5 + - - -
465B GLY* 1.3 81.0 - - - +
467B PHE* 1.3 68.5 + - - +
468B CYS* 4.8 4.7 - - + +
504B ASP* 3.2 41.6 + - + -
505B VAL 3.2 19.1 - - - +
506B PRO* 3.8 5.2 - - + -
507B ASN* 3.1 11.3 + - - -
601B EDO 4.1 0.6 + - - -
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Residues in contact with PHE 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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414B ILE* 4.3 22.7 - - + -
416B LYS* 5.5 2.5 - - + -
458B LEU* 3.7 37.7 - - + -
459B PHE 3.3 18.8 - - - +
460B SER* 4.0 14.4 - - - -
466B HIS* 1.3 76.4 - - - +
468B CYS* 1.3 60.2 + - - +
469B GLY 3.7 3.4 - - - +
503B LYS 3.3 1.0 - - - +
504B ASP* 3.3 3.6 - - - -
505B VAL* 2.8 44.9 + - + +
507B ASN* 3.6 17.5 - - - -
510B LEU* 3.8 24.7 - - + -
523B VAL* 4.6 11.4 - - + -
524B THR* 4.4 16.4 - - + -
540B VAL* 5.5 1.8 - - + -
544B ILE* 4.8 15.3 - - + -
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Residues in contact with CYS 468 (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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423B ILE* 4.2 29.4 - - + -
459B PHE* 2.8 33.0 + - - -
460B SER* 4.4 5.4 - - - -
461B VAL* 4.5 13.0 - - + +
466B HIS* 4.8 4.7 - - + +
467B PHE* 1.3 73.9 - - - +
469B GLY* 1.3 59.4 + - - +
499B TRP* 4.6 3.6 - - - -
502B VAL* 3.6 10.2 - - - +
503B LYS 2.9 29.0 + - - -
504B ASP* 4.0 13.7 - - - +
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Residues in contact with GLY 469 (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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458B LEU* 3.9 1.4 - - - -
459B PHE* 3.0 26.8 + - - +
467B PHE* 3.7 4.3 - - - +
468B CYS* 1.3 82.4 - - - +
470B VAL* 1.3 67.1 + - - +
499B TRP* 4.0 10.8 - - - -
501B PHE* 3.0 16.2 - - - -
503B LYS* 3.6 5.5 + - - -
544B ILE* 5.1 5.3 - - - +
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Residues in contact with VAL 470 (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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403B PHE* 5.5 1.8 - - + -
456B TYR* 4.5 13.2 - - + -
457B LEU 3.4 9.0 - - - +
458B LEU* 4.3 7.0 - - + -
469B GLY* 1.3 78.9 - - - +
471B ALA* 1.3 71.1 + - - +
499B TRP* 3.8 3.8 - - - -
500B ILE* 2.9 29.2 + - + -
501B PHE* 2.7 33.0 + - + +
541B LEU* 4.0 25.6 - - + -
544B ILE* 3.9 36.8 - - + -
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Residues in contact with ALA 471 (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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456B TYR* 3.5 4.9 - - - +
457B LEU* 2.7 40.4 + - + +
459B PHE* 3.7 22.4 - - + -
470B VAL* 1.3 78.2 - - - +
472B GLU* 1.3 60.1 + - - +
497B VAL* 4.1 16.2 - - + -
498B ARG 3.3 13.7 - - - +
499B TRP* 4.0 17.7 - - + -
500B ILE* 4.2 1.3 - - - +
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Residues in contact with GLU 472 (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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454B PRO* 3.7 24.9 - - - +
455B VAL 3.3 15.5 - - - +
456B TYR* 4.0 21.2 + - + -
457B LEU* 4.8 0.2 - - - -
471B ALA* 1.3 74.7 - - - +
473B MET* 1.3 72.5 + - - +
474B LYS* 3.4 27.2 + - + +
497B VAL* 3.1 7.5 - - - -
498B ARG* 2.8 43.7 + - + +
500B ILE* 4.1 12.4 - - + +
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Residues in contact with MET 473 (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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442B LEU* 3.5 48.2 - - + +
443B ASP* 4.0 3.1 - - - +
446B TYR* 3.4 29.5 - - + -
455B VAL* 2.9 38.6 + - + +
457B LEU* 4.3 12.7 - - + +
471B ALA 4.2 0.8 + - - -
472B GLU* 1.3 83.4 - - - +
474B LYS* 1.3 60.7 + - - +
475B SER 3.7 20.6 - - - +
476B ALA* 5.0 0.4 - - - -
477B VAL* 4.1 8.3 - - + -
495B PHE* 3.6 34.5 - - + -
496B ASP 3.8 3.1 - - - -
497B VAL* 4.5 0.9 - - - +
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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