Contacts of the strand formed by residues 495 - 506 (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 PHE 495 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431B ILE* 3.2 4.7 - - - -
432B TRP* 2.9 69.4 + + + -
433B CYS* 4.8 0.2 - - - -
439B ASN* 3.9 18.2 - - - -
442B LEU* 3.8 22.4 - - + -
457B LEU* 3.8 7.6 - - + -
473B MET* 3.6 24.9 - - + -
475B SER* 3.7 11.2 - - - +
476B ALA 3.6 15.7 - - - +
477B VAL* 3.7 21.8 - - + -
494B ARG* 1.3 78.2 - - - +
496B ASP* 1.3 74.8 + - - +
497B VAL* 3.6 20.6 - - + -
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Residues in contact with ASP 496 (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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430B ASN 3.4 7.4 - - - +
431B ILE* 3.9 14.0 - - - +
474B LYS* 2.7 40.2 + - + +
475B SER* 3.1 26.6 + - - +
494B ARG* 5.1 5.4 + - - -
495B PHE* 1.3 80.5 - - - +
497B VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B SER* 3.9 5.6 - - - +
430B ASN* 3.0 40.8 + - - +
431B ILE 3.7 3.4 - - - +
432B TRP* 3.9 11.9 - - + -
457B LEU* 4.1 11.2 - - + -
459B PHE* 5.2 1.6 - - + -
471B ALA* 4.1 9.0 - - + -
472B GLU 3.1 13.0 - - - +
473B MET* 4.5 0.2 - - - -
474B LYS* 3.8 5.9 - - - +
495B PHE* 3.6 25.6 - - + +
496B ASP* 1.3 79.8 - - - +
498B ARG* 1.3 61.2 + - - +
499B TRP* 3.8 25.8 - - + +
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Residues in contact with ARG 498 (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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430B ASN* 4.1 3.4 - - - -
471B ALA* 3.3 3.1 - - - -
472B GLU* 2.8 43.4 + - + +
474B LYS* 3.5 29.2 - - + +
497B VAL* 1.3 74.7 - - - +
499B TRP* 1.3 70.9 + - - +
500B ILE* 3.4 14.2 + - + +
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Residues in contact with TRP 499 (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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398B TYR* 3.9 29.4 - - + -
423B ILE* 4.5 13.2 - - + -
426B SER* 2.8 48.4 + - - -
427B ILE* 3.7 29.4 - - + +
430B ASN* 3.8 13.9 + - - +
459B PHE* 3.4 48.5 - + + -
468B CYS* 4.6 3.8 - - - -
469B GLY* 4.0 13.9 - - - -
470B VAL 3.8 8.7 - - - -
471B ALA* 4.0 6.3 - - + -
497B VAL* 3.8 9.9 - - + +
498B ARG* 1.3 80.4 + - - +
500B ILE* 1.3 60.5 + - - +
501B PHE 3.6 23.3 - - - -
502B VAL* 3.9 10.8 - - + -
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Residues in contact with ILE 500 (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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398B TYR* 3.5 9.3 - - - +
399B ASN 3.1 21.1 + - - -
400B PRO* 3.5 23.1 - - + +
403B PHE* 4.2 16.2 - - + -
456B TYR* 3.7 31.9 - - + +
470B VAL* 2.9 12.5 + - + +
471B ALA 4.7 0.7 - - - -
472B GLU* 4.1 21.3 - - + +
498B ARG* 3.7 20.2 - - + +
499B TRP* 1.3 75.0 - - - +
501B PHE* 1.3 83.5 + - + +
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Residues in contact with PHE 501 (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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399B ASN* 3.6 16.4 - - + +
400B PRO* 3.4 25.8 - - + -
403B PHE* 3.6 42.2 - + + -
469B GLY* 3.0 5.0 - - - -
470B VAL* 2.7 60.1 + - + +
499B TRP* 3.6 5.4 - - - -
500B ILE* 1.3 92.6 - - + +
502B VAL* 1.3 61.0 + - - +
503B LYS* 3.8 25.6 - - + -
541B LEU* 5.6 2.0 - - + -
544B ILE* 4.5 6.5 - - + -
545B ALA* 3.5 38.1 - - + -
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Residues in contact with VAL 502 (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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398B TYR* 3.8 39.8 - - + +
399B ASN* 3.0 21.0 + - - +
427B ILE* 4.0 25.1 - - + -
468B CYS 3.6 9.0 - - - +
469B GLY* 4.3 0.2 - - - -
499B TRP* 3.9 21.3 - - + -
500B ILE 4.1 0.8 + - - -
501B PHE* 1.3 75.7 - - - +
503B LYS* 1.3 65.2 + - - +
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Residues in contact with LYS 503 (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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399B ASN* 4.0 18.8 - - - +
467B PHE 3.3 2.4 - - - +
468B CYS* 2.9 29.3 + - - -
469B GLY* 3.6 1.5 + - - -
501B PHE* 3.8 32.5 - - + -
502B VAL* 1.3 77.2 - - - +
504B ASP* 1.3 63.9 + - - +
505B VAL* 3.7 15.1 + - + +
544B ILE* 3.0 29.1 + - + +
545B ALA 3.4 14.8 + - - -
547B TYR* 3.0 27.7 + - - -
548B LYS* 4.9 9.1 - - - +
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Residues in contact with ASP 504 (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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466B HIS* 3.2 32.0 + - + -
467B PHE 3.3 2.9 - - - -
468B CYS* 4.0 11.6 - - - +
503B LYS* 1.3 77.0 - - - +
505B VAL* 1.3 64.3 + - - +
506B PRO* 4.2 2.4 - - + +
547B TYR* 3.5 17.7 - - - -
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Residues in contact with VAL 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B HIS* 3.7 2.9 - - - +
467B PHE* 2.8 45.8 + - + +
503B LYS* 4.3 11.4 - - - +
504B ASP* 1.3 79.8 - - - +
506B PRO* 1.3 78.4 - - + +
507B ASN* 4.2 0.3 - - - +
509B GLN* 4.3 11.0 - - + -
510B LEU* 4.2 17.0 - - + -
543B ILE* 4.7 2.2 - - + -
544B ILE* 4.1 39.5 - - + +
547B TYR* 4.0 22.2 - - + -
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Residues in contact with PRO 506 (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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465B GLY 3.9 2.9 - - - +
466B HIS* 3.8 10.7 - - + -
504B ASP* 4.2 1.3 - - + +
505B VAL* 1.3 91.7 - - + +
507B ASN* 1.3 63.5 + - - +
508B SER* 3.6 19.3 - - - +
509B GLN* 3.1 21.7 + - + +
510B LEU* 4.0 3.7 + - - +
547B TYR* 3.4 40.2 - - + +
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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