Contacts of the strand formed by residues 431 - 439 (chain A) in PDB entry 6WCZ
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 ILE 431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A PRO* 5.7 7.6 - - + -
342A VAL* 6.0 4.5 - - + -
361A VAL* 3.7 15.0 - - + -
362A SER 3.3 23.1 - - - +
363A ILE* 3.7 21.3 - - + +
376A PHE* 5.7 2.5 - - + -
378A ILE* 6.2 2.2 - - + -
429A HIS 3.8 3.1 + - - +
430A ILE* 1.3 72.9 - - - +
432A SER* 1.3 79.3 + - - +
433A PHE* 3.7 25.7 - - + -
449A ASP 3.7 1.0 - - - -
450A THR* 3.3 35.9 + - + +
453A VAL* 6.1 1.8 - - + -
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Residues in contact with SER 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A SER* 2.5 51.2 + - - -
364A ASP 5.8 0.2 + - - -
365A ARG* 4.7 22.6 + - - +
430A ILE* 4.0 4.5 + - - +
431A ILE* 1.3 78.1 - - - +
433A PHE* 1.3 66.5 + - - +
447A LYS* 5.1 0.7 - - - -
448A THR 3.3 17.5 - - - -
449A ASP* 3.2 24.2 + - - +
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Residues in contact with PHE 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A PHE* 4.3 15.9 - + + -
318A VAL* 6.2 1.3 - - + -
342A VAL* 4.9 18.2 - - + -
344A THR* 4.6 22.0 - - + -
359A VAL* 4.3 10.5 - - + -
360A GLU 3.2 7.0 - - - +
361A VAL* 3.6 32.3 - - + -
362A SER* 3.4 0.4 + - - -
400A PHE* 3.6 24.5 - + + -
431A ILE* 3.7 28.5 - - + -
432A SER* 1.3 84.9 - - - +
434A THR* 1.3 61.8 + - - +
435A VAL* 3.4 3.3 + - - +
446A LEU 3.1 15.6 - - - +
447A LYS* 3.2 12.8 - - - -
448A THR 3.5 16.1 + - - +
449A ASP 5.6 0.9 - - - -
450A THR* 5.6 4.5 - - - -
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Residues in contact with THR 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A VAL* 3.4 4.2 - - - +
360A GLU* 2.5 69.4 + - + +
361A VAL 3.9 0.9 + - - -
362A SER* 3.8 18.2 + - - -
433A PHE* 1.3 69.6 - - - +
435A VAL* 1.3 62.3 + - - +
436A LYS* 4.3 13.3 + - + +
445A GLU* 4.1 15.0 - - - +
447A LYS* 3.7 19.9 - - + +
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Residues in contact with VAL 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A PHE* 3.6 40.6 - - + -
346A LEU* 4.2 20.4 - - + -
358A THR 5.6 0.4 - - - +
359A VAL* 3.7 19.7 - - + -
433A PHE 4.0 0.7 - - - +
434A THR* 1.3 78.7 - - - +
436A LYS* 1.3 61.7 + - - +
437A TYR* 3.4 22.0 + - + +
445A GLU* 2.9 12.0 - - - +
446A LEU* 2.7 50.3 + - + +
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Residues in contact with LYS 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A LEU* 5.3 9.5 - - - +
358A THR 4.6 14.8 + - - +
360A GLU* 5.1 11.2 + - - -
434A THR* 4.1 11.2 + - + +
435A VAL* 1.3 72.2 - - - +
437A TYR* 1.3 59.6 + - - +
438A THR* 4.1 2.4 + - - -
445A GLU* 3.2 30.4 + - - +
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Residues in contact with TYR 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A PHE* 4.6 4.8 - + - -
312A LEU* 3.9 42.7 - - + +
346A LEU* 3.8 27.1 - - + -
348A VAL* 4.9 6.9 + - + +
350A LEU* 3.1 36.2 + - - +
351A GLN* 5.3 3.4 - - + -
357A LEU* 5.7 9.9 - - + -
435A VAL* 3.4 14.7 + - + -
436A LYS* 1.3 73.1 - - - +
438A THR* 1.3 78.4 + - - +
439A TYR* 3.5 30.8 - - + +
442A LEU 5.1 1.6 - - - -
443A LYS* 4.4 0.2 - - - +
444A GLN* 2.8 42.1 + - + +
445A GLU* 4.3 1.4 + - - +
446A LEU* 5.0 6.5 - - + -
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Residues in contact with THR 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A GLU* 3.5 19.6 + - + +
354A ASN* 6.3 0.9 - - - +
357A LEU* 6.0 2.3 - - - +
436A LYS 4.1 2.9 + - - -
437A TYR* 1.3 91.8 + - - +
439A TYR* 1.3 65.5 + - - +
441A GLY* 3.9 18.6 - - - +
442A LEU 3.3 12.3 - - - +
443A LYS* 3.3 34.6 - - + +
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Residues in contact with TYR 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A PHE* 3.2 54.2 - + + -
350A LEU* 3.6 23.5 - - + +
351A GLN* 3.3 34.9 + - - -
352A GLU* 3.2 37.2 - - - -
437A TYR* 3.5 20.2 - - + +
438A THR* 1.3 73.2 - - - +
440A GLN* 1.3 78.7 + - + +
441A GLY 3.1 2.0 - - - +
442A LEU* 2.9 22.4 + - - +
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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