Contacts of the strand formed by residues 405 - 411 (chain A) in PDB entry 2WNW
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 ARG 405 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A PRO* 3.5 34.7 + - + +
39A ARG* 5.1 1.0 - - - +
384A MET* 4.1 5.4 - - + -
398A PHE 3.6 4.5 - - - -
399A VAL* 3.6 20.0 - - + +
403A GLY* 3.0 21.5 + - - -
404A GLU* 1.3 73.8 - - - +
406A VAL* 1.3 62.8 + - - +
441A LEU* 3.3 6.2 - - - -
442A TRP* 2.7 76.8 + - + +
444A GLN* 3.8 31.0 + - - +
1446A PO4 2.7 41.1 + - - -
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Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A HIS 5.3 0.2 - - - +
376A TYR* 4.0 8.5 - - + +
377A VAL* 3.9 24.9 - - + -
384A MET* 3.8 2.9 - - - +
397A GLY* 3.1 3.3 - - - -
398A PHE* 2.7 46.2 + - + +
400A ASN* 3.6 28.5 - - - +
404A GLU* 4.1 6.1 - - - +
405A ARG* 1.3 80.7 - - - +
407A LEU* 1.3 63.7 + - - +
408A VAL* 4.3 2.9 - - + -
439A THR* 3.7 14.6 - - + -
440A LEU 3.4 3.1 - - - -
441A LEU* 3.5 25.8 - - + -
442A TRP* 4.5 0.2 - - - -
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Residues in contact with LEU 407 (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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34A ILE* 4.1 9.4 - - + -
36A VAL* 4.1 15.9 - - + -
384A MET* 5.4 0.2 - - + -
386A SER* 4.8 0.4 - - - +
395A GLU* 3.7 21.8 - - + +
396A VAL 3.6 18.4 - - - +
397A GLY* 3.8 5.8 - - - -
406A VAL* 1.3 74.1 - - - +
408A VAL* 1.3 64.2 + - - +
409A VAL* 3.8 19.4 + - + +
421A VAL* 3.7 41.5 - - + -
438A SER 3.5 1.7 - - - +
439A THR* 3.2 4.8 - - - -
440A LEU* 2.8 42.4 + - + +
442A TRP* 3.9 16.8 - - + -
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Residues in contact with VAL 408 (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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314A LEU* 5.1 4.0 - - + -
318A ILE* 4.5 9.6 - - + -
372A HIS* 3.7 33.0 - - + +
373A PHE* 3.9 46.0 - - + -
394A GLU 4.5 0.2 - - - -
395A GLU* 3.1 8.1 - - - +
396A VAL* 2.9 35.7 + - + +
398A PHE* 4.6 6.3 - - + -
406A VAL* 4.9 4.7 - - + -
407A LEU* 1.3 75.0 - - - +
409A VAL* 1.3 67.9 + - - +
410A TYR* 5.5 0.4 - - + -
437A ALA* 5.7 0.9 - - + -
438A SER 3.5 7.0 - - - +
439A THR* 4.1 5.8 - - + +
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Residues in contact with VAL 409 (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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34A ILE* 4.0 26.7 - - + -
393A LEU* 4.4 14.8 - - + -
394A GLU 3.3 8.5 - - - +
395A GLU* 4.1 2.2 - - + -
407A LEU* 3.8 27.1 - - + +
408A VAL* 1.3 82.4 - - - +
410A TYR* 1.3 63.4 + - - +
419A CYS* 4.7 1.6 - - - -
421A VAL* 5.2 0.2 - - + -
430A LEU* 5.1 11.9 - - + -
432A LEU* 3.6 25.6 - - + +
437A ALA* 3.1 4.9 - - - +
438A SER* 2.8 45.5 + - - +
440A LEU* 6.4 0.2 - - + -
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Residues in contact with TYR 410 (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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310A TRP* 3.8 10.8 - - - -
311A HIS* 2.7 46.1 + + - +
314A LEU* 3.8 34.5 - - + -
315A HIS 4.5 2.0 - - - -
318A ILE* 3.6 17.7 - - + +
392A LEU 3.5 2.6 - - - +
393A LEU 3.7 0.9 - - - -
394A GLU* 2.8 62.4 + - - +
408A VAL* 5.5 0.7 - - + -
409A VAL* 1.3 78.0 - - - +
411A ASN* 1.3 72.6 + - - +
412A ARG* 3.6 22.1 + - + +
435A SER* 3.7 20.0 + - - -
436A GLY 3.5 11.0 - - - -
437A ALA* 4.6 1.8 - - + -
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Residues in contact with ASN 411 (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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392A LEU 3.9 4.3 - - - +
393A LEU* 3.8 15.5 - - + +
410A TYR* 1.3 72.8 - - - +
412A ARG* 1.3 55.9 + - - +
413A ASP* 2.9 23.7 + - - +
415A GLN 2.9 25.5 + - - -
417A ARG* 3.4 16.3 - - - +
432A LEU* 3.3 20.5 + - + +
433A PRO 3.1 24.6 + - - +
434A PRO* 3.8 2.4 - - - +
435A SER* 2.8 35.2 + - - -
436A GLY 2.9 12.5 + - - +
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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