Contacts of the strand formed by residues 33 - 44 (chain B) 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 LEU 33 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A ASP* 4.1 15.5 - - + +
274A HIS* 3.2 10.4 - - + -
26B ARG* 4.5 8.5 - - - +
29B ASP 4.7 0.2 - - - +
30B CYS* 3.3 39.5 + - + +
31B SER 3.2 1.5 - - - +
32B GLU* 1.3 77.0 - - - +
34B ILE* 1.3 62.7 + - - +
35B SER* 3.8 14.4 - - - +
389B TYR* 3.0 32.3 + - - +
420B ARG* 3.4 49.1 - - + +
422B LEU* 4.2 24.0 - - + -
427B GLU* 5.4 0.4 - - - +
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Residues in contact with ILE 34 (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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33B LEU* 1.3 77.0 - - - +
35B SER* 1.3 59.4 + - - +
36B VAL* 3.8 5.5 + - + -
387B SER 3.2 9.0 - - - +
388B SER* 3.9 17.9 - - - +
389B TYR* 4.8 1.6 - - + -
393B LEU* 4.6 6.3 - - + -
395B GLU* 4.0 28.3 - - + +
407B LEU* 4.2 20.9 - - + -
409B VAL* 3.9 24.7 - - + -
419B CYS* 3.8 33.0 - - + -
420B ARG 3.0 9.9 + - - +
421B VAL* 3.4 8.8 - - + +
422B LEU 2.9 21.8 + - - -
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ASP 4.1 7.1 + - - -
274A HIS* 3.7 15.9 - - - -
277A GLN* 3.9 13.3 + - - -
33B LEU* 3.8 13.7 - - - +
34B ILE* 1.3 73.0 - - - +
36B VAL* 1.3 59.3 + - - +
37B LEU* 4.1 8.9 - - - +
386B SER* 3.0 8.0 - - - -
387B SER* 2.8 46.7 + - - +
422B LEU* 3.7 18.0 - - - +
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Residues in contact with VAL 36 (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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34B ILE* 4.2 3.8 - - + +
35B SER* 1.3 79.4 - - - +
37B LEU* 1.3 66.6 + - - +
38B PRO* 3.5 6.5 - - + +
39B ARG* 5.5 0.2 + - - -
384B MET* 4.0 15.0 - - - -
385B LEU 3.8 3.1 - - - -
386B SER* 4.1 11.4 - - - -
407B LEU* 4.1 31.2 - - + -
421B VAL* 4.2 8.1 - - + -
422B LEU 2.9 25.8 + - - +
423B ASP* 3.6 27.3 - - + +
424B GLY 4.5 2.4 + - - -
442B TRP* 3.9 17.7 - - + -
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Residues in contact with LEU 37 (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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246A VAL* 3.8 29.8 - - + -
247A ASP* 3.6 26.5 - - - +
277A GLN* 5.0 9.0 - - + +
35B SER* 4.1 15.0 - - - +
36B VAL* 1.3 88.6 - - - +
38B PRO* 1.3 66.9 - - - +
39B ARG* 3.1 24.7 - - - +
40B HIS* 2.9 31.7 + - + +
384B MET* 4.4 0.6 - - - -
385B LEU* 2.9 36.2 + - + +
386B SER* 4.8 1.3 - - - -
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Residues in contact with PRO 38 (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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36B VAL* 3.5 10.8 - - + +
37B LEU* 1.3 87.2 - - - +
39B ARG* 1.3 62.7 + - - +
40B HIS 3.1 6.6 + - - -
41B ALA* 4.2 4.5 + - - +
384B MET* 3.9 25.3 - - + +
399B VAL* 4.1 13.7 - - + +
405B ARG* 3.5 44.4 + - + +
423B ASP* 3.7 16.2 - - - +
442B TRP* 4.8 0.4 - - + -
1447B PO4 3.9 21.1 - - - +
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Residues in contact with ARG 39 (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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247A ASP* 2.9 29.9 + - - +
250A GLU* 2.9 40.3 + - - -
251A LEU* 6.0 1.8 - - - +
36B VAL 5.5 0.2 + - - -
37B LEU* 3.0 26.5 + - - +
38B PRO* 1.3 80.6 - - - +
40B HIS* 1.3 76.8 + - + +
41B ALA* 3.7 3.7 + - - +
405B ARG* 5.3 0.4 - - - +
424B GLY* 6.3 0.8 - - - -
1447B PO4 5.5 0.8 + - - +
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Residues in contact with HIS 40 (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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246A VAL* 4.2 7.6 - - + +
250A GLU* 2.7 41.1 + - + -
280A TYR* 3.1 31.6 + + + +
37B LEU* 2.9 31.8 + - + +
38B PRO 4.0 2.2 - - - -
39B ARG* 1.3 95.9 + - + +
41B ALA* 1.3 63.0 + - - +
42B LEU* 4.4 1.2 - - - +
384B MET* 3.6 1.4 - - - -
385B LEU* 3.0 44.1 + - + +
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Residues in contact with ALA 41 (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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280A TYR* 5.6 1.4 + - - -
38B PRO 4.7 5.8 - - - +
39B ARG 3.7 5.0 + - - +
40B HIS* 1.3 74.9 - - - +
42B LEU* 1.3 67.9 + - - +
382B ARG* 3.9 30.5 - - + -
383B VAL 3.6 4.9 - - - +
384B MET* 4.6 1.8 - - - +
399B VAL* 6.1 4.3 - - + -
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Residues in contact with LEU 42 (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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280A TYR* 4.1 28.9 - - + -
283A GLN* 5.8 2.2 - - - +
40B HIS 4.6 2.2 - - - +
41B ALA* 1.3 83.0 - - - +
43B GLN* 1.3 75.6 + - - +
322B LYS 5.2 8.1 - - - +
382B ARG* 2.9 23.7 + - - -
383B VAL* 2.7 34.7 + - + +
384B MET 4.1 10.3 - - - +
385B LEU* 4.2 16.4 - - + +
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Residues in contact with GLN 43 (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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42B LEU* 1.3 85.9 - - - +
44B GLN* 1.3 66.5 + - - +
45B ILE* 4.0 0.8 + - + -
282B ALA* 6.3 0.9 - - + -
321B PHE 2.9 27.1 + - - +
322B LYS 5.5 0.5 - - - +
324B GLY* 3.2 36.6 + - - +
325B CYS 2.9 24.4 + - - +
326B SER* 4.9 0.9 - - - +
382B ARG* 3.3 3.9 - - - +
383B VAL* 3.0 45.0 + - - +
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Residues in contact with GLN 44 (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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43B GLN* 1.3 78.2 - - - +
45B ILE* 1.3 68.3 + - - +
46B ASP* 4.8 7.0 + - - +
289B LYS* 6.1 0.9 - - - -
326B SER* 3.9 16.8 - - - -
380B GLY* 2.9 40.5 - - - +
381B ALA 3.4 4.0 - - - +
382B ARG* 3.5 36.2 + - + +
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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