Contacts of the helix formed by residues 37 - 52 (chain A) in PDB entry 2WJW
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 ALA 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 4.4 7.4 - - + +
34A PRO* 3.2 39.7 + - + +
35A ARG 3.3 1.0 + - - -
36A GLY* 1.3 72.5 - - - +
38A ASP* 1.3 63.4 + - - +
40A GLU* 3.4 28.5 + - + +
41A TYR* 3.1 23.4 + - - +
91A PHE* 5.3 1.6 - - + -
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Residues in contact with ASP 38 (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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36A GLY* 2.9 26.3 + - - +
37A ALA* 1.3 70.9 + - - +
39A GLN* 1.3 61.3 + - - +
40A GLU* 4.0 0.2 + - - -
41A TYR* 3.3 7.5 + - - +
42A SER* 2.9 30.8 + - - -
286A PRO* 3.9 28.4 - - + +
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Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA 3.5 0.2 - - - -
38A ASP* 1.3 78.8 - - - +
40A GLU* 1.3 62.2 + - - +
42A SER* 3.2 2.1 + - - -
43A ALA* 2.9 27.9 + - - +
277A TRP* 3.6 24.3 - - + -
286A PRO 3.6 8.5 + - - -
287A GLY* 2.9 31.6 + - - +
290A THR* 4.7 1.0 + - - +
292A THR 4.3 3.6 + - - -
293A ILE* 4.2 6.6 - - - +
294A LYS* 2.9 49.5 + - - +
297A SER* 2.7 21.9 + - - +
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Residues in contact with GLU 40 (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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33A PHE* 4.0 4.5 - - + -
37A ALA* 3.4 31.8 - - + +
39A GLN* 1.3 81.0 + - - +
41A TYR* 1.3 56.4 + - - +
43A ALA* 3.3 1.2 + - - +
44A PHE 2.9 23.6 + - - -
91A PHE* 4.1 20.4 - - + -
213A ARG* 5.5 1.2 + - - -
294A LYS* 3.9 16.8 + - - -
296A THR* 2.6 29.8 + - - +
297A SER* 3.4 31.7 + - - +
300A THR* 3.3 20.3 - - - +
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Residues in contact with TYR 41 (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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33A PHE* 3.7 31.1 - + + -
37A ALA 3.1 17.7 + - - +
38A ASP* 3.3 6.0 + - - +
40A GLU* 1.3 73.8 - - - +
42A SER* 1.3 64.5 + - - +
44A PHE* 3.2 13.8 + + - +
45A ARG* 3.0 61.1 + - + +
48A MET* 5.8 1.6 - - - +
62A ILE* 3.8 39.2 - - + +
64A ASN* 5.9 1.8 - - - -
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Residues in contact with SER 42 (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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38A ASP 2.9 10.4 + - - -
39A GLN 3.2 5.6 + - - -
41A TYR* 1.3 77.0 - - - +
43A ALA* 1.3 57.8 + - - +
45A ARG* 3.2 15.0 + - - +
46A VAL* 2.9 32.6 + - - +
277A TRP* 4.1 10.5 - - - -
285A TYR* 3.2 18.2 - - - -
286A PRO* 2.7 46.9 + - - +
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Residues in contact with ALA 43 (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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39A GLN 2.9 16.9 + - - +
40A GLU 3.6 4.0 - - - +
42A SER* 1.3 72.9 - - - +
44A PHE* 1.3 61.3 + - - +
46A VAL* 3.4 1.9 + - - +
47A GLY* 2.9 26.0 + - - -
273A PHE* 5.5 0.2 - - + -
277A TRP* 3.9 19.9 - - + -
293A ILE* 4.3 4.7 - - + -
297A SER* 3.3 34.8 - - - +
301A TYR* 3.7 17.3 - - + +
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Residues in contact with PHE 44 (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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29A ILE* 4.1 13.7 - - + -
31A GLY* 5.3 2.7 - - - -
33A PHE* 3.7 18.2 - + + -
40A GLU 2.9 13.7 + - - +
41A TYR* 3.3 25.6 - + - +
43A ALA* 1.3 78.1 - - - +
45A ARG* 1.3 57.4 + - - +
47A GLY* 3.2 2.9 + - - -
48A MET* 3.0 53.6 + - + +
60A PRO* 3.9 24.2 - - + -
62A ILE* 4.2 12.8 - - + -
89A PHE* 3.9 27.6 - + + -
300A THR* 3.6 16.7 - - + +
304A VAL* 3.7 26.5 - - + +
307A MET* 4.3 4.5 - - + -
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Residues in contact with ARG 45 (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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41A TYR* 3.0 61.6 + - + +
42A SER* 3.7 24.7 + - - +
44A PHE* 1.3 73.8 - - + +
46A VAL* 1.3 65.5 + - - +
48A MET* 3.2 22.5 + - + +
49A VAL* 3.1 25.9 + - - +
284A GLU* 2.5 42.4 + - - +
285A TYR* 3.7 22.6 - - + +
286A PRO* 4.1 5.1 - - - +
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Residues in contact with VAL 46 (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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42A SER 2.9 21.7 + - - +
43A ALA* 3.8 6.5 - - - +
44A PHE 3.4 0.4 - - - -
45A ARG* 1.3 74.7 - - - +
47A GLY* 1.3 57.5 + - - +
49A VAL* 3.3 8.0 + - + +
50A GLN* 3.0 29.7 + - + +
273A PHE* 4.3 12.1 - - + -
276A ARG* 5.0 15.3 - - + -
277A TRP* 4.0 9.0 - - + -
280A LEU* 3.7 26.5 - - + -
285A TYR* 3.7 22.2 - - + -
301A TYR* 4.1 14.6 - - + -
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Residues in contact with GLY 47 (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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43A ALA 2.9 11.4 + - - -
44A PHE 3.6 4.3 - - - -
45A ARG 3.2 0.2 - - - -
46A VAL* 1.3 78.1 - - - +
48A MET* 1.3 56.1 + - - +
50A GLN 4.5 0.2 - - - -
51A PHE* 2.9 41.5 + - - +
301A TYR* 3.5 24.8 - - - -
304A VAL* 3.6 13.5 - - - -
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Residues in contact with MET 48 (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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41A TYR* 5.8 1.6 - - - +
44A PHE* 3.0 35.3 + - + +
45A ARG* 3.2 26.0 + - + +
47A GLY* 1.3 75.4 - - - +
49A VAL* 1.3 59.4 + - + +
52A SER* 2.9 34.2 + - - +
58A LEU* 4.1 20.0 - - + +
60A PRO* 3.1 40.4 - - + -
304A VAL* 4.1 14.6 - - + -
308A THR* 6.2 0.4 - - - -
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Residues in contact with VAL 49 (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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45A ARG 3.1 14.0 + - - +
46A VAL* 3.6 9.6 - - + +
47A GLY 3.2 0.4 - - - -
48A MET* 1.3 79.6 - - + +
50A GLN* 1.3 63.7 + - - +
52A SER* 3.6 14.5 + - - +
276A ARG* 6.5 0.7 - - - -
285A TYR* 4.4 15.0 - - - +
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Residues in contact with GLN 50 (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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46A VAL* 3.0 19.0 + - + +
47A GLY 3.3 2.9 + - - +
49A VAL* 1.3 80.1 - - - +
51A PHE* 1.3 78.8 + - + +
52A SER 3.9 3.6 + - - +
276A ARG* 4.8 15.1 + - - -
301A TYR* 3.4 26.2 + - + +
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Residues in contact with PHE 51 (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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47A GLY* 2.9 28.0 + - - +
50A GLN* 1.3 89.1 - - + +
52A SER* 1.3 64.7 + - - +
53A THR* 4.3 0.5 - - - +
301A TYR* 3.6 51.8 - + - -
302A ASP* 6.0 0.2 - - - -
304A VAL* 4.2 0.9 - - + -
305A GLN* 3.6 58.3 - - + -
308A THR* 3.7 34.6 - - + +
312A ARG* 4.2 13.5 + - - -
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Residues in contact with SER 52 (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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48A MET* 2.9 24.5 + - - +
49A VAL* 3.6 13.2 + - - +
50A GLN 3.5 3.7 - - - +
51A PHE* 1.3 81.2 - - - +
53A THR* 1.3 66.2 + - - +
56A PHE 4.0 8.3 - - - -
57A ARG* 4.6 16.6 - - - +
58A LEU 5.3 1.8 - - - +
308A THR* 5.5 2.5 - - - -
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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