Contacts of the helix formed by residues 47 - 61 (chain A) in PDB entry 2WXW
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 ASP 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A PRO 3.4 5.7 + - - +
46A VAL* 1.3 69.1 - - - +
48A GLU* 1.3 57.4 + - - +
49A LYS* 3.4 13.2 + - - +
50A ALA* 3.1 32.3 + - + +
51A LEU* 2.9 27.4 + - - +
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Residues in contact with GLU 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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46A VAL* 3.1 12.6 + - + +
47A ASP* 1.3 69.3 + - - +
49A LYS* 1.3 64.6 + - + +
51A LEU* 3.4 8.7 + - + +
52A GLN* 3.1 25.1 + - - +
171A LEU* 3.4 28.3 - - + +
173A SER* 2.6 29.5 + - - +
228A TRP* 3.2 22.1 - - + -
250A HIS* 3.2 25.4 + - - -
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Residues in contact with LYS 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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47A ASP* 3.3 8.9 + - - +
48A GLU* 1.3 77.7 - - + +
50A ALA* 1.3 62.7 + - - +
51A LEU 3.2 0.2 + - - -
52A GLN* 3.3 16.6 + - - +
53A ASP* 3.0 38.2 + - - +
171A LEU* 6.3 0.2 - - - -
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Residues in contact with ALA 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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47A ASP* 3.1 31.9 + - + +
49A LYS* 1.3 78.3 - - - +
51A LEU* 1.3 60.7 + - - +
53A ASP* 3.8 7.1 + - - +
54A GLN* 3.3 22.2 + - - +
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Residues in contact with LEU 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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46A VAL* 5.7 5.2 - - + -
47A ASP 2.9 13.6 + - - +
48A GLU* 3.5 11.2 - - - +
49A LYS 3.1 0.4 - - - -
50A ALA* 1.3 73.9 - - - +
52A GLN* 1.3 61.1 + - + +
54A GLN* 3.0 9.9 + - + +
55A LEU* 3.0 40.2 + - + +
171A LEU* 6.2 0.7 - - + -
172A LEU 5.2 0.2 - - - +
173A SER* 4.0 35.4 - - - +
174A THR* 4.4 6.5 - - - +
175A VAL* 5.1 2.9 - - + -
198A THR* 5.4 0.7 - - - +
199A PRO* 3.8 36.3 - - + -
200A VAL* 4.2 22.9 - - + -
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Residues in contact with GLN 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 GLU 3.1 12.1 + - - +
49A LYS* 3.4 21.8 - - - +
51A LEU* 1.3 79.2 - - - +
53A ASP* 1.3 69.7 + - - +
55A LEU* 3.1 14.9 + - + +
56A VAL* 2.9 37.8 + - + +
159A VAL* 3.9 23.8 - - + +
167A GLN* 6.3 1.2 - - - +
170A LEU 4.0 3.6 - - - +
171A LEU* 3.6 35.1 - - + +
172A LEU 5.8 0.7 - - - +
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Residues in contact with ASP 53 (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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49A LYS* 3.0 30.6 + - - +
50A ALA* 4.1 7.1 + - - +
52A GLN* 1.3 86.3 + - - +
54A GLN* 1.3 57.5 + - - +
56A VAL* 3.1 25.5 - - + +
57A LEU* 3.6 8.8 + - - +
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Residues in contact with GLN 54 (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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50A ALA 3.3 12.3 + - - +
51A LEU* 3.0 13.8 + - + +
53A ASP* 1.3 77.9 - - - +
55A LEU* 1.3 59.8 + - + +
56A VAL 3.3 0.4 - - - -
57A LEU* 3.4 16.6 + - + +
58A VAL* 3.1 37.9 + - - +
152A GLN* 4.4 2.9 + - - -
199A PRO* 3.8 23.6 - - + +
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Residues in contact with LEU 55 (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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51A LEU* 3.0 34.6 + - + +
52A GLN* 3.1 12.5 + - - +
54A GLN* 1.3 75.9 - - - +
56A VAL* 1.3 60.4 + - - +
58A VAL* 3.4 5.4 + - + +
59A ALA 3.0 21.5 + - - -
152A GLN* 3.2 45.3 - - + +
155A GLN* 4.2 16.8 - - + +
156A GLY* 3.5 20.2 - - - -
159A VAL* 4.6 11.2 - - + -
172A LEU 3.7 22.9 - - - +
174A THR* 5.6 2.5 - - - +
199A PRO* 4.6 8.5 - - + -
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Residues in contact with VAL 56 (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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52A GLN* 2.9 21.4 + - + +
53A ASP* 3.1 29.8 - - + +
55A LEU* 1.3 73.3 - - - +
57A LEU* 1.3 56.3 + - + +
59A ALA* 3.4 8.0 + - - +
60A ALA* 2.8 34.8 + - - +
159A VAL* 3.4 31.4 - - + +
160A ALA* 4.8 8.7 - - - +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ASP 3.8 10.3 - - - +
54A GLN* 3.4 22.8 + - + +
55A LEU 3.3 0.6 - - - -
56A VAL* 1.3 80.4 - - + +
58A VAL* 1.3 62.2 + - + +
60A ALA* 4.2 6.7 - - + -
61A LYS* 2.8 69.6 + - + +
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Residues in contact with VAL 58 (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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54A GLN* 3.1 40.3 + - - +
55A LEU* 3.5 9.6 - - + +
56A VAL 3.3 0.2 - - - -
57A LEU* 1.3 79.0 - - + +
59A ALA* 1.3 60.7 + - - +
61A LYS* 3.3 18.8 - - - +
62A LEU* 3.6 13.5 - - + +
149A SER 5.4 1.8 - - - +
152A GLN* 3.8 35.9 - - + +
153A ALA* 4.6 13.5 - - + -
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Residues in contact with ALA 59 (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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55A LEU 3.0 11.2 + - - +
56A VAL* 3.6 7.0 - - - +
58A VAL* 1.3 75.7 - - - +
60A ALA* 1.3 66.4 + - - +
62A LEU* 3.3 18.1 - - - +
67A LYS* 5.4 4.5 - - - -
153A ALA 5.1 1.1 - - - -
156A GLY* 3.4 37.2 - - - +
157A LEU* 4.0 15.7 - - + +
160A ALA* 5.8 2.9 - - + -
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Residues in contact with ALA 60 (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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56A VAL 2.8 21.1 + - - +
57A LEU* 3.2 10.3 + - + +
59A ALA* 1.3 75.6 - - - +
61A LYS* 1.3 62.6 + - + +
62A LEU* 2.8 13.0 + - - +
67A LYS* 6.0 0.3 - - - -
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Residues in contact with LYS 61 (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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57A LEU* 2.8 49.3 + - + +
58A VAL* 3.3 11.7 - - - +
60A ALA* 1.3 70.6 - - + +
62A LEU* 1.3 60.4 + - - +
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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