Contacts of the helix formed by residues 59 - 69 (chain B) in PDB entry 2WA2
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 GLY 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B SER* 3.0 7.7 + - - -
58B ARG* 1.3 75.9 - - - +
60B THR* 1.3 65.1 + - - +
62B LYS* 3.2 11.2 + - - +
63B LEU 3.1 11.4 + - - -
87B SER* 3.0 12.3 - - - -
88B TRP* 3.1 23.8 + - - -
147B ASP* 5.3 1.3 - - - -
1267B SAM 3.5 12.6 - - - -
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Residues in contact with THR 60 (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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55B ALA* 3.6 20.8 - - - +
57B SER 3.5 1.0 + - - -
58B ARG 3.3 1.4 - - - -
59B GLY* 1.3 77.2 - - - +
61B ALA* 1.3 59.9 + - - +
63B LEU* 3.2 1.9 + - - +
64B ALA* 2.8 26.0 + - - +
87B SER* 2.7 40.8 + - - -
88B TRP* 4.7 1.3 - - - -
90B TYR* 5.1 0.2 - - - +
91B TYR* 3.9 14.6 - - + -
258B TYR* 3.6 34.8 - - + -
260B PHE* 3.6 18.6 - - + -
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Residues in contact with ALA 61 (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 31.6 - - + -
58B ARG 3.5 7.4 + - - +
59B GLY 3.3 0.4 - - - -
60B THR* 1.3 80.3 - - - +
62B LYS* 1.3 57.6 + - - +
64B ALA* 3.7 8.3 - - - +
65B TRP* 3.0 27.7 + - - +
213B LEU* 3.7 11.8 - - + +
257B ASP* 3.7 12.4 + - - +
258B TYR* 4.3 10.1 - - + +
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Residues in contact with LYS 62 (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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58B ARG* 3.6 33.4 + - - +
59B GLY* 3.2 14.2 + - - +
61B ALA* 1.3 74.2 - - - +
63B LEU* 1.3 66.3 + - - +
65B TRP* 3.1 4.7 + - - +
66B ILE* 3.1 29.0 + - + +
88B TRP* 4.7 5.6 - - + +
147B ASP* 6.0 1.1 - - - +
211B VAL* 4.3 13.5 - - + +
213B LEU* 3.8 40.5 + - + +
214B SER* 3.8 11.4 - - - +
215B ARG 5.6 0.4 - - - +
220B GLU* 3.7 23.8 - - - +
222B TYR* 4.2 14.8 - - + +
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Residues in contact with LEU 63 (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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59B GLY 3.1 4.0 + - - -
60B THR 3.8 5.4 - - - +
62B LYS* 1.3 77.4 - - - +
64B ALA* 1.3 57.9 + - - +
66B ILE* 3.2 5.6 + - + -
67B ASP* 2.9 30.8 + - - +
72B VAL* 4.3 16.8 - - + -
74B LEU* 4.8 4.7 - - + -
88B TRP* 3.6 64.7 - - + +
91B TYR* 3.7 23.6 - - + -
92B ALA 4.9 0.7 - - - +
145B LEU* 4.0 15.5 - - + -
182B CYS* 4.1 27.6 - - + -
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Residues in contact with ALA 64 (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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60B THR 2.8 20.9 + - - +
61B ALA* 3.7 7.0 - - - +
63B LEU* 1.3 71.5 - - - +
65B TRP* 1.3 58.3 + - - +
67B ASP* 3.2 0.5 + - - +
68B GLU* 2.9 44.9 + - - +
91B TYR* 3.6 31.1 - - + -
258B TYR* 3.7 22.0 - - + -
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Residues in contact with TRP 65 (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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61B ALA 3.0 17.9 + - - +
62B LYS 3.1 5.1 + - - +
64B ALA* 1.3 79.6 - - - +
66B ILE* 1.3 69.4 + - + +
68B GLU* 4.7 2.2 - - - -
69B ARG* 3.1 81.0 + - + +
209B ILE* 4.1 22.2 - - + -
210B ARG 3.7 17.5 - - - -
211B VAL* 3.8 17.3 - - + -
212B PRO* 3.3 33.6 - - + +
213B LEU* 3.9 19.7 - - + -
227B ILE* 6.2 0.2 - - + -
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Residues in contact with ILE 66 (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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62B LYS* 3.1 15.8 + - + +
63B LEU* 3.6 9.9 - - + +
65B TRP* 1.3 82.5 - - + +
67B ASP* 1.3 62.7 + - - +
69B ARG* 3.2 8.8 + - - +
71B GLY* 2.9 42.7 + - - -
72B VAL* 4.1 13.7 - - + -
88B TRP* 5.1 2.0 - - + -
182B CYS* 3.5 22.4 - - - -
209B ILE* 4.1 8.1 - - + -
211B VAL* 3.7 29.8 - - + -
222B TYR* 3.9 19.7 - - + -
224B VAL* 4.0 15.9 - - + -
227B ILE* 5.3 0.2 - - - +
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Residues in contact with ASP 67 (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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63B LEU 2.9 16.7 + - - +
64B ALA 3.2 0.6 + - - +
66B ILE* 1.3 77.3 - - - +
68B GLU* 1.3 59.4 + - - +
69B ARG 3.0 0.2 - - - -
70B GLY* 2.9 21.4 + - - +
72B VAL* 3.2 27.5 - - + +
73B GLU* 5.3 0.2 - - - -
74B LEU* 3.7 19.8 + - + +
91B TYR* 2.6 35.8 + - + +
95B GLN* 3.8 9.2 - - - +
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Residues in contact with GLU 68 (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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64B ALA* 2.9 38.5 + - - +
65B TRP* 4.0 4.6 - - - +
66B ILE 3.3 0.2 - - - -
67B ASP* 1.3 76.4 - - - +
69B ARG* 1.3 75.1 + - - +
70B GLY 3.3 1.4 + - - -
91B TYR* 4.6 7.8 + - - +
258B TYR* 4.5 10.2 - - - -
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Residues in contact with ARG 69 (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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65B TRP* 3.1 86.2 + - + +
66B ILE* 3.2 5.5 + - - +
67B ASP 3.0 1.0 - - - -
68B GLU* 1.3 96.6 + - - +
70B GLY* 1.3 61.6 + - - +
71B GLY 3.3 1.9 + - - +
227B ILE* 3.8 18.9 - - + +
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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