Contacts of the helix formed by residues 59 - 68 (chain B) in PDB entry 2WOE
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 THR 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B ASP* 2.6 24.8 + - - +
25B ALA* 3.5 28.5 - - + -
28B GLU* 5.2 0.7 + - - -
51B LEU* 4.2 11.8 - - + +
53B LEU* 3.9 19.3 - - + -
57B GLN 4.3 0.2 - - - +
58B ILE* 1.3 79.9 - - - +
60B ASP* 1.3 76.8 + - - +
61B ASP* 3.2 11.0 + - - -
62B THR* 3.4 1.9 + - - -
63B GLU* 3.0 31.3 + - - +
96B VAL* 4.0 14.4 - - + -
245B ASP* 3.9 5.9 + - - +
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Residues in contact with ASP 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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59B THR* 1.3 80.9 + - - +
61B ASP* 1.3 60.7 + - - +
63B GLU* 4.2 1.7 + - - -
64B MET* 2.8 33.6 + - - +
90B TRP* 3.7 22.7 - - + -
96B VAL* 4.9 0.4 - - - +
97B ASN* 3.0 45.6 + - - +
99B GLY 4.1 5.7 + - - -
130B MET* 3.5 14.3 - - + +
245B ASP* 4.0 0.5 - - - +
401B AR6 2.5 33.6 + - - -
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Residues in contact with ASP 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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17B LEU* 4.8 2.5 - - + -
21B ASP* 3.4 11.9 - - + +
59B THR* 3.2 11.3 + - - -
60B ASP* 1.3 76.8 - - - +
62B THR* 1.3 55.5 - - - +
64B MET* 4.3 1.2 - - - +
65B SER* 2.8 30.3 + - - -
130B MET* 3.5 28.4 - - + +
131B ARG* 4.7 1.0 - - - +
245B ASP* 2.6 31.4 - - - +
246B THR* 2.7 39.0 + - - +
249B ALA* 3.9 14.3 - - + +
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Residues in contact with THR 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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14B PHE* 4.8 7.0 - - + -
17B LEU* 4.1 5.2 + - + -
18B ALA* 3.4 31.0 + - + +
21B ASP* 2.6 35.4 + - - +
58B ILE* 3.6 25.3 - - + +
61B ASP* 1.3 75.0 - - - +
63B GLU* 1.3 59.4 + - - +
65B SER* 3.3 5.9 + - - -
66B LEU* 2.8 41.5 + - + +
280B ILE* 4.5 6.5 - - + -
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Residues in contact with GLU 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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57B GLN* 5.9 1.0 + - - -
58B ILE* 3.8 23.0 - - + +
59B THR* 3.0 28.2 + - - +
60B ASP* 4.2 1.7 + - - +
62B THR* 1.3 77.6 - - - +
64B MET* 1.3 57.9 + - - +
66B LEU* 3.3 8.5 + - + +
67B ALA* 3.0 26.7 + - - +
70B ARG* 4.9 1.9 + - - -
90B TRP* 3.0 37.5 + - + +
95B PRO* 3.7 15.5 - - - +
96B VAL* 4.7 6.6 + - - +
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Residues in contact with MET 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 ASP* 2.8 23.7 + - - +
61B ASP 4.4 0.2 - - - +
63B GLU* 1.3 69.8 - - - +
65B SER* 1.3 63.9 + - - +
67B ALA* 3.2 8.8 + - - +
68B LEU* 3.0 21.0 + - - +
87B PHE* 3.7 36.0 - - + -
90B TRP* 3.6 42.4 - - + -
102B CYS* 3.9 14.8 - - + -
106B ILE* 4.0 11.2 - - + -
130B MET* 3.5 23.8 - - + -
131B ARG* 3.8 33.2 - - + +
157B THR* 4.9 0.4 - - + -
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Residues in contact with SER 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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14B PHE* 4.1 10.5 - - - -
17B LEU* 3.6 20.2 - - - +
61B ASP 2.8 21.4 + - - -
62B THR 3.3 5.3 + - - -
64B MET* 1.3 79.2 - - - +
66B LEU* 1.3 57.1 + - - +
68B LEU* 3.3 2.7 + - - -
69B GLY* 2.9 24.8 + - - -
130B MET 3.5 3.8 + - - -
131B ARG* 3.3 25.3 - - - +
133B LEU* 5.4 0.2 - - - +
134B PRO* 3.3 22.8 - - - +
283B GLN* 4.2 0.3 - - - +
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Residues in contact with LEU 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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14B PHE* 3.8 17.0 - - + -
58B ILE* 4.5 11.0 - - + -
62B THR* 2.8 36.8 + - + +
63B GLU* 3.8 7.2 - - + +
64B MET 3.3 0.2 - - - -
65B SER* 1.3 73.8 - - - +
67B ALA* 1.3 57.0 + - - +
70B ARG* 2.9 39.2 + - - +
276B VAL* 4.6 9.4 - - + +
279B GLU* 3.9 19.5 - - + -
280B ILE* 4.0 21.1 - - + -
283B GLN* 3.0 36.7 + - - +
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Residues in contact with ALA 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 GLU 3.0 14.2 + - - +
64B MET* 3.2 11.0 + - - +
66B LEU* 1.3 75.2 - - - +
68B LEU* 1.3 62.0 + - - +
70B ARG* 3.4 22.7 + - - +
71B SER* 3.4 16.3 + - - -
86B GLU* 3.7 27.9 - - + +
87B PHE* 3.9 20.0 - - + -
90B TRP* 4.8 8.1 - - + -
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Residues in contact with LEU 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 MET 3.0 12.3 + - - +
65B SER* 3.6 7.6 - - - +
67B ALA* 1.3 77.4 - - - +
69B GLY* 1.3 62.7 + - - +
71B SER* 3.2 4.2 + - - -
72B LEU* 3.0 31.8 + - + +
78B LEU* 5.5 1.1 - - + -
83B ILE* 3.5 39.5 - - + -
87B PHE* 4.0 11.2 - - + -
131B ARG* 3.3 26.5 - - + +
134B PRO* 4.0 16.2 - - + -
135B ALA* 4.3 8.5 - - + +
153B GLN* 3.7 32.3 - - + +
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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