Contacts of the helix formed by residues 132 - 139 (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 CYS 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 5.1 0.4 - - - -
128B ALA 3.7 0.9 - - - -
129B ALA 3.4 16.6 + - - +
130B MET 3.5 1.0 - - - -
131B ARG* 1.3 76.8 - - - +
133B LEU* 1.3 66.2 + - - +
134B PRO* 3.5 0.4 - - - -
135B ALA* 3.3 9.0 + - - +
136B ALA* 3.3 17.5 + - - +
150B VAL* 3.9 13.1 - - + +
153B GLN* 3.6 17.7 - - - +
167B CYS* 3.4 53.2 - - - +
170B LEU* 4.9 9.2 - - + -
171B GLY* 5.1 4.0 - - - +
250B LEU* 5.9 0.2 - - - +
253B MET* 5.7 3.1 - - + -
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Residues in contact with LEU 133 (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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13B ALA* 3.5 20.4 - - + +
14B PHE* 3.4 50.9 - - + +
17B LEU* 4.5 12.6 - - + -
130B MET 5.2 0.6 + - - -
131B ARG 3.3 1.0 - - - -
132B CYS* 1.3 77.2 - - - +
134B PRO* 1.3 65.4 - - + +
136B ALA* 3.0 8.6 + - - +
137B LEU* 2.9 45.3 + - + +
174B VAL* 3.9 23.3 - - + -
253B MET* 3.7 27.9 - - + -
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Residues in contact with PRO 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PHE* 4.2 11.4 - - + -
65B SER* 3.3 34.8 - - - +
68B LEU* 4.0 9.0 - - + -
69B GLY* 3.9 23.6 - - - +
72B LEU* 3.6 5.3 - - + +
131B ARG 3.3 14.8 - - - +
132B CYS 3.5 0.7 - - - -
133B LEU* 1.3 94.8 - - + +
135B ALA* 1.3 55.7 + - - +
137B LEU* 3.4 4.7 + - + +
138B ALA* 2.9 30.7 + - - +
287B LEU* 3.9 16.4 - - + +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 4.3 13.6 - - + +
72B LEU* 3.8 12.9 - - + +
78B LEU* 6.3 0.7 - - + -
132B CYS 3.3 8.6 + - - +
133B LEU 3.3 0.6 - - - -
134B PRO* 1.3 78.1 - - - +
136B ALA* 1.3 60.5 + - - +
138B ALA* 3.6 1.4 + - - +
139B THR* 2.8 32.4 + - - +
146B LEU* 4.2 3.6 - - - +
149B TRP* 4.3 12.6 - - + +
150B VAL* 3.8 30.5 - - + +
153B GLN* 4.7 2.7 - - + -
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B CYS 3.3 9.3 + - - +
133B LEU* 3.0 10.9 + - - +
135B ALA* 1.3 75.7 - - - +
137B LEU* 1.3 65.9 + - - +
139B THR* 3.3 4.3 + - - -
140B LEU* 3.5 3.0 + - - +
146B LEU* 3.7 14.9 - - + +
150B VAL* 4.5 0.4 - - + +
171B GLY* 4.0 17.3 - - - +
174B VAL* 3.8 30.5 - - + -
175B HIS* 2.7 25.8 + - + -
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ALA* 3.9 25.1 - - + +
13B ALA* 5.0 0.2 - - + -
14B PHE* 4.1 20.9 - - + -
133B LEU* 2.9 45.3 + - + +
134B PRO 3.8 4.0 - - - +
136B ALA* 1.3 75.8 - - - +
138B ALA* 1.3 63.0 + - - +
139B THR 3.2 1.0 + - - -
140B LEU* 3.5 20.0 + - + +
174B VAL* 4.6 0.9 - - + -
178B ILE* 3.4 33.4 - - + -
284B VAL* 4.7 7.2 - - + +
287B LEU* 3.7 26.3 - - + +
288B LEU* 5.5 2.7 - - + +
291B ALA* 3.5 13.0 - - - +
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Residues in contact with ALA 138 (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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72B LEU* 4.1 6.3 - - + -
134B PRO 2.9 17.8 + - - +
135B ALA 4.1 2.9 - - - +
136B ALA 3.3 0.6 - - - -
137B LEU* 1.3 76.4 - - - +
139B THR* 1.3 57.6 + - - +
140B LEU 3.6 0.2 - - - -
142B HIS* 2.9 23.2 + - - -
149B TRP* 3.9 21.3 - - + -
287B LEU* 3.8 19.9 - - + +
290B LEU* 4.0 18.6 - - + +
291B ALA* 3.8 10.2 + - - -
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Residues in contact with THR 139 (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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135B ALA 2.8 22.6 + - - +
137B LEU 3.2 0.2 - - - -
138B ALA* 1.3 77.3 - - - +
140B LEU* 1.3 64.6 + - - +
141B GLY 3.2 3.1 - - - -
142B HIS* 3.0 33.2 + - + -
143B PRO 3.2 2.6 - - - -
145B ASP* 3.6 26.9 - - + +
146B LEU* 3.5 13.8 - - - +
149B TRP* 3.5 29.4 - - + -
175B HIS* 3.1 22.4 + - - -
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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