Contacts of the strand formed by residues 140 - 146 (chain B) in PDB entry 3WBR
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 TYR 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B ILE* 3.6 13.9 - - + -
98B SER 4.4 0.9 - - - -
134B LEU* 3.6 33.3 - - + -
135B LYS* 2.6 51.0 + - - -
138B SER* 3.3 26.4 - - - -
139B SER* 1.3 75.7 + - - +
141B PHE* 1.3 63.4 + - - +
182B ILE* 3.1 6.8 - - - -
183B ILE* 2.8 47.2 + - + +
191B TRP* 4.4 1.3 - + - -
203B LYS* 3.2 32.3 - - + +
204B SER* 3.8 13.0 - - - -
205B ILE* 3.7 25.6 - - + -
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Residues in contact with PHE 141 (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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102B GLN 3.3 26.7 - - - -
104B TRP* 3.3 39.7 - + + -
107B SER* 3.9 6.5 - - - -
118B LEU* 4.1 8.1 - - + +
140B TYR* 1.3 73.7 - - - +
142B LEU* 1.3 63.4 + - - +
180B CYS* 3.8 17.5 - - + -
181B ALA 3.6 5.8 - - - -
182B ILE* 3.4 22.6 - - + +
196B ILE* 3.8 12.1 - - + -
197B HIS 4.6 0.2 - - - -
198B CYS 3.7 13.0 - - - -
200B VAL 3.2 22.0 - - - -
202B GLN* 3.6 19.0 - - + +
203B LYS 2.8 14.0 + - - +
204B SER* 4.2 7.9 - - - -
205B ILE* 3.4 23.6 + - - +
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Residues in contact with LEU 142 (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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155A TRP* 4.7 6.1 - - + -
104B TRP* 2.8 24.3 + - - -
118B LEU* 4.1 4.0 - - - -
119B VAL* 3.7 27.6 - - + +
121B ILE* 3.7 17.5 - - + -
141B PHE* 1.3 76.3 - - - +
143B GLY* 1.3 59.6 + - - +
144B LEU 3.0 10.2 + - - +
181B ALA* 3.1 27.3 + - + +
182B ILE 4.4 2.9 - - - -
183B ILE* 3.6 30.1 - - + +
193B TRP* 3.6 46.4 - - + +
205B ILE* 4.3 2.9 - - + -
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Residues in contact with GLY 143 (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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154A GLN 3.6 0.5 - - - +
155A TRP* 3.3 11.8 - - - -
156A VAL* 2.9 33.9 + - - +
104B TRP* 4.1 9.1 - - - -
118B LEU* 3.5 26.1 - - - +
119B VAL 2.8 20.6 + - - -
142B LEU* 1.3 69.3 - - - +
144B LEU* 1.3 57.2 + - - +
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Residues in contact with LEU 144 (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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153A TRP* 3.9 11.7 - - + -
154A GLN 3.4 17.7 - - - +
155A TRP* 3.6 36.6 - - + +
161A TYR* 3.7 22.4 - - + -
168A TRP* 3.7 30.3 - - + -
104B TRP* 4.1 0.3 + - - -
142B LEU* 3.0 8.1 + - + +
143B GLY* 1.3 77.6 - - - +
145B SER* 1.3 64.0 + - - +
180B CYS* 3.5 1.0 - - - -
181B ALA* 2.9 42.1 + - + -
193B TRP* 3.9 22.2 - - + -
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Residues in contact with SER 145 (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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153A TRP* 3.5 8.0 - - - -
154A GLN* 2.7 45.6 + - - +
156A VAL* 6.1 0.2 - - - -
104B TRP* 3.6 25.1 - - - -
144B LEU* 1.3 78.2 - - - +
146B ASP* 1.3 62.8 + - - +
147B PRO* 3.9 10.1 - - - +
179B ARG 3.2 13.2 - - - -
180B CYS* 3.7 15.7 - - - -
198B CYS* 4.7 0.7 - - - -
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Residues in contact with ASP 146 (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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151A ARG* 3.4 40.4 + - + +
152A HIS* 3.5 22.6 + - - +
153A TRP* 3.7 6.6 - - + -
154A GLN* 5.3 0.2 + - - -
176A LEU* 5.2 2.4 - - - +
145B SER* 1.3 74.5 - - - +
147B PRO* 1.3 66.9 - - - +
148B GLY* 2.9 24.7 + - - +
152B HIS* 6.0 1.6 - - - -
176B LEU* 5.1 10.0 - - - +
177B ASP 5.2 2.7 - - - -
178B GLU* 3.4 1.4 - - - +
179B ARG* 2.7 35.2 + - + +
198B CYS* 5.0 0.2 - - - -
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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