Contacts of the strand formed by residues 145 - 149 (chain B) in PDB entry 2WU4
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 VAL 145 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B VAL* 4.1 10.1 - - + -
102B TRP 3.3 8.3 - - - +
103B THR* 3.7 21.1 - - + -
104B PRO* 4.4 4.3 - - + -
108B PRO* 4.5 0.7 - - + -
112B THR* 3.9 6.9 - - - +
113B PRO 3.4 11.7 + - - +
114B VAL* 3.3 12.9 - - + +
115B LEU 3.0 24.6 + - - -
143B GLY 3.9 0.4 + - - -
144B ALA* 1.3 75.0 - - - +
146B LEU* 1.3 59.5 + - - +
147B VAL* 4.5 1.6 - - + -
187B ILE* 4.0 33.0 - - + -
190B PHE* 4.2 1.6 - - + +
191B GLY 4.1 7.4 - - - +
192B GLY* 4.0 22.4 - - - +
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 3.1 4.5 - - - +
102B TRP* 2.7 65.4 + - + +
115B LEU* 3.5 18.6 - - + +
117B TRP* 5.0 3.6 - - + -
133B TYR 4.3 0.7 - - - +
135B GLY* 3.5 34.3 - - - +
138B LEU* 3.8 33.9 - - + -
139B ALA 5.4 0.2 - - - +
144B ALA* 3.8 3.5 + - + +
145B VAL* 1.3 73.9 - - - +
147B VAL* 1.3 71.2 + - - +
148B SER* 5.2 0.4 - - - -
200B PHE* 3.8 18.2 - - + -
455B PHE* 3.8 15.3 - - + -
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.5 17.0 - - + -
100B ASN 3.1 9.4 - - - +
101B VAL* 4.2 6.1 - - + -
114B VAL* 4.0 15.3 - - + -
115B LEU 2.9 10.4 + - - +
116B ILE* 3.3 14.6 - - + -
117B TRP* 2.8 27.2 + - - +
145B VAL* 4.5 1.8 - - + -
146B LEU* 1.3 81.6 - - - +
148B SER* 1.3 72.0 + - - +
149B MET* 5.6 2.0 - - + -
179B ALA* 5.9 0.9 - - + -
183B VAL* 4.0 20.4 - - + -
187B ILE* 3.8 28.9 - - + -
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Residues in contact with SER 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 3.0 3.9 - - - +
100B ASN* 2.7 56.0 + - - -
102B TRP* 3.6 17.9 - - - -
116B ILE* 5.2 0.4 - - - -
117B TRP* 3.7 27.4 - - - -
128B ALA* 3.4 19.4 + - - +
133B TYR 5.6 2.0 - - - -
146B LEU* 5.2 1.1 - - - -
147B VAL* 1.3 77.0 - - - +
149B MET* 1.3 61.4 + - - +
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Residues in contact with MET 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 4.0 4.0 - - + -
98B TYR 3.7 4.3 - - - -
99B LEU* 3.9 9.2 - - + +
116B ILE* 3.6 31.6 - - + -
117B TRP 3.7 12.5 + - - +
118B ILE* 4.1 19.1 - - + -
119B TYR* 3.3 17.8 - - - -
128B ALA* 3.9 3.6 - - - +
147B VAL* 5.6 0.9 - - + -
148B SER* 1.3 77.1 - - - +
150B ASN* 1.3 76.8 + - - +
151B TYR* 3.8 3.3 + - - +
176B GLN* 4.2 26.0 - - + +
179B ALA* 3.7 35.9 - - + -
180B LEU* 4.1 9.2 - - + -
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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
------------------------------------------------------------
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