Contacts of the strand formed by residues 159 - 166 (chain B) in PDB entry 2B3T
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 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ARG* 5.2 7.4 + - - +
25A GLU* 4.7 6.1 + - - -
36A ARG* 5.6 2.1 + - - -
40A LEU* 3.5 28.5 - - + +
115B VAL 4.7 0.2 - - - +
117B ALA* 3.7 7.1 - - - +
125B ALA* 3.2 14.0 + - - +
128B ALA* 3.1 26.2 - - + +
129B GLY* 4.0 25.4 - - - -
132B PHE* 5.8 4.9 - + + -
151B ALA* 4.0 23.1 - - + -
152B SER 3.0 10.1 - - - -
153B GLU* 5.1 7.6 - - + -
158B GLY* 1.3 92.7 - - - -
160B LYS* 1.3 63.7 + - - +
161B GLU* 2.9 21.0 - - - +
162B ILE* 3.9 24.9 - - + -
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Residues in contact with LYS 160 (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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115B VAL 4.1 0.7 - - - -
116B ARG* 3.3 7.1 - - - +
117B ALA* 3.0 37.5 + - + +
125B ALA* 4.5 3.2 - - - +
152B SER* 2.8 28.6 + - - +
153B GLU 5.6 1.8 - - - +
154B GLY* 4.7 1.9 - - - +
159B TYR* 1.3 72.8 - - - +
161B GLU* 1.3 67.3 + - + +
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Residues in contact with GLU 161 (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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114B GLU* 4.2 2.8 - - - +
115B VAL 3.3 7.0 - - - +
116B ARG* 2.5 53.6 + - + +
150B SER* 5.3 6.3 - - - +
151B ALA 5.2 0.9 - - - -
152B SER* 3.2 31.2 + - - +
159B TYR* 2.9 14.7 - - - +
160B LYS* 1.3 92.1 - - + +
162B ILE* 1.3 72.6 + - - +
163B ILE* 6.2 1.6 - - + -
256B GLU* 5.3 9.4 - - - +
277B ARG* 5.1 7.4 + - - -
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Residues in contact with ILE 162 (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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113B LEU 4.0 0.2 - - - +
114B GLU* 3.0 4.2 - - - +
115B VAL* 2.9 55.2 + - + +
128B ALA 5.0 0.7 - - - +
132B PHE* 3.4 49.0 - - + -
148B ILE* 4.0 25.1 - - + -
150B SER 3.2 8.6 + - - -
151B ALA* 4.2 4.5 - - + -
159B TYR* 3.9 36.1 - - + -
161B GLU* 1.3 80.3 + - - +
163B ILE* 1.3 60.5 + - - +
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Residues in contact with ILE 163 (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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112B PHE* 4.7 2.0 - - + -
113B LEU 3.2 5.4 - - - +
114B GLU* 3.0 36.8 - - + +
132B PHE* 4.9 0.4 - - - -
148B ILE* 3.4 2.6 - - - -
149B MET* 2.8 38.7 + - + +
150B SER* 3.1 35.8 + - - +
161B GLU* 5.8 2.2 - - + +
162B ILE* 1.3 79.7 - - - +
164B ALA* 1.3 66.2 + - - +
206B MET* 4.6 2.2 - - + -
256B GLU 5.4 1.1 - - - +
257B CYS* 6.4 0.2 - - - -
273B VAL* 4.0 27.6 - - + -
277B ARG* 4.2 14.4 - - - +
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Residues in contact with ALA 164 (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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112B PHE* 3.5 5.0 - - - -
113B LEU* 2.8 32.7 + - + +
132B PHE* 3.7 29.2 - - + -
146B VAL* 4.1 13.7 - - + -
147B GLU 3.1 15.9 - - - +
148B ILE* 3.9 0.4 - - - +
149B MET* 4.5 1.8 - - - -
163B ILE* 1.3 78.0 - - - +
165B LYS* 1.3 60.9 + - - +
166B ILE* 3.7 12.6 - - + -
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Residues in contact with LYS 165 (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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110B ASN* 6.0 0.4 - - - +
111B ALA 3.7 4.0 - - - +
112B PHE* 3.8 20.2 - - + -
145B ARG* 2.7 21.9 - - - +
147B GLU* 2.5 37.8 + - + +
149B MET* 3.4 22.9 - - - -
164B ALA* 1.3 73.0 - - - +
166B ILE* 1.3 55.0 + - - +
167B SER* 3.8 14.1 + - - +
208B GLU* 2.9 35.8 + - - +
272B SER* 5.8 0.9 - - - -
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Residues in contact with ILE 166 (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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110B ASN* 3.5 1.9 - - - +
111B ALA* 2.9 33.9 + - + +
113B LEU* 3.9 23.1 - - + -
135B TYR* 5.3 6.5 - - + -
136B SER* 6.4 0.2 - - - -
139B ALA* 4.1 13.0 - - + -
144B TRP* 3.3 39.7 - - + -
145B ARG 3.1 5.8 - - - +
146B VAL* 4.2 8.3 - - + +
164B ALA* 4.5 15.7 - - + -
165B LYS* 1.3 71.7 - - - +
167B SER* 1.3 72.4 + - - +
171B VAL* 4.4 9.2 - - + -
175B LEU* 3.6 26.7 - - + -
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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