Contacts of the strand formed by residues 149 - 156 (chain E) in PDB entry 2V8W
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 149 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E TRP* 4.6 7.0 - - + -
95E LYS* 2.9 31.9 + - - +
98E ILE* 5.1 0.7 - - - +
137E LEU* 3.6 28.3 - - + -
142E PHE* 3.6 33.0 - - + -
146E SER* 3.1 15.1 + - - +
147E ASP 3.9 2.3 - - - +
148E ASP* 1.3 77.0 - - - +
150E CYS* 1.3 63.4 + - - +
151E GLY* 3.5 15.5 - - - +
165E ILE* 4.3 8.5 - - + -
166E TRP 3.7 7.4 - - - +
167E THR* 4.4 0.7 - - - +
179E ILE* 4.0 15.9 - - + -
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Residues in contact with CYS 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E TRP* 4.0 0.4 - - - -
94E PHE* 3.3 16.6 - - + -
95E LYS* 2.8 32.5 + - - +
98E ILE* 4.0 21.5 - - + +
106E LYS* 3.4 19.7 - - - -
107E ASN* 3.3 28.5 - - - +
149E VAL* 1.3 75.7 - - - +
151E GLY* 1.3 58.5 + - - +
166E TRP 2.9 11.2 + - - +
167E THR 3.9 1.8 - - - -
168E THR* 3.7 25.8 - - - -
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Residues in contact with GLY 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E TRP* 4.3 0.9 - - - -
93E LEU 2.9 15.7 - - - -
94E PHE* 3.9 8.0 - - - -
137E LEU* 3.7 13.0 - - - -
149E VAL* 3.5 3.6 - - - +
150E CYS* 1.3 80.4 - - - +
152E ALA* 1.3 56.1 + - - +
165E ILE* 3.7 5.5 - - - +
166E TRP* 2.8 34.9 + - - +
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Residues in contact with ALA 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E SER* 3.2 3.6 - - - -
93E LEU 2.8 31.0 + - - -
94E PHE* 3.8 1.1 - - - -
130E TRP* 3.5 12.8 - - + -
133E THR* 3.5 29.4 - - + -
134E LEU* 5.3 0.4 - - + -
137E LEU* 3.6 17.0 - - + +
151E GLY* 1.3 74.7 - - - +
153E VAL* 1.3 66.4 + - - +
164E ALA 3.1 14.4 - - - +
165E ILE* 4.4 1.1 - - + -
166E TRP 4.5 0.4 - - - +
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Residues in contact with VAL 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E ASP* 4.5 4.3 - - + -
91E TYR 3.3 9.9 - - - +
92E SER* 3.8 11.4 - - - +
94E PHE* 3.6 21.8 - - + -
100E PRO* 5.3 2.2 - - + +
112E ARG* 6.0 2.2 - - - +
130E TRP* 3.7 4.5 - - - -
152E ALA* 1.3 78.3 - - - +
154E VAL* 1.3 63.5 + - - +
155E ASN* 3.5 30.0 - - - +
162E LYS 3.8 0.7 - - - +
163E ILE* 3.4 2.9 - - - -
164E ALA* 2.9 34.8 + - + +
166E TRP* 3.5 35.2 - - + +
1218E MGO 6.3 2.0 - - - -
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Residues in contact with VAL 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E SER* 3.7 19.3 - - - +
90E ASP* 3.1 7.4 - - - +
91E TYR* 2.8 45.0 + - + +
126E LEU* 4.0 20.6 - - + -
130E TRP* 3.5 38.8 - - + -
153E VAL* 1.3 73.7 - - - +
155E ASN* 1.3 69.5 + - - +
156E VAL* 4.1 3.9 + - + +
162E LYS 3.1 11.0 - - - +
163E ILE* 3.8 13.5 - - + -
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Residues in contact with ASN 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E ASP* 2.7 34.1 + - - +
112E ARG* 4.2 13.5 + - - -
153E VAL* 3.5 20.1 - - - +
154E VAL* 1.3 73.5 - - - +
156E VAL* 1.3 62.0 + - - +
157E ARG* 3.5 26.4 + - + +
161E ASP* 3.4 5.2 - - - +
162E LYS* 2.7 58.0 + - + +
164E ALA* 6.1 0.9 - - - +
1218E MGO 4.3 14.0 + - - -
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Residues in contact with VAL 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E SER* 3.4 27.6 - - - +
83E SER 6.2 0.2 - - - -
85E LEU* 3.3 41.7 - - + +
86E MET 3.8 11.4 - - - +
87E PRO* 4.1 3.1 - - + -
88E GLY 2.7 29.9 + - - -
89E CYS 2.9 14.7 + - - +
119E LYS* 4.4 8.5 - - - +
126E LEU* 4.5 6.7 - - + -
154E VAL* 4.7 6.7 - - + +
155E ASN* 1.3 71.3 - - - +
157E ARG* 1.3 66.0 + - - +
161E ASP* 3.4 16.8 - - - +
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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