Contacts of the strand formed by residues 176 - 187 (chain E) in PDB entry 2VIG
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 SER 176 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172E ALA* 3.5 3.3 - - - -
173E GLU 2.7 33.3 + - - +
174E GLY 3.1 3.6 + - - -
175E ASP* 1.3 81.1 - - - +
177E TRP* 1.3 66.5 + - - +
178E VAL* 4.2 0.3 - - - +
247E ARG* 2.7 41.2 + - - +
248E ILE 3.1 23.1 - - - -
249E PRO* 4.5 0.7 - - - -
250E LYS* 4.0 7.6 - - - +
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Residues in contact with TRP 177 (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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170E ALA 4.1 11.7 - - - -
171E ARG 3.4 13.2 - - - -
172E ALA* 3.3 38.4 - - + -
176E SER* 1.3 72.7 + - - +
178E VAL* 1.3 60.8 + - - +
179E LEU* 3.9 17.0 - - + -
201E THR* 4.1 16.4 - - + -
213E PHE* 3.6 27.2 - + + -
246E CYS 3.4 1.6 - - - +
247E ARG* 3.3 4.7 - - - -
248E ILE* 2.8 39.0 + - + +
249E PRO 3.6 6.7 - - - -
250E LYS* 3.1 54.5 + - + +
253E ILE* 3.9 25.4 - - + +
257E PRO* 4.9 12.1 - - + -
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Residues in contact with VAL 178 (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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169E THR* 3.4 3.1 + - - +
170E ALA* 3.4 2.4 - - - -
171E ARG* 2.8 38.6 + - + +
173E GLU* 3.7 30.3 - - + -
176E SER* 4.2 7.9 - - - +
177E TRP* 1.3 76.1 - - - +
179E LEU* 1.3 62.6 + - - +
180E ASN* 3.8 19.9 + - - +
245E ASP* 3.9 23.3 - - + -
246E CYS 3.3 3.4 - - - +
247E ARG* 4.2 15.9 - - + +
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Residues in contact with LEU 179 (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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168E THR* 5.3 2.0 - - + -
169E THR 3.2 4.3 - - - +
170E ALA* 3.8 23.8 - - + -
177E TRP* 3.9 20.2 - - + +
178E VAL* 1.3 77.5 - - - +
180E ASN* 1.3 66.1 + - - +
197E VAL* 4.5 13.7 - - + -
199E ALA* 4.8 5.2 - - + -
213E PHE* 4.7 8.5 - - + -
215E VAL* 4.0 27.6 - - + -
243E PHE* 3.6 34.8 - - + +
245E ASP 3.6 1.9 + - - -
246E CYS 2.8 37.1 + - - +
248E ILE* 4.3 13.9 - - + -
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Residues in contact with ASN 180 (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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167E SER 4.4 1.4 - - - +
168E THR* 3.4 6.1 - - - +
169E THR* 2.9 47.2 + - - +
178E VAL* 3.8 22.4 + - - +
179E LEU* 1.3 82.3 + - - +
181E GLY* 1.3 57.6 + - - +
243E PHE* 3.6 4.0 - - - +
244E GLU* 3.8 8.1 - - - +
245E ASP* 3.1 20.8 + - - +
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Residues in contact with GLY 181 (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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168E THR* 3.6 8.1 - - - -
180E ASN* 1.3 74.1 - - - +
182E THR* 1.3 63.0 + - - -
183E LYS 4.2 0.2 - - - -
242E ILE* 4.7 0.7 - - - -
243E PHE* 2.9 42.0 + - - +
504E EDO 3.2 19.1 - - - -
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Residues in contact with THR 182 (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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156E GLU* 3.4 10.2 - - - +
157E PRO* 3.5 14.7 - - + +
168E THR* 3.5 3.5 + - - -
181E GLY* 1.3 73.3 - - - -
183E LYS* 1.3 75.5 + - - +
240E ASN* 3.7 24.9 - - + +
241E LEU 3.4 7.9 - - - +
242E ILE* 4.1 20.3 - - + +
504E EDO 2.7 44.3 + - - -
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Residues in contact with LYS 183 (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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153E ALA* 3.3 39.0 - - + -
154E LEU* 2.8 28.4 + - - +
155E SER 3.3 8.5 - - - +
156E GLU* 2.7 20.9 + - - +
166E ALA* 4.0 5.3 - - - +
168E THR* 3.4 24.9 - - + +
182E THR* 1.3 74.5 - - - +
184E ALA* 1.3 60.5 + - - +
186E ILE* 4.2 3.8 - - + -
197E VAL* 4.3 2.2 - - + -
198E PHE* 2.7 24.1 + - - +
240E ASN* 3.1 11.1 - - - +
241E LEU* 2.9 33.7 + - + +
243E PHE* 4.0 22.7 - - + -
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Residues in contact with ALA 184 (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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155E SER* 2.8 20.0 + - - -
156E GLU* 3.6 5.4 - - - +
157E PRO* 3.5 30.5 - - + -
183E LYS* 1.3 73.0 - - - +
185E TRP* 1.3 81.7 + - + +
186E ILE* 3.0 19.6 - - - +
240E ASN* 3.2 15.9 - - - +
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Residues in contact with TRP 185 (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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155E SER* 4.0 8.1 - - - -
156E GLU 4.6 6.2 + - - -
157E PRO* 5.2 4.9 + - + +
184E ALA* 1.3 96.3 - - + +
186E ILE* 1.3 61.4 + - - +
187E THR 3.2 0.2 + - - -
228E GLU* 4.0 21.9 + - + -
238E THR* 3.4 22.8 - - + +
239E ALA 4.0 3.4 + - - +
240E ASN* 3.8 6.3 + - - -
501E FAD 2.8 91.3 + + + +
297F ARG* 6.0 0.2 - - - +
369F GLY* 3.5 39.7 - - - -
370F MET* 3.7 28.0 - - + -
373F VAL* 3.9 22.4 - - + -
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Residues in contact with ILE 186 (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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151E CYS* 3.8 28.9 - - - -
152E PHE 3.8 13.2 - - - +
153E ALA* 3.5 33.2 - - + -
154E LEU 4.4 0.4 - - - +
155E SER 4.5 0.2 - - - +
183E LYS* 4.2 12.3 - - + -
184E ALA 3.0 25.8 - - - +
185E TRP* 1.3 73.8 - - - +
187E THR* 1.3 67.6 + - - +
188E ASN 3.5 0.5 + - - -
189E ALA* 3.2 19.1 + - + +
238E THR* 3.5 4.1 - - - +
239E ALA 3.1 26.7 + - - +
241E LEU* 4.1 19.5 - - + -
501E FAD 3.8 9.4 - - - +
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Residues in contact with THR 187 (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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114E VAL* 4.3 12.7 - - + +
118E VAL* 3.8 24.6 - - + +
151E CYS* 3.3 20.3 - - - +
185E TRP 3.2 1.4 + - - -
186E ILE* 1.3 70.8 - - - +
188E ASN* 1.3 81.0 + - - +
189E ALA 3.2 0.2 - - - -
233E ILE* 5.6 1.4 - - + +
236E SER* 4.3 17.0 + - - +
237E SER 3.2 10.1 - - - +
238E THR* 4.5 2.5 + - - +
391E TYR* 4.9 4.5 - - - -
501E FAD 3.0 44.5 + - - +
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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