Contacts of the strand formed by residues 178 - 187 (chain E) in PDB entry 3VI4
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 178 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110E GLU* 2.7 35.9 + - - +
142E ASN 2.6 21.1 - - - +
144E PHE* 3.0 48.9 + - + +
145E TYR* 3.9 16.1 - + - -
147E LYS* 3.3 46.3 - - + +
169E THR* 4.1 14.1 - - - -
170E ASP* 4.8 1.6 - - - -
171E GLN* 3.4 43.9 + - + +
176E SER 3.8 13.9 - - - -
177E THR* 1.3 75.6 - - - +
179E SER* 1.3 57.7 + - - +
169F HIS* 5.5 0.4 - - - -
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Residues in contact with SER 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E LEU 3.4 5.6 - - - -
142E ASN* 2.1 30.7 + - - -
144E PHE* 3.8 3.3 - - - -
168E TRP* 3.5 7.1 - - - +
169E THR* 3.1 40.1 + - - +
178E TYR* 1.3 72.9 + - - +
180E MET* 1.3 62.6 + - - +
169F HIS* 2.8 33.3 + - - -
171F PHE* 3.7 15.0 - - - -
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Residues in contact with MET 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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139E CYS 4.7 0.2 - - - -
140E PHE* 3.7 0.9 - - - -
141E LEU* 2.8 41.9 + - + +
144E PHE* 4.1 12.3 - - + -
149E ILE* 3.3 27.1 - - + +
150E ASN* 5.6 0.2 - - - -
151E VAL* 3.7 29.4 - - + +
166E ASN* 3.8 22.9 - - - +
167E SER 3.4 7.0 - - - +
168E TRP* 3.2 45.1 - - + +
179E SER* 1.3 75.1 - - - +
181E SER* 1.3 68.1 + - - +
182E SER* 5.2 0.7 - - - -
171F PHE* 3.2 12.1 - - - -
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Residues in contact with SER 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E VAL* 4.4 4.5 - - - +
139E CYS 3.8 2.7 - - - -
140E PHE* 3.5 14.7 - - - -
165E LEU 3.9 1.1 - - - +
166E ASN* 3.2 6.6 - - - +
167E SER* 2.8 39.5 + - - +
180E MET* 1.3 75.8 - - - +
182E SER* 1.3 62.0 + - - +
183E THR* 4.8 2.8 + - - -
171F PHE* 3.5 26.9 - - - -
183F SER* 3.3 22.3 + - - -
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Residues in contact with SER 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E CYS* 2.8 48.8 + - - -
141E LEU* 5.9 0.9 - - - -
151E VAL* 4.3 21.1 - - - +
153E TRP* 2.8 35.9 + - - -
164E VAL* 5.1 0.7 - - - +
165E LEU 3.7 0.2 - - - -
166E ASN* 2.7 23.3 + - - -
180E MET* 4.3 2.0 - - - -
181E SER* 1.3 74.1 + - - +
183E THR* 1.3 63.4 + - - +
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Residues in contact with THR 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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136E SER* 4.0 14.6 - - - +
137E VAL 3.5 8.7 - - - +
138E VAL* 3.9 19.9 - - + +
153E TRP* 4.5 1.3 - - - -
163E GLY 3.1 6.2 - - - +
164E VAL* 3.2 2.3 - - - -
165E LEU* 2.8 46.7 + - + +
181E SER* 4.8 3.6 + - - -
182E SER* 1.3 77.0 + - - +
184E LEU* 1.3 65.4 + - - +
185E THR* 3.4 19.4 + - - +
146F LEU* 4.9 9.1 - - + +
148F LYS* 6.3 0.9 - - - -
176F GLN* 6.1 0.4 - - - +
181F THR* 6.0 5.6 - - + +
183F SER* 4.8 3.3 + - - -
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Residues in contact with LEU 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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135E ALA 3.7 1.6 - - - +
136E SER* 3.4 3.5 - - - -
137E VAL* 2.9 41.4 + - + +
153E TRP* 3.9 42.7 - - + -
155E ILE* 3.8 31.4 - - + -
160E ARG* 5.6 5.6 - - + -
162E ASN* 4.9 3.6 - - + +
163E GLY 3.4 17.5 - - - +
164E VAL* 3.8 20.0 - - + +
183E THR* 1.3 70.9 - - - +
185E THR* 1.3 63.4 + - - +
186E LEU* 4.1 21.5 - - + +
197E TYR* 4.2 11.0 - - + -
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Residues in contact with THR 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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129E GLN* 5.2 1.1 - - - +
134E GLY* 6.3 0.4 - - - -
135E ALA 3.5 6.5 - - - +
136E SER* 3.2 22.3 + - - +
163E GLY* 2.7 31.0 + - - -
165E LEU* 5.6 1.6 - - - +
183E THR* 3.4 13.5 + - - +
184E LEU* 1.3 73.2 - - - +
186E LEU* 1.3 68.9 + - - +
148F LYS* 4.5 11.8 - - - +
176F GLN* 4.0 25.6 + - - +
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Residues in contact with LEU 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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134E GLY* 3.9 2.1 - - - -
135E ALA* 2.9 31.8 + - - +
137E VAL* 6.1 1.3 - - + -
155E ILE* 4.2 13.7 - - + -
162E ASN* 5.8 4.0 - - + -
163E GLY 4.9 6.1 - - - +
184E LEU* 4.1 24.2 - - + +
185E THR* 1.3 85.9 - - - +
187E THR* 1.3 69.1 + - - +
190E GLU* 4.5 15.9 - - + +
191E TYR* 4.5 18.6 - - + +
194E HIS* 5.2 2.5 - - + -
197E TYR* 4.1 25.8 - - + +
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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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133E GLY 4.2 7.4 - - - +
134E GLY* 4.7 0.4 - - - -
135E ALA 4.4 0.7 - - - -
186E LEU* 1.3 77.6 - - - +
188E LYS* 1.3 65.6 + - - +
189E ASP* 4.1 7.2 + - - +
190E GLU* 3.1 26.4 + - - +
191E TYR* 2.9 20.6 + - - +
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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