Contacts of the strand formed by residues 180 - 189 (chain F) 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 180 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115F THR* 4.2 21.0 - - - +
149F GLY 2.8 23.9 + - - -
150F TYR* 2.7 55.3 + - + +
151F PHE* 4.2 21.9 - + - -
152F PRO* 4.1 14.6 - - + -
153F GLU* 3.4 40.1 + - + +
173F ALA* 4.4 6.3 - - + -
174F VAL* 3.3 18.4 - - - -
175F LEU* 3.3 29.3 - - + +
179F LEU* 1.3 71.6 - - - +
181F THR* 1.3 63.3 + - - +
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Residues in contact with THR 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E LEU* 5.5 4.7 - - + -
183E THR* 6.0 4.9 - - + +
146F LEU* 3.9 17.9 - - + -
147F VAL 3.4 4.7 - - - +
148F LYS* 3.4 25.7 - - + +
149F GLY 3.9 0.7 + - - -
150F TYR* 4.1 1.3 - - - -
172F PRO 4.5 0.5 - - - +
173F ALA* 3.3 1.8 - - - -
174F VAL* 2.8 41.9 + - - +
176F GLN* 2.7 37.2 + - - +
180F TYR* 1.3 78.3 + - - +
182F LEU* 1.3 65.8 + - - +
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Residues in contact with LEU 182 (chain F).
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* 6.5 0.2 - - - -
146F LEU* 3.8 4.1 - - - +
147F VAL* 2.8 39.2 + - + +
150F TYR* 3.1 24.4 - - + +
155F VAL* 3.9 27.6 - - + +
157F VAL* 4.6 7.0 - - + -
170F THR* 3.6 25.4 - - + -
171F PHE* 3.6 22.2 - - - +
172F PRO 5.1 1.6 - - - -
173F ALA* 3.8 10.1 - - + +
181F THR* 1.3 77.2 - - - +
183F SER* 1.3 86.8 + - - +
184F SER 4.5 0.4 - - - +
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Residues in contact with SER 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E VAL* 4.0 5.1 - - - +
140E PHE* 3.5 12.6 - - - -
181E SER* 3.3 22.7 + - - -
183E THR* 4.8 2.6 + - - -
129F LEU* 4.5 3.1 - - - -
145F CYS 3.1 15.3 - - - -
146F LEU* 3.8 20.9 - - - +
147F VAL* 4.5 0.7 - - - +
171F PHE* 3.3 34.6 + - - +
182F LEU* 1.3 80.0 - - - +
184F SER* 1.3 61.6 + - - +
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Residues in contact with SER 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E PHE* 3.8 4.0 - - - -
144F GLY* 3.1 4.7 - - - -
145F CYS* 2.8 39.7 + - - -
147F VAL* 6.6 0.2 - - - -
157F VAL* 3.7 19.4 - - - +
159F TRP* 3.3 21.5 + - - -
168F VAL* 3.9 0.9 - - - +
169F HIS 3.0 9.7 + - - -
170F THR* 2.8 35.8 + - - -
183F SER* 1.3 75.8 - - - +
185F SER* 1.3 57.7 + - - +
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Residues in contact with SER 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E PHE* 3.6 39.2 - - - -
142E ASN* 3.4 19.1 + - - -
142F THR* 4.0 8.6 - - - +
143F LEU 3.3 5.2 - - - -
159F TRP* 4.5 0.9 - - - -
168F VAL* 3.4 8.0 - - - +
169F HIS* 2.8 42.9 + - - +
184F SER* 1.3 73.2 - - - +
186F VAL* 1.3 62.2 + - - +
187F THR* 4.9 1.2 + - - -
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Residues in contact with VAL 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F VAL 3.6 1.0 - - - +
142F THR* 3.5 3.8 - - - -
143F LEU* 2.7 55.1 + - + +
159F TRP* 3.7 39.7 - - + +
164F LEU* 3.8 27.1 - - + -
166F SER 5.0 0.2 - - - +
167F GLY 3.5 4.3 - - - +
168F VAL* 3.7 19.5 - - + -
185F SER* 1.3 75.5 - - - +
187F THR* 1.3 69.0 + - - +
188F VAL* 3.7 5.5 + - + +
198F VAL* 4.5 6.1 - - + -
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Residues in contact with THR 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E THR* 6.4 1.8 - - + -
142E ASN* 4.5 13.7 + - - -
143E ASN* 5.7 2.6 + - - -
140F MET* 3.6 42.6 - - + +
141F VAL 3.4 4.0 - - - +
142F THR* 4.0 16.4 + - - +
164F LEU* 5.2 1.6 - - - +
166F SER 4.4 6.1 - - - +
167F GLY* 2.9 26.9 + - - +
169F HIS* 5.4 3.3 + - - -
185F SER* 4.3 1.1 + - - -
186F VAL* 1.3 73.5 - - - +
188F VAL* 1.3 65.5 + - - +
189F PRO* 4.6 2.5 - - - +
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Residues in contact with VAL 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F MET* 4.1 2.9 - - - -
141F VAL* 2.7 48.2 + - + +
143F LEU* 5.2 4.5 - - + -
164F LEU* 3.7 32.5 - - + -
186F VAL* 3.9 13.0 - - + +
187F THR* 1.3 80.8 - - - +
189F PRO* 1.4 68.9 - - + +
192F THR* 3.2 35.0 - - - +
193F TRP* 4.7 9.2 - - + -
198F VAL* 4.9 13.0 - - + -
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Residues in contact with PRO 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C THR* 5.8 3.4 - - + +
139F SER* 3.3 15.3 - - - +
140F MET* 3.7 24.5 - - + -
141F VAL* 5.1 0.3 - - - +
164F LEU* 6.4 1.6 - - + -
187F THR 4.6 1.8 - - - +
188F VAL* 1.4 91.5 - - + +
190F SER* 1.3 64.3 + - - +
191F SER* 3.1 6.0 + - - +
192F THR* 2.8 31.3 + - + +
193F TRP 4.3 0.5 + - - -
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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