Contacts of the strand formed by residues 140 - 150 (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 MET 140 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C THR* 5.4 7.4 - - - -
136F GLN* 3.2 20.3 - - - +
137F THR 4.4 1.4 + - - -
138F ASN* 2.9 18.7 + - + +
139F SER* 1.3 88.7 - - - +
141F VAL* 1.3 60.9 + - - +
142F THR* 5.1 1.2 + - - -
167F GLY* 6.4 0.9 - - - -
187F THR* 3.6 36.4 - - + +
188F VAL 3.5 5.6 - - - +
189F PRO* 3.7 32.5 - - + -
190F SER* 4.4 0.2 - - - -
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Residues in contact with VAL 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F PRO* 4.6 18.6 - - + -
134F ALA* 5.9 1.3 - - - -
135F ALA 5.6 4.3 - - - +
136F GLN* 4.2 23.1 - - + +
139F SER 4.2 1.0 + - - -
140F MET* 1.3 73.0 - - - +
142F THR* 1.3 70.2 + - - +
143F LEU* 4.1 6.9 + - + -
186F VAL 3.6 1.2 - - - +
187F THR* 3.4 1.9 - - - -
188F VAL* 2.7 53.7 + - + +
190F SER* 4.4 12.6 + - - +
193F TRP* 4.3 35.4 - - + +
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Residues in contact with THR 142 (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* 5.4 6.4 - - - +
121E SER* 3.9 21.1 + - - +
123E PHE* 3.3 31.7 - - + -
140E PHE* 4.4 4.3 - - + -
142E ASN* 4.5 10.6 + - - +
131F PRO* 4.7 3.8 - - - +
140F MET 4.3 1.4 + - - -
141F VAL* 1.3 82.6 - - - +
143F LEU* 1.3 77.3 + - - +
185F SER* 4.0 20.4 - - - +
186F VAL 3.5 7.2 - - - +
187F THR* 4.0 14.3 + - - +
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Residues in contact with LEU 143 (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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123E PHE* 4.2 2.2 - - - -
140E PHE* 5.0 0.2 - - - -
129F LEU 3.9 8.5 - - - +
130F ALA* 4.5 2.0 - - - -
131F PRO* 4.1 9.0 - - + -
141F VAL* 4.7 7.4 - - + -
142F THR* 1.3 83.5 - - - +
144F GLY* 1.3 58.2 + - - +
185F SER* 3.3 2.9 - - - -
186F VAL* 2.7 50.6 + - + +
188F VAL* 5.2 4.5 - - + -
193F TRP* 3.5 55.4 - - + -
198F VAL* 3.9 27.4 - - + -
215F ILE* 3.5 28.3 - - + -
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Residues in contact with GLY 144 (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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123E PHE* 4.4 0.4 - - - -
140E PHE* 4.2 4.0 - - - -
129F LEU* 2.9 49.0 + - - +
143F LEU* 1.3 75.7 - - - +
145F CYS* 1.3 64.2 - - - +
159F TRP* 3.6 6.0 - - - -
184F SER 3.1 11.4 - - - -
215F ILE* 3.8 9.2 - - - +
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Residues in contact with CYS 145 (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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126F VAL* 4.1 12.1 - - + -
127F TYR 3.6 7.6 - - - -
129F LEU* 3.9 2.9 - - - +
144F GLY* 1.3 78.1 - - - -
146F LEU* 1.3 61.3 + - - +
147F VAL* 4.1 7.0 + - + +
157F VAL* 5.4 1.6 - - + -
159F TRP* 3.7 7.4 - - + -
183F SER* 3.1 6.4 - - - -
184F SER* 2.8 36.0 + - - +
200F CYS* 2.0 52.3 - - + -
202F VAL* 5.3 0.7 - - + -
213F LYS* 4.6 10.8 - - - -
215F ILE* 4.7 4.3 - - - -
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Residues in contact with LEU 146 (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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129E GLN* 4.1 11.7 - - - +
136E SER* 3.8 28.3 - - - -
138E VAL* 4.5 12.6 - - + -
183E THR* 4.9 9.4 - - + +
125F SER 3.2 3.8 - - - +
126F VAL* 3.4 2.3 - - - -
127F TYR* 2.8 51.1 + - + +
129F LEU* 4.0 15.0 - - + +
145F CYS* 1.3 73.2 - - - +
147F VAL* 1.3 63.5 + - - +
148F LYS* 4.0 21.7 + - + -
181F THR* 3.9 19.5 - - + -
182F LEU 3.8 4.7 - - - +
183F SER* 3.8 19.3 - - - +
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Residues in contact with VAL 147 (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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124F PRO* 3.5 27.6 - - + -
125F SER 3.2 3.4 - - - +
126F VAL* 4.3 7.2 - - + -
145F CYS* 4.8 6.1 - - + +
146F LEU* 1.3 78.0 - - - +
148F LYS* 1.3 59.2 + - - +
150F TYR* 3.6 14.0 - - + -
155F VAL* 4.3 9.4 - - + -
157F VAL* 4.5 11.2 - - + -
181F THR* 3.4 2.3 - - - +
182F LEU* 2.8 47.6 + - + +
183F SER* 5.6 0.2 - - - -
202F VAL* 3.6 37.9 - - + -
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Residues in contact with LYS 148 (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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129E GLN* 4.0 7.2 + - + +
136E SER* 4.1 15.5 - - - -
183E THR* 6.3 0.7 - - - -
185E THR* 4.5 8.9 - - - +
123F PRO 4.7 0.2 - - - +
125F SER* 2.9 37.2 + - - +
127F TYR* 3.9 30.7 - - + +
146F LEU* 4.0 15.9 - - + -
147F VAL* 1.3 76.1 - - - +
149F GLY* 1.3 62.9 + - - +
150F TYR* 3.5 3.1 - - - -
176F GLN* 3.3 34.9 + - - +
180F TYR 3.6 3.6 - - - -
181F THR* 3.4 17.3 - - + +
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Residues in contact with GLY 149 (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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122F THR* 3.5 13.3 - - - +
123F PRO 4.0 3.3 - - - +
148F LYS* 1.3 78.3 - - - +
150F TYR* 1.3 57.1 + - - +
176F GLN* 5.8 2.9 - - - -
179F LEU* 3.3 43.2 - - - +
180F TYR 2.8 9.1 + - - -
181F THR* 3.9 2.8 + - - -
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Residues in contact with TYR 150 (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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122F THR 3.5 13.5 - - - +
123F PRO 4.0 1.1 - - - -
124F PRO* 3.5 36.6 - - + -
147F VAL* 3.6 25.8 - - + -
149F GLY* 1.3 79.5 - - - +
151F PHE* 1.3 63.1 + - - +
152F PRO 3.5 14.4 - - - -
153F GLU 3.6 22.2 + - - -
155F VAL* 3.6 15.9 - - + +
173F ALA* 3.1 28.1 - - - +
179F LEU* 3.6 1.4 - - - -
180F TYR* 2.7 75.5 + + + +
181F THR* 3.9 1.6 - - - -
182F LEU* 3.1 17.5 - - + +
204F HIS* 4.1 2.5 - - + -
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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