Contacts of the helix formed by residues 171 - 187 (chain A) in PDB entry 4BLV
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 THR 171 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A MET* 3.7 17.0 - - + +
170A LYS* 1.3 82.2 - - + +
172A ASP* 1.3 67.4 + - - +
173A TYR 3.1 0.4 - - - -
174A GLN* 3.0 18.9 + - - +
175A ALA* 2.8 25.1 + - - +
1292A EDO 5.2 7.3 + - - -
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Residues in contact with ASP 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A HIS* 5.3 0.4 + - - -
145A PHE* 3.8 17.4 - - - -
165A PRO* 3.6 20.0 - - + +
166A PRO* 3.8 5.2 - - - +
167A TYR* 2.9 45.3 + - + -
168A GLU 3.8 1.7 + - - -
169A MET* 3.0 22.2 + - - +
171A THR* 1.3 81.6 + - - +
173A TYR* 1.3 57.7 + - - +
175A ALA* 4.0 6.0 - - - +
176A VAL* 2.9 35.0 + - - +
1281A SAM 5.8 1.8 + - - -
1292A EDO 5.2 1.6 + - - -
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Residues in contact with TYR 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A TYR* 3.3 40.3 + + + +
170A LYS* 3.0 32.8 + - + +
172A ASP* 1.3 78.0 - - - +
174A GLN* 1.3 63.6 + - - +
176A VAL* 3.6 14.7 - - - +
177A VAL* 3.7 10.9 - - - +
197A PRO* 3.6 22.9 + - + +
199A VAL* 5.1 11.1 + - - +
200A LEU 5.7 0.5 + - - -
203A GLN* 3.2 53.6 - - + +
204A ILE* 3.9 19.0 - - + +
207A MET* 3.7 21.6 - - + +
210A ASP* 5.4 1.2 - - - +
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Residues in contact with GLN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LYS* 3.9 6.2 + - - +
171A THR* 3.0 30.3 + - - +
173A TYR* 1.3 88.8 - - - +
175A ALA* 1.3 66.0 + - - +
176A VAL 3.3 0.4 - - - -
177A VAL* 3.0 17.7 + - - +
178A SER* 3.0 15.2 + - - -
203A GLN* 4.2 14.5 + - - +
206A ARG* 5.1 7.9 - - - +
210A ASP* 4.8 13.1 + - - +
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A PHE* 3.8 21.0 - - + -
171A THR 2.8 15.3 + - - +
172A ASP* 3.2 3.8 + - - +
174A GLN* 1.3 78.2 - - - +
176A VAL* 1.3 55.7 + - - +
178A SER* 3.5 8.1 + - - -
179A GLY* 2.9 27.0 + - - -
1292A EDO 3.2 39.2 + - - -
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE* 4.0 13.2 - - + -
163A ILE* 4.2 5.7 - - + +
165A PRO* 3.6 29.6 - - + -
167A TYR* 3.8 4.3 - - + +
172A ASP 2.9 24.4 + - - +
173A TYR* 3.6 12.1 - - - +
175A ALA* 1.3 75.7 - - - +
177A VAL* 1.3 68.5 + - + +
179A GLY* 4.0 0.6 - - - -
180A ILE* 3.1 32.0 + - - +
194A LEU* 3.6 29.4 - - + -
207A MET* 3.7 24.2 - - - -
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Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A TYR 3.7 18.4 - - - +
174A GLN* 3.0 7.4 + - - +
176A VAL* 1.3 76.6 - - + +
178A SER* 1.3 65.3 + - - +
180A ILE* 3.4 6.7 + - - +
181A ALA* 3.1 21.9 + - - +
194A LEU* 6.0 1.1 - - + -
207A MET* 3.7 30.1 - - + +
210A ASP* 3.5 41.5 - - + +
211A LEU* 3.8 16.4 - - + +
214A THR* 3.9 10.1 - - + +
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Residues in contact with SER 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLN 3.0 12.7 + - - -
175A ALA* 3.5 13.2 + - - -
177A VAL* 1.3 77.2 - - - +
179A GLY* 1.3 59.2 + - - +
181A ALA* 3.5 6.4 + - - +
182A GLU* 3.0 35.4 + - - +
1292A EDO 5.5 3.5 - - - -
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Residues in contact with GLY 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A PHE* 5.0 7.0 - - - -
148A LEU* 3.5 28.5 - - - +
175A ALA 2.9 18.9 + - - -
176A VAL 4.0 0.4 - - - -
178A SER* 1.3 78.9 + - - +
180A ILE* 1.3 55.7 + - - +
182A GLU* 3.2 7.6 + - - +
183A GLY 2.9 24.6 + - - -
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 4.2 2.0 - - - +
163A ILE* 3.6 24.0 - - + -
176A VAL 3.1 19.9 + - - +
177A VAL* 3.7 4.5 - - - +
179A GLY* 1.3 74.2 - - - +
181A ALA* 1.3 57.7 + - - +
183A GLY* 3.2 2.7 + - - +
184A TYR* 2.8 31.2 + - + +
192A TYR* 4.9 13.4 - - + -
194A LEU* 4.1 35.0 - - + -
211A LEU* 4.3 15.9 - - + -
214A THR* 6.3 0.2 - - + -
216A ILE* 4.0 11.9 - - + -
241A ILE* 6.0 0.9 - - + -
243A ILE* 3.4 33.9 - - + -
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A VAL 3.1 17.0 + - - +
178A SER* 3.8 7.9 - - - +
180A ILE* 1.3 76.4 - - - +
182A GLU* 1.3 63.3 + - + +
184A TYR* 3.9 1.2 - - - +
185A LYS* 3.1 23.7 + - - +
214A THR* 4.2 22.2 - - + +
216A ILE* 4.3 11.4 - - - +
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Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 4.3 3.4 - - + +
149A LYS* 3.6 34.9 + - + -
178A SER* 3.0 22.0 + - - +
179A GLY* 3.2 9.6 + - - +
181A ALA* 1.3 74.2 - - + +
183A GLY* 1.3 64.9 + - - +
185A LYS* 3.5 16.5 + - - +
186A ARG* 2.6 66.7 + - - +
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Residues in contact with GLY 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 3.6 19.2 + - - -
152A LEU* 3.8 12.7 - - - +
179A GLY 2.9 14.0 + - - -
180A ILE 3.2 2.7 + - - -
182A GLU* 1.3 77.2 - - - +
184A TYR* 1.3 49.7 + - - +
186A ARG* 2.9 8.3 + - - +
187A PHE* 2.8 31.7 + - - +
192A TYR* 3.1 14.8 + - - -
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Residues in contact with TYR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ILE* 2.8 21.4 + - + +
181A ALA 3.9 2.9 - - - +
183A GLY* 1.3 67.8 - - - +
185A LYS* 1.3 68.0 + - - +
187A PHE 3.9 1.3 - - - -
188A ALA* 3.1 67.0 + - + +
192A TYR* 3.5 18.5 + + + -
216A ILE* 3.7 53.9 - - + +
217A ARG* 4.6 8.0 + - - +
243A ILE* 4.0 10.8 - - + -
244A ASN* 3.9 15.1 + - - -
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Residues in contact with LYS 185 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A ALA 3.1 18.4 + - - +
182A GLU* 3.5 16.4 + - - +
184A TYR* 1.3 80.2 - - - +
186A ARG* 1.3 82.4 + - + +
188A ALA* 5.1 1.0 + - - +
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Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU 3.7 9.0 - - - -
149A LYS* 3.3 46.2 + - - +
152A LEU* 3.5 22.9 - - + +
153A PRO* 3.7 20.1 - - + +
182A GLU* 2.6 50.5 + - - +
183A GLY 2.9 7.8 + - - +
185A LYS* 1.3 95.6 - - + +
187A PHE* 1.3 58.9 + - - +
188A ALA 4.1 0.7 - - - -
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Residues in contact with PHE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A LEU* 4.1 8.3 - - + -
153A PRO* 3.9 20.2 - - + -
154A PRO* 3.7 25.1 - - + -
157A ARG* 3.5 35.4 - - + -
158A ARG* 3.7 9.2 - - - -
159A GLY* 3.9 8.5 - - - -
161A ILE* 4.1 15.5 - - + -
183A GLY 2.8 5.2 + - - +
184A TYR 3.4 2.1 - - - +
186A ARG* 1.3 81.2 - - - +
188A ALA* 1.3 57.7 + - - +
189A THR* 3.2 24.5 - - - -
190A GLY* 3.2 37.0 + - - -
192A TYR* 2.7 34.7 + - - +
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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