Contacts of the helix formed by residues 178 - 190 (chain A) in PDB entry 4BPW
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 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A LYS 3.5 3.9 + - - -
177A LEU* 1.3 78.2 - - - +
179A SER* 1.3 63.8 + - - +
180A ALA* 3.2 9.5 + - - +
181A VAL* 3.3 27.0 + - - +
182A ARG* 3.1 20.3 + - - +
313A ILE* 4.3 6.1 - - - -
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Residues in contact with SER 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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178A SER* 1.3 74.1 - - - +
180A ALA* 1.3 55.8 + - - +
182A ARG* 3.4 5.5 + - - +
183A SER* 2.9 29.1 + - - -
311A LYS* 2.6 44.1 + - - +
312A GLY* 4.1 3.3 - - - -
313A ILE* 3.9 18.3 - - - +
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Residues in contact with ALA 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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178A SER* 3.1 9.6 - - - +
179A SER* 1.3 77.6 - - - +
181A VAL* 1.3 61.1 + - + +
183A SER* 3.4 7.1 + - - -
184A GLY* 3.0 20.6 + - - -
311A LYS* 5.4 2.7 - - - +
192B LEU* 3.5 26.1 - - + +
196B ARG* 5.8 0.2 - - - -
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Residues in contact with VAL 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 LEU* 3.7 28.5 - - + -
178A SER* 3.3 22.4 + - - +
180A ALA* 1.3 74.6 - - - +
182A ARG* 1.3 66.2 + - - +
184A GLY* 3.0 1.7 + - - -
185A ILE* 2.9 26.2 + - + +
188B PHE* 3.8 24.7 - - + -
189B ALA* 4.3 23.3 - - + +
192B LEU* 3.7 19.3 - - + -
195B PHE* 4.4 5.2 - - + -
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Residues in contact with ARG 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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102A GLN 5.4 0.2 + - - -
103A GLU* 4.9 0.2 - - - +
104A LYS* 2.9 26.8 + - - +
105A GLU 3.4 16.8 + - - -
106A LEU* 3.8 23.7 - - + +
174A VAL 3.7 1.4 + - - -
175A ARG 3.0 27.7 + - - -
176A LYS 4.1 0.4 - - - -
177A LEU* 2.6 42.5 + - + +
178A SER 3.1 12.3 + - - +
179A SER 3.6 7.0 - - - +
181A VAL* 1.3 77.2 - - - +
183A SER* 1.3 61.4 + - - +
185A ILE* 3.3 18.7 + - - +
186A VAL* 3.3 16.6 + - - +
310A SER 3.2 22.0 - - - +
311A LYS 3.7 13.9 - - - +
312A GLY 4.9 1.3 + - - -
313A ILE* 3.5 27.1 - - - +
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Residues in contact with SER 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A SER 2.9 16.9 + - - -
180A ALA* 3.7 7.2 - - - -
181A VAL 3.2 0.2 - - - -
182A ARG* 1.3 76.7 - - - +
184A GLY* 1.3 61.4 + - - +
186A VAL* 3.3 9.6 + - - +
187A GLU* 3.2 33.9 + - - +
307A ILE* 3.7 18.0 - - - +
311A LYS* 3.9 34.3 + - - +
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Residues in contact with GLY 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 ALA 3.0 15.1 + - - -
181A VAL 3.0 4.4 + - - -
183A SER* 1.3 75.4 - - - +
185A ILE* 1.3 64.1 + - - +
187A GLU* 3.3 4.3 + - - -
188A TYR 3.1 17.7 + - - -
192B LEU* 4.1 7.2 - - - -
195B PHE* 3.5 14.1 - - - -
196B ARG* 3.6 26.8 - - - -
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Residues in contact with ILE 185 (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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106A LEU* 3.7 25.1 - - + -
108A PHE* 4.2 14.6 - - + -
146A LEU* 4.6 3.8 - - + -
150A PHE* 4.0 26.2 - - + -
152A PHE* 3.9 19.3 - - + -
177A LEU* 4.0 15.5 - - + -
181A VAL 2.9 20.3 + - - +
182A ARG* 3.6 8.7 - - - +
184A GLY* 1.3 75.5 - - - +
186A VAL* 1.3 62.6 + - - +
188A TYR* 3.4 3.7 + - - +
189A LEU* 3.2 38.5 + - + +
188B PHE* 4.2 6.7 - - + -
195B PHE* 3.9 11.2 - - + -
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Residues in contact with VAL 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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108A PHE* 4.3 10.3 - - + -
182A ARG 3.3 10.0 + - - +
183A SER* 3.3 9.6 + - - +
184A GLY 3.2 0.4 - - - -
185A ILE* 1.3 79.2 - - - +
187A GLU* 1.3 60.5 + - - +
189A LEU* 3.2 8.1 + - - +
190A SER* 2.9 40.0 + - - +
305A LEU* 5.0 11.2 - - + +
307A ILE* 3.7 43.5 - - + +
310A SER* 3.4 35.0 - - - +
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Residues in contact with GLU 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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183A SER* 3.2 28.4 + - - +
184A GLY* 3.7 3.5 - - - +
185A ILE 3.3 0.2 - - - -
186A VAL* 1.3 75.7 - - - +
188A TYR* 1.3 62.8 + - - +
190A SER* 3.5 13.8 + - - +
193A LYS* 6.2 0.2 - - - -
307A ILE* 4.8 11.2 - - + -
196B ARG* 2.7 66.1 + - - +
197B GLY* 5.7 0.3 - - - -
198B ARG* 3.2 13.7 + - - -
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Residues in contact with TYR 188 (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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149A ASP* 2.7 34.4 + - + +
150A PHE* 3.4 31.4 - + - -
184A GLY 3.1 10.8 + - - +
185A ILE 3.6 8.3 - - - +
187A GLU* 1.3 78.4 - - - +
189A LEU* 1.3 64.3 + - + +
209A HIS* 3.7 26.6 - + - -
211A PHE* 3.5 35.6 - + + +
195B PHE* 3.1 38.6 - + + +
196B ARG 4.1 1.1 + - - -
198B ARG* 2.4 38.3 + - + +
200B VAL 5.0 0.9 - - - -
202B LEU* 3.8 22.1 + - + +
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Residues in contact with LEU 189 (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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108A PHE* 3.8 35.2 - - + -
142A ILE* 4.4 21.6 - - + +
145A ALA* 3.6 31.6 - - + -
146A LEU* 4.5 4.7 - - + -
150A PHE* 4.3 4.9 - - + -
185A ILE* 3.2 22.9 + - + +
186A VAL 3.2 4.4 + - - +
188A TYR* 1.3 91.5 - - + +
190A SER* 1.3 58.2 + - - +
211A PHE* 3.7 13.9 - - + -
302A PHE* 3.1 27.2 - - - -
303A PRO* 5.1 1.4 - - - +
305A LEU* 4.0 20.0 - - + +
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Residues in contact with SER 190 (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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186A VAL* 2.9 30.7 + - - +
187A GLU* 3.5 8.9 + - - +
188A TYR 3.2 2.6 - - - -
189A LEU* 1.3 78.1 - - - +
191A LEU* 1.3 61.8 + - - +
192A VAL 5.3 2.5 - - - -
193A LYS* 5.0 14.9 - - - -
302A PHE* 4.4 1.3 - - - -
303A PRO 5.6 1.3 - - - -
305A LEU* 4.3 17.4 + - - +
198B ARG* 2.9 22.9 + - - -
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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