Contacts of the helix formed by residues 178 - 195 (chain A) in PDB entry 2B4M
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 TRP 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.6 26.0 - - + -
22A ASP* 3.0 37.9 - - - -
25A SER* 4.2 9.4 - - - -
50A SER* 3.9 25.6 - - - -
72A TRP* 4.7 5.6 - + - +
176A VAL* 2.9 42.9 + - + +
177A ALA* 1.3 78.3 - - - +
179A ASP* 1.3 67.6 + - - +
180A SER* 3.1 5.6 - - - +
181A GLU* 2.9 29.9 + - - +
182A ILE* 3.0 11.5 + - - +
206A ALA* 5.6 3.2 - - - +
230A HIS* 5.9 0.8 + - - -
311A PBE 3.6 50.6 + - + +
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Residues in contact with ASP 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A SER* 5.5 4.4 + - - -
75A HIS* 3.9 16.6 + - + +
76A TRP* 3.1 37.7 + - + +
132A MET* 3.7 15.0 - - + +
135A VAL* 5.4 8.0 - - - +
136A GLU* 4.1 10.1 - - - +
177A ALA 4.0 1.7 + - - +
178A TRP* 1.3 71.8 - - - +
180A SER* 1.3 61.8 + - - +
182A ILE* 3.5 21.0 + - - +
183A ALA* 3.2 20.6 + - - +
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TRP* 5.1 2.4 + - - -
74A PRO 3.9 16.8 + - - -
75A HIS* 5.7 1.4 - - - -
128A MET* 3.4 30.2 - - - +
132A MET* 3.8 6.1 - - - -
178A TRP* 3.8 7.6 - - - +
179A ASP* 1.3 73.9 - - - +
181A GLU* 1.3 85.3 + - - +
183A ALA* 3.0 22.5 - - - +
184A SER* 3.1 8.8 + - - -
225A TRP* 4.0 12.9 - - - -
311A PBE 4.8 1.9 - - - -
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Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 3.9 10.4 - - - +
128A MET* 4.4 0.9 - - - +
175A TYR* 4.4 1.8 - - - +
176A VAL 3.4 23.1 - - - +
178A TRP* 2.9 16.2 + - + +
180A SER* 1.3 103.0 + - - +
182A ILE* 1.3 60.2 + - - +
183A ALA 3.2 1.1 - - - -
184A SER* 3.3 7.5 + - - +
185A THR* 2.4 37.2 + - - +
222A LEU 3.6 16.9 - - - +
223A SER* 3.3 29.4 - - - +
225A TRP* 3.1 30.5 + - - -
311A PBE 4.0 4.9 - - - +
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Residues in contact with ILE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE* 5.3 0.6 - - - +
135A VAL* 4.9 11.9 - - + -
141A PRO* 4.0 29.7 - - + +
175A TYR* 4.5 14.8 - - + -
177A ALA* 4.3 24.9 - - + +
178A TRP 3.0 17.6 + - - +
179A ASP* 3.7 25.1 - - - +
180A SER 3.3 0.2 - - - -
181A GLU* 1.3 74.1 - - - +
183A ALA* 1.3 67.5 + - - +
185A THR* 4.9 0.7 - - - -
186A ASN* 2.9 34.9 + - - +
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TRP* 4.1 5.2 - - + -
128A MET* 3.7 22.0 - - + -
131A ILE* 3.8 33.4 - - + +
132A MET* 4.1 6.1 - - + -
179A ASP 3.2 12.6 + - - +
180A SER 3.0 12.5 + - - +
182A ILE* 1.3 80.0 - - - +
184A SER* 1.3 63.5 + - - +
186A ASN* 3.9 1.9 - - - +
187A VAL* 3.2 21.5 + - - +
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Residues in contact with SER 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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99A ILE* 6.3 1.6 - - - -
121A PHE* 4.0 17.0 - - - -
123A TRP* 3.7 16.8 - - - -
128A MET* 4.4 5.2 - - - -
180A SER 3.1 3.7 + - - -
181A GLU* 3.3 22.2 + - - +
183A ALA* 1.3 75.4 - - - +
185A THR* 1.3 71.7 + - - +
187A VAL* 3.1 12.9 - - - +
188A ILE* 3.0 27.2 + - - +
222A LEU* 3.7 18.0 + - - +
247A SER* 6.0 0.4 - - - -
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Residues in contact with THR 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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173A LEU* 4.2 17.7 - - + +
174A ALA 4.8 2.6 + - - +
175A TYR* 3.3 33.4 - - + +
181A GLU* 2.4 27.4 + - - +
184A SER* 1.3 79.6 + - - +
186A ASN* 1.3 61.9 + - - +
188A ILE* 4.1 0.2 - - - -
189A GLY* 2.8 26.0 + - - -
201A LEU* 3.6 25.8 - - + +
222A LEU* 3.7 17.3 - - + +
223A SER* 4.5 2.8 + - - -
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Residues in contact with ASN 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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131A ILE* 6.2 1.6 - - + -
141A PRO* 3.3 29.4 - - + +
142A ALA* 3.6 15.4 - - - +
145A ALA* 3.6 14.8 - - + +
175A TYR* 5.7 4.5 - - - -
182A ILE* 2.9 33.4 + - - +
183A ALA 3.9 1.6 - - - +
184A SER 3.2 0.6 - - - -
185A THR* 1.3 78.3 - - - +
187A VAL* 1.3 60.1 + - - +
189A GLY* 3.6 1.7 - - - +
190A LYS* 2.8 31.4 + - - +
201A LEU* 4.3 20.9 - - - +
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 4.2 13.5 - - + -
123A TRP* 3.7 15.0 - - + -
131A ILE* 4.0 9.9 - - + -
145A ALA* 3.9 10.2 - - + +
148A TYR* 3.8 31.6 - - + -
149A VAL* 3.9 14.3 - - + +
159A TRP* 4.0 14.1 - - + -
183A ALA 3.2 14.1 + - - +
184A SER* 3.1 24.0 - - - +
186A ASN* 1.3 75.1 - - - +
188A ILE* 1.3 62.3 + - - +
190A LYS* 3.2 4.5 + - - +
191A VAL* 3.1 25.6 + - - +
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Residues in contact with ILE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 4.7 15.0 - - + +
118A LEU* 4.0 19.3 - - + -
121A PHE* 3.5 54.3 - - + -
159A TRP* 4.1 15.9 - - + -
173A LEU* 4.1 5.2 - - + -
184A SER 3.0 14.0 + - - +
187A VAL* 1.3 74.5 - - - +
189A GLY* 1.3 67.3 + - - +
191A VAL* 3.0 10.0 + - + +
192A LEU* 3.0 41.1 + - + +
222A LEU* 3.8 14.4 - - + -
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Residues in contact with GLY 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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173A LEU* 4.1 14.6 - - - -
185A THR 2.8 21.0 + - - -
186A ASN* 3.3 2.9 + - - -
188A ILE* 1.3 78.2 - - - +
190A LYS* 1.3 55.3 + - - +
192A LEU* 3.4 3.9 + - - +
193A GLU* 3.0 34.6 + - - +
199A VAL* 3.8 12.4 - - - +
201A LEU* 4.7 4.7 - - - -
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Residues in contact with LYS 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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142A ALA* 4.5 5.8 - - + +
145A ALA* 4.1 9.0 - - + -
146A ALA* 3.7 39.7 - - - +
149A VAL* 4.4 8.9 - - + +
150A ASN* 5.5 2.8 - - - +
186A ASN 2.8 17.8 + - - +
187A VAL 3.5 5.4 - - - +
189A GLY* 1.3 73.2 - - - +
191A VAL* 1.3 61.3 + - - +
193A GLU* 3.1 18.9 + - + +
194A ASP* 2.8 57.4 + - - +
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Residues in contact with VAL 191 (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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117A LEU* 3.8 30.5 - - + -
149A VAL* 4.1 18.6 - - + -
156A ILE* 4.2 10.3 - - + -
159A TRP* 4.2 22.0 - - + -
160A THR* 3.8 17.9 - - + -
187A VAL 3.1 17.0 + - - +
188A ILE* 3.0 11.8 + - + +
190A LYS* 1.3 75.1 - - - +
192A LEU* 1.3 58.0 + - - +
194A ASP* 3.3 11.2 + - + +
195A LEU* 3.1 28.2 + - + +
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Residues in contact with LEU 192 (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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114A ALA* 4.7 12.3 - - + +
117A LEU* 3.6 23.6 - - + -
118A LEU* 4.8 3.8 - - + -
171A ILE* 4.5 16.2 - - + -
173A LEU* 3.9 22.7 - - + -
188A ILE* 3.0 34.8 + - + +
189A GLY* 3.6 6.7 - - - +
191A VAL* 1.3 74.9 - - - +
193A GLU* 1.3 59.0 + - - +
195A LEU* 3.0 17.4 + - + +
196A GLY 3.2 0.7 + - - -
197A TYR* 3.0 58.3 + - + +
199A VAL* 3.7 10.8 - - + -
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Residues in contact with GLU 193 (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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189A GLY 3.0 20.4 + - - +
190A LYS* 3.1 25.7 + - + +
192A LEU* 1.3 76.2 - - - +
194A ASP* 1.3 63.3 + - - +
195A LEU 3.1 0.4 - - - -
196A GLY* 3.2 12.5 + - - -
197A TYR 3.9 12.4 + - - +
199A VAL* 3.6 26.4 + - + +
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Residues in contact with ASP 194 (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 VAL* 3.8 16.3 - - - +
150A ASN* 5.0 3.3 - - - +
165A LYS* 4.3 16.3 + - - -
190A LYS* 2.8 51.9 + - - +
191A VAL* 3.5 8.9 - - + +
193A GLU* 1.3 77.0 - - - +
195A LEU* 1.3 59.9 + - + +
196A GLY 3.6 0.3 + - - -
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Residues in contact with LEU 195 (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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117A LEU* 4.2 25.4 - - + -
160A THR* 4.6 15.0 - - + -
163A VAL* 3.9 29.2 - - + +
164A GLN 4.0 13.7 - - - +
165A LYS* 3.7 31.9 - - + +
166A VAL* 3.3 24.4 + - - +
167A LYS* 5.6 0.2 + - - -
191A VAL* 3.1 15.9 + - + +
192A LEU* 3.0 13.1 + - - +
194A ASP* 1.3 81.1 - - + +
196A GLY* 1.3 55.9 + - - +
197A TYR* 3.6 15.7 - - + -
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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
------------------------------------------------------------
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