Contacts of the helix formed by residues 182 - 194 (chain B) in PDB entry 6CDS
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 GLU 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B ARG* 3.5 42.2 + - - +
161B GLY* 3.5 28.2 + - - -
164B ALA* 5.8 3.5 - - - +
180B THR* 3.3 4.7 + - - -
181B PRO* 1.4 84.3 - - + +
183B MET* 1.4 58.1 + - - +
184B TRP* 3.3 4.9 - - - +
185B GLU* 3.6 24.1 - - + +
186B GLU* 3.1 33.6 + - + +
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Residues in contact with MET 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A TYR* 3.3 29.2 - - + +
172A ARG* 4.4 8.3 - - - +
177B TYR* 3.9 38.6 - - + +
179B MET* 3.4 36.8 - - + -
180B THR* 3.3 32.8 + - + +
181B PRO 3.5 0.8 - - - -
182B GLU* 1.4 76.9 - - - +
184B TRP* 1.4 58.8 + - - +
186B GLU* 3.6 9.2 + - - +
187B ARG* 3.1 40.9 + - + +
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Residues in contact with TRP 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 6.2 0.2 - - - -
163B LEU* 3.1 29.2 - - + -
164B ALA* 4.5 11.7 - - - -
166B GLU 3.6 14.6 - - - -
168B LEU* 4.0 17.0 - - + -
169B LEU* 3.7 26.3 - - + +
174B ILE* 4.7 24.6 - - + +
177B TYR* 3.9 27.0 - - + +
181B PRO 3.7 22.0 + - - -
182B GLU* 4.7 2.2 - - - +
183B MET* 1.4 77.3 - - - +
185B GLU* 1.3 77.5 + - + +
187B ARG* 3.5 7.1 + - - +
188B ILE* 3.2 49.9 + - + +
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Residues in contact with GLU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ARG* 3.7 6.6 - - - +
161B GLY* 2.7 42.5 + - - -
162B PHE* 3.8 7.1 + - - -
163B LEU* 3.9 22.0 - - + -
164B ALA* 3.8 13.5 + - - +
182B GLU* 3.5 27.2 + - + +
183B MET 3.4 0.2 - - - -
184B TRP* 1.3 96.9 - - + +
186B GLU* 1.3 60.4 + - + +
188B ILE* 3.3 5.9 + - - +
189B THR* 2.9 44.0 + - - +
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Residues in contact with GLU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ARG* 3.6 22.6 + - - +
180B THR* 4.6 10.0 + - - -
182B GLU* 3.1 24.2 + - + +
183B MET* 3.8 6.8 - - - +
185B GLU* 1.3 74.8 - - + +
187B ARG* 1.4 60.0 + - - +
189B THR* 3.4 6.0 + - - -
190B ALA* 3.0 29.8 + - - +
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Residues in contact with ARG 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A TYR* 4.4 10.3 + - - -
134A PRO* 5.0 2.4 - - - +
135A PRO* 3.6 26.7 - - - +
172A ARG* 5.4 0.2 - - - +
176A LEU* 4.0 11.9 - - - +
177A TYR* 4.4 4.7 + - - -
136B GLU* 3.1 36.6 + - - -
139B VAL* 4.0 15.5 - - + -
177B TYR* 3.5 30.9 - - + -
183B MET* 3.1 25.9 + - + +
184B TRP* 3.6 11.7 - - - +
185B GLU 3.3 0.2 - - - -
186B GLU* 1.4 73.8 - - - +
188B ILE* 1.3 65.7 + - - +
190B ALA* 3.5 9.0 + - - +
191B TRP* 3.4 27.7 + - - -
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Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 4.2 15.9 - - + +
142B ALA* 3.9 14.8 - - + -
143B SER* 3.7 22.9 - - - +
146B VAL* 4.2 6.3 - - + -
163B LEU* 3.8 20.0 - - + -
168B LEU* 3.6 34.3 - - + -
169B LEU* 4.0 10.5 - - + -
184B TRP* 3.2 33.2 + - + +
185B GLU* 3.6 6.7 - - - +
187B ARG* 1.3 74.6 - - - +
189B THR* 1.3 53.5 + - - +
191B TRP* 3.2 4.5 + - - +
192B TYR* 2.8 35.6 + - + +
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Residues in contact with THR 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B TYR* 3.7 39.0 - - + +
158B HIS 5.5 0.7 - - - +
162B PHE* 3.6 25.1 - - + -
163B LEU* 4.1 2.1 - - - +
185B GLU* 2.9 21.7 + - - +
186B GLU* 3.8 6.5 - - - -
188B ILE* 1.3 75.0 - - - +
190B ALA* 1.3 65.4 + - - +
192B TYR* 3.8 7.2 - - + -
193B ALA* 3.0 24.5 + - + +
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B GLU 3.0 17.6 + - - +
187B ARG* 3.7 9.6 - - - +
188B ILE 3.3 0.2 - - - -
189B THR* 1.3 75.7 - - - +
191B TRP* 1.3 63.4 + - + +
193B ALA* 3.5 14.8 - - - +
194B GLU* 3.6 14.9 - - - +
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Residues in contact with TRP 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B GLU* 3.5 19.3 + - + -
139B VAL* 3.7 25.5 - - + +
140B LEU* 3.6 37.1 - - + +
143B SER* 3.5 18.6 - - - +
187B ARG* 3.4 9.7 + - - +
188B ILE* 3.2 5.0 + - - +
190B ALA* 1.3 78.6 - - + +
192B TYR* 1.4 58.1 + - - +
194B GLU* 2.9 46.7 + - + +
195B HIS* 3.4 15.8 + + - -
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Residues in contact with TYR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B SER* 3.6 9.1 - - - +
146B VAL* 3.4 30.3 - - + -
147B GLN* 3.6 27.5 - - + +
150B TYR* 3.3 7.9 - - + +
151B GLY 2.9 28.0 + - - -
153B TYR* 3.4 37.9 - + + +
158B HIS* 3.2 22.5 - - - -
162B PHE* 3.6 23.6 - + - -
163B LEU* 5.3 0.4 - - + -
188B ILE 2.8 22.1 + - - +
189B THR* 3.5 8.7 - - - +
191B TRP* 1.4 70.5 - - - +
193B ALA* 1.4 52.2 + - - +
195B HIS* 2.9 36.6 + - - +
196B ARG 4.1 1.9 + - - -
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Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B TYR* 3.9 31.1 - - + +
189B THR 3.0 11.4 + - - +
190B ALA* 3.5 14.4 - - - +
192B TYR* 1.4 75.3 - - - +
194B GLU* 1.3 65.3 + - - +
195B HIS 3.3 1.0 + - - -
196B ARG* 3.6 17.0 + - - +
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Residues in contact with GLU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ALA 3.6 15.2 - - - +
191B TRP* 2.9 36.7 + - + +
193B ALA* 1.3 78.9 - - - +
195B HIS* 1.3 66.5 + - + +
196B ARG* 3.4 3.2 + - - +
198B ARG* 4.3 8.4 + - - +
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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