Contacts of the helix formed by residues 175 - 189 (chain B) in PDB entry 2I6A
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 175 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B TYR* 3.8 18.7 + - - -
145B LYS* 4.9 0.3 - - - -
146B LYS 4.4 3.8 + - - -
171B PHE* 3.1 22.8 + - - +
174B VAL* 1.3 79.4 - - - +
176B PRO* 1.3 65.3 - - - +
177B GLU* 2.9 16.5 + - - +
178B SER* 2.6 37.2 + - - -
179B VAL* 3.3 14.2 + - - +
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Residues in contact with PRO 176 (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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172B LEU* 3.1 28.9 - - + +
173B THR 4.8 0.7 - - - -
174B VAL 3.7 4.5 - - - +
175B SER* 1.3 89.6 - - - +
177B GLU* 1.3 70.6 + - + +
179B VAL* 3.5 11.1 + - + +
180B LEU* 2.8 40.1 + - + +
209B SER* 3.6 28.3 - - - +
213B VAL* 5.0 1.4 - - + +
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Residues in contact with GLU 177 (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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146B LYS* 4.1 21.3 - - + +
174B VAL 5.0 0.3 - - - +
175B SER* 3.4 12.3 + - - +
176B PRO* 1.3 98.1 - - + +
178B SER* 1.3 58.1 + - - +
180B LEU* 3.4 10.5 + - + +
181B LYS* 2.8 30.0 + - - +
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Residues in contact with SER 178 (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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12B MET* 3.7 18.8 - - - -
144B TYR* 3.5 8.8 - - - -
146B LYS* 3.3 18.6 + - - +
150B LEU* 3.7 20.6 - - - -
171B PHE* 4.2 1.1 - - - -
175B SER* 2.6 30.2 + - - -
177B GLU* 1.3 75.4 - - - +
179B VAL* 1.3 60.4 + - - +
181B LYS* 3.1 2.4 + - - +
182B VAL* 2.8 36.6 + - - +
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Residues in contact with VAL 179 (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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12B MET* 4.8 0.6 - - - -
167B ILE* 4.1 21.1 - - + -
171B PHE* 4.0 25.4 - - + +
172B LEU* 4.3 11.9 - - + -
175B SER 3.3 14.3 + - - +
176B PRO* 3.6 12.1 - - + +
178B SER* 1.3 76.4 - - - +
180B LEU* 1.3 52.8 + - - +
182B VAL* 3.2 1.2 + - - +
183B ALA* 2.8 34.0 + - - +
193B PHE* 3.9 14.7 - - + -
195B LEU* 4.4 8.7 - - + -
213B VAL* 3.7 31.0 - - + -
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Residues in contact with LEU 180 (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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176B PRO* 2.8 29.8 + - + +
177B GLU* 3.6 9.4 - - + +
179B VAL* 1.3 74.8 - - - +
181B LYS* 1.3 62.6 + - - +
183B ALA* 4.5 2.9 - - - +
184B HIS* 2.9 27.1 + - + +
212B LYS* 3.9 37.2 - - + +
213B VAL* 4.3 11.7 - - + -
216B TYR* 3.8 31.2 - - + +
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Residues in contact with LYS 181 (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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146B LYS* 4.2 16.3 - - + +
150B LEU* 4.1 9.4 - - + -
151B ASP* 2.6 39.0 + - - +
156B TRP* 3.1 47.8 - - + -
177B GLU 2.8 20.7 + - - +
178B SER* 3.1 4.9 + - - +
180B LEU* 1.3 73.3 - - - +
182B VAL* 1.3 57.8 + - - +
184B HIS* 3.9 4.4 - - - +
185B HIS* 3.2 26.9 + - - +
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Residues in contact with VAL 182 (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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10B PHE* 3.9 26.7 - - + -
12B MET* 4.1 13.2 - - - -
150B LEU* 3.8 24.9 - - + -
156B TRP* 4.4 4.3 - - + -
159B VAL* 4.2 10.5 - - + -
165B CYS* 4.1 16.7 - - + -
167B ILE* 4.3 13.0 - - + -
178B SER 2.8 26.2 + - - +
179B VAL 3.7 2.9 - - - +
181B LYS* 1.3 72.7 - - - +
183B ALA* 1.3 66.6 + - - +
185B HIS* 3.2 9.3 + - + +
186B ALA* 3.0 22.2 + - - +
193B PHE* 4.4 1.6 - - + -
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Residues in contact with ALA 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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179B VAL 2.8 16.6 + - - +
180B LEU* 4.4 2.0 - - - +
182B VAL* 1.3 73.2 - - - +
184B HIS* 1.3 61.1 + - - +
186B ALA* 3.4 3.7 + - - +
187B SER* 3.1 20.6 + - - -
193B PHE* 3.2 49.8 - - + +
213B VAL* 4.4 6.1 - - + -
216B TYR* 3.7 23.4 - - + +
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Residues in contact with HIS 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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180B LEU* 2.9 20.9 + - + +
181B LYS* 3.9 5.2 - - - +
183B ALA* 1.3 75.1 - - - +
185B HIS* 1.3 65.5 + - - +
187B SER* 2.9 12.9 + - - -
188B GLU* 3.0 57.0 + - + -
216B TYR* 3.1 40.6 - + + -
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Residues in contact with HIS 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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156B TRP* 3.6 23.6 - + + -
159B VAL* 4.6 14.4 - - + -
160B GLU* 2.7 44.1 + - + -
162B ALA 5.9 0.4 + - - -
165B CYS* 6.0 3.8 - - - -
181B LYS 3.2 12.5 + - - +
182B VAL* 3.2 9.8 + - - +
184B HIS* 1.3 83.1 + - - +
186B ALA* 1.3 65.3 + - - +
188B GLU* 4.7 4.3 - - - -
189B ASN* 2.8 60.5 + - + +
191B ARG* 4.4 15.6 + - + -
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Residues in contact with ALA 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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165B CYS* 5.3 6.1 - - - -
182B VAL 3.0 12.0 + - - +
183B ALA* 3.7 8.7 - - - +
184B HIS 3.3 0.2 - - - -
185B HIS* 1.3 77.3 - - + +
187B SER* 1.3 53.2 + - - +
190B ASN* 2.6 31.7 + - - -
191B ARG* 2.6 45.0 + - + +
192B ILE 4.5 1.6 - - - +
193B PHE* 4.0 22.9 - - + +
218B ASP* 5.2 0.4 - - - +
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Residues in contact with SER 187 (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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183B ALA 3.1 11.9 + - - -
184B HIS* 2.9 11.4 + - - -
186B ALA* 1.3 75.6 - - - +
188B GLU* 1.3 66.1 + - - +
190B ASN* 2.9 15.9 + - - +
191B ARG 5.2 0.2 - - - -
216B TYR* 3.8 23.6 - - - -
218B ASP* 5.8 1.5 + - - -
254B MET* 4.3 4.5 - - - +
255B ASN* 3.3 42.2 + - - +
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Residues in contact with GLU 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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184B HIS* 3.0 46.4 + - + +
185B HIS* 4.0 7.0 - - - +
187B SER* 1.3 77.2 + - - +
189B ASN* 1.3 68.8 + - - +
190B ASN 3.9 0.3 + - - -
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Residues in contact with ASN 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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185B HIS* 2.8 50.7 + - - +
187B SER 3.0 0.4 - - - -
188B GLU* 1.3 87.0 + - - +
190B ASN* 1.3 71.7 + - - +
191B ARG* 2.9 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