Contacts of the helix formed by residues 175 - 189 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A TYR* 3.6 18.9 + - - -
145A LYS* 4.7 0.7 - - - -
146A LYS 4.4 4.0 + - - -
171A PHE* 3.0 23.9 + - - -
174A VAL* 1.3 80.7 - - - +
176A PRO* 1.3 67.3 - - - +
177A GLU* 3.1 12.1 + - - +
178A SER* 2.8 38.2 + - - -
179A VAL* 3.2 14.7 + - - +
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Residues in contact with PRO 176 (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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172A LEU* 3.3 29.8 - - + +
173A THR 5.0 0.7 - - - -
174A VAL 3.8 4.0 - - - +
175A SER* 1.3 88.7 - - - +
177A GLU* 1.3 74.1 + - - +
179A VAL* 3.8 2.2 - - + +
180A LEU* 2.8 39.9 + - + +
209A SER* 2.9 33.7 - - - +
213A VAL* 4.9 1.8 - - + +
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Residues in contact with GLU 177 (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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146A LYS* 4.0 22.0 - - + +
174A VAL 4.9 1.0 - - - +
175A SER* 3.1 10.8 + - - +
176A PRO* 1.3 99.7 - - - +
178A SER* 1.3 63.6 + - - +
180A LEU* 3.5 6.5 + - - +
181A LYS* 3.1 24.6 + - - +
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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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12A MET* 4.3 4.0 - - - -
144A TYR* 3.5 14.9 - - - -
146A LYS* 3.4 19.6 + - - +
150A LEU* 3.7 17.0 - - - +
171A PHE* 4.0 12.6 - - - -
175A SER* 2.8 31.3 + - - -
177A GLU* 1.3 76.9 - - - +
179A VAL* 1.3 65.8 + - - +
181A LYS* 3.6 2.3 + - - +
182A VAL* 2.9 28.6 + - - +
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Residues in contact with VAL 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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167A ILE* 3.9 22.9 - - + -
171A PHE* 3.7 25.6 - - + -
172A LEU* 4.4 15.5 - - + -
175A SER 3.2 16.7 + - - +
176A PRO 3.8 5.6 - - - +
177A GLU 3.4 0.2 - - - -
178A SER* 1.3 73.0 - - - +
180A LEU* 1.3 55.0 + - - +
182A VAL* 2.9 4.9 + - - +
183A ALA* 2.6 33.4 + - + +
193A PHE* 3.6 24.7 - - + -
195A LEU* 4.3 9.4 - - + -
213A VAL* 4.1 21.5 - - + -
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Residues in contact with LEU 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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176A PRO* 2.8 23.6 + - + +
177A GLU* 3.9 6.3 - - - +
179A VAL* 1.3 76.5 - - - +
181A LYS* 1.3 54.5 + - - +
183A ALA* 3.0 3.7 + - + -
184A HIS* 2.6 41.0 + - + +
212A LYS* 3.9 45.1 - - + +
213A VAL* 4.1 13.9 - - + -
216A TYR* 4.0 24.0 - - + -
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Residues in contact with LYS 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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146A LYS* 4.3 15.5 - - + +
150A LEU* 3.4 17.7 - - + -
151A ASP* 2.8 29.3 + - - +
156A TRP* 3.2 48.2 - - + -
177A GLU 3.1 17.2 + - - +
178A SER* 3.6 4.3 - - - +
179A VAL 3.3 0.2 - - - -
180A LEU* 1.3 73.9 - - - +
182A VAL* 1.3 63.6 + - - +
184A HIS* 3.5 5.5 + - - +
185A HIS* 3.0 25.3 + - - +
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Residues in contact with VAL 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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10A PHE* 4.2 14.4 - - + -
12A MET* 4.1 13.7 - - - -
150A LEU* 4.1 25.6 - - + -
156A TRP* 4.5 3.8 - - + -
159A VAL* 4.3 10.8 - - + -
165A CYS* 4.1 25.8 - - + -
167A ILE* 4.2 3.8 - - + -
178A SER 2.9 19.3 - - - +
179A VAL 2.9 4.6 + - - +
181A LYS* 1.3 73.1 - - - +
183A ALA* 1.3 65.2 + - - +
185A HIS* 3.1 9.3 + - + +
186A ALA* 3.0 21.0 + - - +
193A PHE* 4.1 12.8 - - + -
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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
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179A VAL* 2.6 21.1 + - + +
180A LEU* 3.5 9.9 - - + +
182A VAL* 1.3 73.0 - - - +
184A HIS* 1.3 63.1 + - - +
186A ALA* 3.1 14.2 + - - +
187A SER* 3.2 11.8 + - - -
193A PHE* 3.6 31.4 - - + +
213A VAL* 4.9 2.9 - - + +
216A TYR* 3.6 32.7 - - + +
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Residues in contact with HIS 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 LEU* 2.6 22.8 + - + +
181A LYS* 3.9 5.2 - - - +
183A ALA* 1.3 73.6 - - - +
185A HIS* 1.3 57.3 + - - +
187A SER* 3.3 4.0 + - - -
188A GLU* 3.0 65.0 + - + +
216A TYR* 3.8 36.6 + + + -
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Residues in contact with HIS 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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156A TRP* 3.5 27.0 - + + -
159A VAL* 4.5 13.4 + - + -
160A GLU* 3.0 43.6 + - - -
162A ALA 5.9 0.2 + - - -
165A CYS* 5.9 4.9 - - - -
181A LYS 3.0 18.4 + - - +
182A VAL* 3.1 6.0 + - - +
184A HIS* 1.3 76.3 + - - +
186A ALA* 1.3 69.4 + - - +
188A GLU* 3.6 4.7 + - - -
189A ASN* 2.7 58.1 + - - +
191A ARG* 4.2 15.4 + - + +
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Residues in contact with ALA 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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165A CYS* 5.3 4.9 - - - -
182A VAL 3.0 11.5 + - - +
183A ALA 3.1 8.9 + - - +
185A HIS* 1.3 79.1 - - - +
187A SER* 1.3 53.8 + - - +
189A ASN 3.3 0.3 + - - -
190A ASN* 2.8 15.8 + - - -
191A ARG* 2.6 60.2 + - + +
192A ILE 4.4 1.6 - - - +
193A PHE* 3.7 25.4 - - + +
218A ASP* 5.0 0.7 - - - +
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Residues in contact with SER 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 ALA 3.2 2.2 + - - -
184A HIS* 3.3 10.5 - - - -
186A ALA* 1.3 78.6 - - - +
188A GLU* 1.3 65.5 + - - +
190A ASN* 3.1 13.5 + - - +
216A TYR* 3.5 35.1 - - - +
218A ASP* 6.0 1.1 - - - -
254A MET* 4.1 2.6 - - - +
255A ASN* 3.3 41.2 + - - +
257A LYS* 5.9 2.6 - - - -
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Residues in contact with GLU 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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184A HIS* 3.0 44.7 + - + +
185A HIS* 4.1 6.4 - - - +
187A SER* 1.3 80.5 - - - +
189A ASN* 1.3 68.8 + - - +
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Residues in contact with ASN 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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185A HIS* 2.7 54.6 + - - +
187A SER 3.1 0.8 - - - -
188A GLU* 1.3 87.5 - - - +
190A ASN* 1.3 64.5 + - - +
191A ARG* 2.7 46.0 + - - +
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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