Contacts of the helix formed by residues 175 - 189 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144C TYR* 3.4 20.0 + - - -
145C LYS* 4.7 0.3 - - - -
146C LYS* 4.4 3.3 + - - +
171C PHE* 3.0 28.5 + - - -
174C VAL* 1.3 78.8 - - - +
176C PRO* 1.3 67.4 - - - +
177C GLU* 3.1 11.0 + - - +
178C SER* 2.2 37.8 + - - -
179C VAL* 3.2 14.6 + - - +
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Residues in contact with PRO 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C LEU* 3.3 24.9 - - + +
173C THR 5.2 0.2 - - - -
174C VAL 3.8 3.8 - - - +
175C SER* 1.3 89.1 - - - +
177C GLU* 1.3 71.1 + - - +
179C VAL* 3.3 12.2 + - + +
180C LEU* 3.0 40.4 + - + +
209C SER* 3.8 29.8 - - - +
212C LYS* 6.2 0.9 - - + +
213C VAL* 4.8 1.4 - - + +
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Residues in contact with GLU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C LYS* 3.8 24.5 - - + +
174C VAL 4.8 0.9 - - - +
175C SER* 3.6 10.8 + - - +
176C PRO* 1.3 99.2 - - - +
178C SER* 1.3 63.2 + - - +
180C LEU* 3.4 8.5 + - - +
181C LYS* 3.1 22.5 + - - +
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Residues in contact with SER 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C MET* 4.2 7.9 - - - -
144C TYR* 3.8 13.8 - - - -
146C LYS* 3.4 16.6 - - - +
150C LEU* 3.4 24.7 - - - -
171C PHE* 4.4 1.6 - - - -
175C SER* 2.2 36.8 + - - -
177C GLU* 1.3 77.1 - - - +
179C VAL* 1.3 64.4 + - - +
181C LYS* 3.3 2.8 + - - +
182C VAL* 3.0 30.2 + - - +
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Residues in contact with VAL 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C ILE* 4.4 16.4 - - + +
171C PHE* 3.8 27.6 - - + +
172C LEU* 3.8 32.1 - - + -
175C SER 3.2 17.2 + - - +
176C PRO 3.3 6.3 + - - +
178C SER* 1.3 76.5 - - - +
180C LEU* 1.3 58.1 + - - +
182C VAL* 3.5 2.3 + - - +
183C ALA* 2.9 30.4 + - - +
193C PHE* 3.8 12.7 - - + -
195C LEU* 4.7 7.2 - - + -
213C VAL* 3.9 20.4 - - + -
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C PRO* 3.0 25.3 + - + +
177C GLU* 3.7 7.2 - - - +
178C SER 3.2 0.2 - - - -
179C VAL* 1.3 74.5 - - - +
181C LYS* 1.3 57.8 + - - +
183C ALA* 4.1 2.0 - - + -
184C HIS* 2.5 41.3 + - + +
212C LYS* 3.8 50.3 - - + +
213C VAL* 4.0 16.4 - - + -
216C TYR* 4.2 22.4 - - + -
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Residues in contact with LYS 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C LYS* 3.5 18.6 - - - +
150C LEU* 4.0 8.2 + - + -
151C ASP* 2.7 39.4 + - - +
156C TRP* 3.1 52.9 - - + -
177C GLU 3.1 13.6 + - - +
178C SER* 3.4 9.9 - - - +
180C LEU* 1.3 75.4 - - - +
182C VAL* 1.3 68.6 + - - +
184C HIS* 3.7 5.5 - - - +
185C HIS* 3.0 19.4 + - - +
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Residues in contact with VAL 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C PHE* 4.2 15.3 - - + -
12C MET* 4.1 16.2 - - - -
150C LEU* 3.9 17.9 - - + -
156C TRP* 4.4 10.3 - - + -
159C VAL* 4.7 6.7 - - + -
165C CYS* 3.7 30.7 - - + -
167C ILE* 4.7 3.6 - - + -
178C SER 3.0 17.2 + - - +
179C VAL* 3.7 4.5 - - - +
181C LYS* 1.3 72.7 - - - +
183C ALA* 1.3 55.3 + - - +
185C HIS* 2.8 30.1 + - + +
186C ALA* 2.9 11.3 + - - +
193C PHE* 3.9 12.8 - - + -
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Residues in contact with ALA 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C VAL 2.9 22.9 + - - +
180C LEU* 3.6 6.7 - - + +
182C VAL* 1.3 70.6 - - - +
184C HIS* 1.3 63.6 + - - +
186C ALA* 3.1 12.3 + - - +
187C SER* 3.1 13.0 + - - -
193C PHE* 3.5 31.4 - - + +
213C VAL* 4.5 5.4 - - + -
216C TYR* 3.6 32.1 - - + +
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Residues in contact with HIS 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C LEU* 2.5 23.6 + - + +
181C LYS* 3.7 5.2 - - - +
183C ALA* 1.3 73.3 - - - +
185C HIS* 1.3 62.3 + - - +
187C SER* 3.2 4.6 - - - -
188C GLU* 3.0 61.5 + - + +
216C TYR* 3.5 37.3 + + + -
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Residues in contact with HIS 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C TRP* 3.5 25.9 - + + -
159C VAL* 4.5 14.5 + - + -
160C GLU* 2.9 47.4 + - + -
165C CYS* 5.9 5.4 - - - -
181C LYS 3.0 11.6 + - - +
182C VAL 2.8 15.8 + - - +
184C HIS* 1.3 72.3 + - - +
186C ALA* 1.3 69.6 + - - +
188C GLU* 3.4 4.3 + - - -
189C ASN* 3.1 56.3 + - - +
191C ARG* 4.4 14.2 + - + +
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Residues in contact with ALA 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C CYS* 5.2 6.7 - - - -
182C VAL 2.9 10.3 + - - +
183C ALA 3.1 8.9 + - - +
185C HIS* 1.3 78.9 - - - +
187C SER* 1.3 52.0 - - - +
189C ASN 3.3 0.5 + - - -
190C ASN* 2.8 16.5 + - - -
191C ARG* 2.7 50.7 + - + +
192C ILE 4.7 0.2 - - - -
193C PHE* 3.5 33.9 - - + +
216C TYR 5.5 0.2 - - - +
218C ASP* 5.0 0.9 - - - +
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Residues in contact with SER 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C ALA 3.1 1.6 + - - -
184C HIS* 3.2 11.2 - - - -
186C ALA* 1.3 77.4 - - - +
188C GLU* 1.3 61.8 + - - +
190C ASN* 2.8 22.3 + - - +
216C TYR* 3.7 32.3 - - - -
254C MET* 4.2 2.1 - - - +
255C ASN* 3.4 39.0 + - - +
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Residues in contact with GLU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C HIS* 3.0 44.9 + - + +
185C HIS* 4.0 6.3 - - - +
187C SER* 1.3 80.5 - - - +
189C ASN* 1.3 68.2 + - - +
190C ASN 3.5 0.4 + - - -
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Residues in contact with ASN 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C HIS* 3.1 48.2 + - - +
187C SER 3.1 0.6 - - - -
188C GLU* 1.3 87.4 + - - +
190C ASN* 1.3 71.6 + - - +
191C ARG* 3.0 38.3 + - - +
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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