Contacts of the helix formed by residues 194 - 207 (chain C) in PDB entry 1C7G
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 MET 194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193C SER* 1.3 70.1 - - - +
195C ALA* 1.3 64.5 + - - +
197C MET* 3.3 7.7 + - - +
198C ARG* 3.0 27.2 + - - +
225C ILE* 3.9 7.7 - - + +
229C GLU* 2.8 21.9 + - - +
232C TYR* 3.2 31.2 - - + +
240C ILE* 3.4 42.8 - - + +
243C GLU* 3.5 27.8 - - + +
244C MET* 3.8 31.4 - - + -
247C TYR* 3.9 9.2 - - + -
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Residues in contact with ALA 195 (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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193C SER* 3.2 6.0 - - - +
194C MET* 1.3 78.2 - - - +
196C ASN* 1.3 55.7 + - - +
198C ARG* 3.4 19.8 + - - +
199C ALA* 2.9 29.6 + - - +
229C GLU* 3.1 15.7 + - - +
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Residues in contact with ASN 196 (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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157C ASP* 3.5 19.3 + - - +
158C ILE* 2.7 55.7 + - - +
160C LEU* 4.3 17.0 - - - +
180C LEU* 4.9 1.2 - - - +
192C VAL* 4.0 7.3 - - + +
193C SER* 3.2 21.4 + - - +
194C MET 3.2 0.4 - - - -
195C ALA* 1.3 76.9 - - - +
197C MET* 1.3 60.6 + - - +
199C ALA* 3.2 3.6 + - - +
200C VAL* 2.8 38.2 + - - +
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Residues in contact with MET 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C LEU* 4.0 16.1 - - + +
182C VAL* 4.4 5.6 - - + -
192C VAL* 3.2 43.3 - - + +
193C SER 3.2 13.7 + - - +
194C MET* 3.3 10.5 + - - +
196C ASN* 1.3 79.7 - - - +
198C ARG* 1.3 56.7 + - - +
200C VAL* 3.8 1.9 + - - +
201C HIS* 3.2 27.0 + - - +
211C ILE* 5.6 0.2 - - - +
213C TYR* 3.5 36.3 + - - +
221C ASN* 3.8 13.5 - - - +
225C ILE* 3.8 11.0 - - + -
244C MET* 3.9 24.2 - - + -
247C TYR* 3.6 14.4 - - + +
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Residues in contact with ARG 198 (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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194C MET* 3.0 19.9 + - - +
195C ALA* 3.6 24.9 - - - +
197C MET* 1.3 75.6 - - - +
199C ALA* 1.3 59.0 + - - +
201C HIS* 3.4 4.6 + - + +
202C GLU* 3.0 42.3 + - + +
229C GLU* 5.6 0.6 + - - -
232C TYR* 3.1 18.4 + - - -
243C GLU* 3.0 21.4 + - - -
247C TYR* 3.0 38.8 + - + +
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Residues in contact with ALA 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C LEU* 3.6 31.7 - - + +
195C ALA 2.9 18.1 + - - +
196C ASN* 3.7 4.7 - - - +
198C ARG* 1.3 73.9 - - - +
200C VAL* 1.3 66.7 + - - +
202C GLU* 3.2 12.8 + - - +
203C MET* 3.1 25.0 + - + +
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Residues in contact with VAL 200 (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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158C ILE* 3.9 25.8 - - + -
160C LEU* 3.9 20.6 - - + -
163C LEU* 4.5 7.4 - - + +
178C ILE* 4.4 21.8 - - + -
180C LEU* 4.2 17.3 - - + -
196C ASN* 2.8 29.2 + - - +
197C MET 4.0 3.6 - - - +
199C ALA* 1.3 75.2 - - - +
201C HIS* 1.3 58.9 + - - +
203C MET* 3.9 2.0 - - - +
204C ALA* 2.9 28.4 + - - +
211C ILE* 4.0 16.6 - - + -
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Residues in contact with HIS 201 (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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197C MET 3.2 16.7 + - - +
198C ARG* 3.5 5.2 - - + +
199C ALA 3.2 0.4 - - - -
200C VAL* 1.3 78.8 - - - +
202C GLU* 1.3 65.4 + - + +
204C ALA* 4.1 0.3 - - - +
205C SER* 2.9 41.8 + - - -
211C ILE* 3.6 14.1 - - - +
246C SER 4.7 6.0 + - - -
247C TYR* 3.6 51.1 + + + +
248C ALA 6.3 0.2 - - - -
249C ASP* 6.0 2.5 - - - -
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Residues in contact with GLU 202 (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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198C ARG* 3.0 30.2 + - + +
199C ALA* 3.2 13.8 + - - +
201C HIS* 1.3 83.3 - - + +
203C MET* 1.3 62.5 + - - +
205C SER* 3.7 6.3 + - - -
206C THR* 3.2 24.8 + - - -
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Residues in contact with MET 203 (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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160C LEU* 3.8 35.2 - - + +
163C LEU* 4.0 23.1 - - + -
164C ALA* 3.9 27.4 - - + -
167C ILE* 4.2 6.5 - - + -
199C ALA 3.1 10.6 + - - +
200C VAL 3.9 3.4 - - - +
202C GLU* 1.3 80.6 - - - +
204C ALA* 1.3 63.9 + - - +
206C THR* 2.9 23.0 + - - -
207C TYR* 3.1 30.1 - - + -
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Residues in contact with ALA 204 (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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163C LEU* 5.5 0.8 - - - +
167C ILE* 5.5 1.1 - - - -
178C ILE* 3.8 18.8 - - + -
200C VAL 2.9 18.6 + - - +
203C MET* 1.3 76.4 - - - +
205C SER* 1.3 57.9 + - - +
207C TYR* 3.3 1.5 + - - +
208C GLY 2.8 9.2 + - - -
209C ILE* 2.8 49.7 + - + +
211C ILE* 3.5 24.0 - - + -
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Residues in contact with SER 205 (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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201C HIS* 2.9 37.4 + - - -
202C GLU* 3.7 6.3 + - - -
203C MET 3.2 0.2 - - - -
204C ALA* 1.3 77.1 - - - +
206C THR* 1.3 64.4 + - - +
208C GLY* 3.4 10.2 + - - +
209C ILE 5.2 0.9 - - - -
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Residues in contact with THR 206 (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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202C GLU 3.2 13.5 + - - -
203C MET* 2.9 14.2 + - - -
205C SER* 1.3 81.2 + - - +
207C TYR* 1.3 82.6 + - + +
208C GLY 3.3 0.4 + - - -
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Residues in contact with TYR 207 (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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164C ALA* 6.4 0.2 - - - -
167C ILE* 3.7 36.8 - - + -
172C ALA* 3.7 29.6 - - + +
203C MET* 3.1 40.2 + - + -
204C ALA 4.2 0.4 - - - +
206C THR* 1.3 91.8 - - + +
208C GLY* 1.3 63.1 + - - +
209C ILE* 3.3 12.0 + - + -
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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