Contacts of the helix formed by residues 194 - 207 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A SER* 1.3 70.1 - - - +
195A ALA* 1.3 60.3 + - - +
197A MET* 3.5 7.6 + - - +
198A ARG* 3.0 33.6 + - - +
225A ILE* 3.9 7.1 - - + +
229A GLU* 2.7 21.4 + - - +
232A TYR* 3.4 31.2 - - + +
240A ILE* 3.5 40.6 - - + +
243A GLU* 3.6 32.3 - - + +
244A MET* 3.9 27.6 - - + -
247A TYR* 3.9 9.0 - - + -
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Residues in contact with ALA 195 (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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193A SER* 3.1 5.8 - - - +
194A MET* 1.3 78.1 - - - +
196A ASN* 1.3 56.9 + - - +
198A ARG* 3.5 21.9 + - - +
199A ALA* 2.9 30.0 + - - +
229A GLU* 2.9 14.6 + - - +
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Residues in contact with ASN 196 (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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157A ASP* 3.5 20.5 + - - +
158A ILE* 2.7 55.1 + - - +
160A LEU* 4.2 16.2 - - - +
180A LEU* 5.0 1.0 - - - +
192A VAL* 3.8 8.4 - - + +
193A SER* 3.2 20.7 + - - +
195A ALA* 1.3 76.2 - - - +
197A MET* 1.3 56.3 + - - +
199A ALA* 3.0 4.8 + - - +
200A VAL* 2.7 40.7 + - - +
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Residues in contact with MET 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 4.1 17.4 - - + +
182A VAL* 4.5 3.4 - - + -
192A VAL* 3.3 41.5 - - + +
193A SER 3.3 10.9 + - - +
194A MET* 3.8 9.2 - - - +
195A ALA 3.5 0.2 - - - -
196A ASN* 1.3 78.5 - - - +
198A ARG* 1.3 63.3 + - - +
200A VAL* 3.9 1.3 - - - +
201A HIS* 3.0 25.6 + - - +
211A ILE* 5.5 0.5 - - - +
213A TYR* 3.4 34.3 + - - +
221A ASN* 3.7 15.3 - - - +
225A ILE* 3.8 12.8 - - + -
244A MET* 3.8 27.4 - - + +
247A TYR* 3.9 11.8 - - + +
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Residues in contact with ARG 198 (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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194A MET* 3.0 25.3 + - - +
195A ALA* 3.6 25.8 - - - +
197A MET* 1.3 78.5 - - - +
199A ALA* 1.3 57.3 + - - +
201A HIS* 3.4 4.3 + - + +
202A GLU* 3.1 42.5 + - + +
229A GLU* 5.6 0.2 + - - -
232A TYR* 3.1 28.5 + - - -
243A GLU* 3.2 11.1 + - - -
247A TYR* 3.1 34.8 + - + +
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Residues in contact with ALA 199 (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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160A LEU* 3.6 29.7 - - + +
195A ALA 2.9 18.1 + - - +
196A ASN* 3.5 5.4 - - - +
198A ARG* 1.3 74.3 - - - +
200A VAL* 1.3 64.7 + - - +
202A GLU* 3.3 13.1 + - - +
203A MET* 3.2 22.9 + - - +
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Residues in contact with VAL 200 (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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158A ILE* 3.8 36.6 - - + -
160A LEU* 3.8 15.3 - - + -
163A LEU* 4.2 5.8 - - + +
178A ILE* 4.2 28.3 - - + -
180A LEU* 4.5 12.1 - - + -
196A ASN* 2.7 28.0 + - - +
197A MET 3.9 3.8 - - - +
199A ALA* 1.3 73.0 - - - +
201A HIS* 1.3 58.3 + - - +
203A MET* 3.3 1.9 + - - +
204A ALA* 2.9 28.6 + - - +
211A ILE* 4.1 15.5 - - + -
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Residues in contact with HIS 201 (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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197A MET 3.0 19.4 + - - +
198A ARG* 3.5 5.6 - - + +
200A VAL* 1.3 78.6 - - - +
202A GLU* 1.3 64.2 + - + +
205A SER* 2.8 49.1 + - - -
211A ILE* 3.6 14.0 - - + +
246A SER 4.6 4.7 + - - -
247A TYR* 3.3 51.4 + + + +
249A ASP* 6.0 2.2 - - - -
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Residues in contact with GLU 202 (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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198A ARG* 3.1 35.2 + - + +
199A ALA* 3.5 13.1 - - - +
200A VAL 3.2 0.2 - - - -
201A HIS* 1.3 84.7 - - + +
203A MET* 1.3 61.6 + - - +
205A SER* 3.7 4.5 + - - -
206A THR* 3.1 25.1 + - - -
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Residues in contact with MET 203 (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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160A LEU* 3.7 31.4 - - + +
163A LEU* 4.0 15.3 - - + -
164A ALA* 3.7 38.4 - - + -
167A ILE* 4.1 14.4 - - + -
199A ALA 3.2 8.8 + - - +
200A VAL 3.8 5.4 - - - +
202A GLU* 1.3 76.7 - - - +
204A ALA* 1.3 66.3 + - - +
206A THR* 3.0 21.7 + - - -
207A TYR* 3.2 22.1 - - + -
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Residues in contact with ALA 204 (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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163A LEU* 5.2 0.6 - - - +
167A ILE* 5.4 1.3 - - - -
178A ILE* 4.0 17.3 - - + -
200A VAL 2.9 20.5 + - - +
203A MET* 1.3 73.2 - - - +
205A SER* 1.3 58.8 + - - +
207A TYR* 3.1 3.7 + - - +
208A GLY 2.9 9.2 + - - -
209A ILE* 2.9 53.5 + - + +
211A ILE* 3.7 21.8 - - + -
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Residues in contact with SER 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A HIS* 2.8 40.8 + - - -
202A GLU* 3.7 6.4 + - - -
204A ALA* 1.3 75.7 - - - +
206A THR* 1.3 63.0 + - - +
208A GLY* 3.5 9.6 + - - +
209A ILE 4.6 2.0 + - - +
211A ILE* 5.5 0.2 - - - +
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Residues in contact with THR 206 (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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202A GLU 3.1 15.4 + - - -
203A MET* 3.0 13.8 + - - -
205A SER* 1.3 79.3 + - - +
207A TYR* 1.3 81.8 + - + +
208A GLY 3.4 0.8 + - - -
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Residues in contact with TYR 207 (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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164A ALA* 6.3 0.7 - - + -
167A ILE* 3.8 41.7 - - + -
172A ALA* 3.6 31.4 - - + +
203A MET* 3.2 33.7 - - + -
204A ALA 3.1 2.6 + - - +
206A THR* 1.3 93.2 - - + +
208A GLY* 1.3 63.7 + - - +
209A ILE* 3.3 11.2 + - + -
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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