Contacts of the helix formed by residues 194 - 212 (chain A) in PDB entry 1C1C
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 GLU 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A LYS* 4.3 17.9 + - - -
192A ASP 4.3 5.8 - - - +
193A LEU* 1.3 75.7 - - - +
195A ILE* 1.3 55.9 + - + +
196A GLY* 3.1 4.0 - - - +
197A GLN* 2.7 39.8 + - + +
198A HIS 2.8 9.7 + - - -
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Residues in contact with ILE 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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104A LYS* 5.1 6.3 - - + +
105A SER* 4.1 17.0 - - - +
193A LEU 3.5 2.7 + - - +
194A GLU* 1.3 71.1 - - - +
196A GLY* 1.3 62.3 + - - +
198A HIS* 3.5 11.4 - - + +
199A ARG* 2.9 30.5 + - - +
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Residues in contact with GLY 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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194A GLU* 2.9 5.1 + - - +
195A ILE* 1.3 78.5 - - - +
197A GLN* 1.3 54.5 + - - +
199A ARG* 3.2 25.0 + - - +
200A THR* 2.7 41.2 + - - -
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Residues in contact with GLN 197 (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 LEU* 3.7 30.1 - - + +
194A GLU* 2.7 28.2 + - + +
196A GLY* 1.3 67.8 - - - -
198A HIS* 1.3 67.0 + - - +
200A THR* 3.0 9.1 + - - -
201A LYS* 2.9 35.0 + - - +
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Residues in contact with HIS 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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105A SER* 3.4 34.6 - - - -
107A THR* 3.1 28.2 + - - -
178A ILE* 6.1 1.0 - - + +
189A VAL* 3.6 19.1 - - + -
190A GLY* 3.9 2.0 - - - -
191A SER* 2.6 33.6 + - - +
193A LEU* 4.0 12.2 - - - +
194A GLU 2.8 11.4 + - - +
195A ILE* 3.5 15.0 - - + +
197A GLN* 1.3 78.9 - - - +
199A ARG* 1.3 67.4 + - + +
201A LYS* 3.0 3.9 + - - +
202A ILE* 2.9 40.8 + - + +
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Residues in contact with ARG 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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195A ILE* 2.9 18.2 + - - +
196A GLY* 3.5 19.9 - - - +
198A HIS* 1.3 77.3 - - + +
200A THR* 1.3 75.7 + - - +
202A ILE* 3.3 11.2 + - + +
203A GLU* 3.1 24.1 + - + +
206A ARG* 5.2 1.6 + - - +
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Residues in contact with THR 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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196A GLY 2.7 24.4 + - - -
197A GLN* 3.0 12.3 + - - -
199A ARG* 1.3 86.2 + - - +
201A LYS* 1.3 69.0 + - - +
203A GLU* 3.0 10.8 + - - +
204A GLU* 2.9 20.7 + - + +
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Residues in contact with LYS 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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171A PHE* 3.8 9.5 - - + -
175A ASN* 3.1 30.2 + - - +
178A ILE* 3.9 20.0 - - + -
193A LEU* 3.8 20.6 - - + -
197A GLN* 2.9 23.7 + - - +
198A HIS* 3.3 8.1 - - - +
200A THR* 1.3 76.2 - - - +
202A ILE* 1.3 69.6 + - + +
204A GLU* 2.8 44.1 + - - +
205A LEU 2.8 10.0 + - - -
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Residues in contact with ILE 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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107A THR* 4.0 17.7 - - + +
109A LEU* 3.9 25.4 - - + -
171A PHE* 5.5 1.3 - - + -
178A ILE* 6.0 1.1 - - + -
189A VAL* 3.9 29.4 - - + -
198A HIS* 2.9 55.3 + - + +
199A ARG* 3.4 10.1 - - + +
200A THR 3.2 0.2 - - - -
201A LYS* 1.3 77.0 - - + +
203A GLU* 1.3 56.0 + - - +
205A LEU* 2.8 28.8 + - + +
206A ARG* 2.8 29.1 + - - +
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Residues in contact with GLU 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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199A ARG* 3.1 10.9 + - + +
200A THR* 3.0 13.6 + - + +
202A ILE* 1.3 79.5 - - - +
204A GLU* 1.3 62.7 + - - +
206A ARG* 3.1 37.7 + - - +
207A GLN* 3.0 45.5 + - + +
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Residues in contact with GLU 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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171A PHE* 4.3 14.1 - - + -
174A GLN* 4.9 9.5 + - - -
175A ASN* 4.7 4.9 + - - -
200A THR* 2.9 10.2 + - + +
201A LYS* 2.8 47.8 + - - +
203A GLU* 1.3 76.7 - - - +
205A LEU* 1.3 61.8 + - - +
207A GLN* 3.2 11.5 + - + +
208A HIS* 2.9 22.8 + - + +
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Residues in contact with LEU 205 (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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109A LEU* 4.1 13.5 - - + -
168A LEU* 3.9 26.9 - - + -
171A PHE* 3.3 42.5 - - + -
180A ILE* 3.8 22.9 - - + -
187A LEU* 5.1 3.8 - - + -
189A VAL* 4.0 20.9 - - + -
201A LYS 2.8 5.9 + - - +
202A ILE* 2.8 13.3 + - + +
204A GLU* 1.3 77.4 - - - +
206A ARG* 1.3 63.3 + - - +
208A HIS* 2.9 9.8 + - - +
209A LEU* 2.8 36.8 + - + +
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Residues in contact with ARG 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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107A THR* 5.7 0.2 - - - +
109A LEU* 3.0 42.8 - - + +
199A ARG* 5.2 1.2 + - - +
202A ILE* 2.8 24.4 + - - +
203A GLU* 3.1 41.8 + - - +
205A LEU* 1.3 76.2 - - - +
207A GLN* 1.3 57.8 + - - +
209A LEU* 3.2 15.2 + - + +
210A LEU* 2.8 27.0 + - - +
214A LEU 5.0 0.7 - - - +
216A THR* 3.4 42.2 + - + +
217A PRO* 4.5 11.6 - - + +
222A GLN* 5.2 3.2 + - - +
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Residues in contact with GLN 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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203A GLU* 3.0 41.6 + - - +
204A GLU* 3.5 9.9 - - + +
206A ARG* 1.3 74.8 - - - +
208A HIS* 1.3 65.5 + - - +
210A LEU* 3.2 18.5 + - + +
211A ARG* 2.9 22.9 + - - +
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Residues in contact with HIS 208 (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* 3.2 31.5 + - + +
168A LEU* 5.6 0.2 - - - +
170A PRO* 4.6 17.4 - - + +
171A PHE* 4.6 17.2 - - + +
204A GLU* 2.9 12.8 + - + +
205A LEU* 2.9 18.6 + - - +
207A GLN* 1.3 76.9 - - - +
209A LEU* 1.3 58.7 + - - +
211A ARG* 2.8 44.2 + - - +
212A TRP* 2.9 42.4 + + - -
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Residues in contact with LEU 209 (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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109A LEU* 4.2 19.1 - - + -
111A VAL* 4.6 12.1 - - + -
164A MET* 4.4 8.7 - - - -
167A ILE* 4.3 14.6 - - + -
168A LEU* 4.0 16.6 - - + -
187A LEU* 4.2 21.5 - - + -
205A LEU* 2.8 34.6 + - + +
206A ARG* 3.3 10.1 - - + +
208A HIS* 1.3 74.4 - - - +
210A LEU* 1.3 54.7 + - - +
211A ARG 2.8 4.7 - - - -
212A TRP* 2.6 30.9 + - - +
214A LEU* 3.3 32.8 + - + +
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Residues in contact with LEU 210 (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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206A ARG 2.8 14.0 + - - +
207A GLN* 3.3 22.7 - - + +
209A LEU* 1.3 75.9 - - - +
211A ARG* 1.3 61.0 + - - +
213A GLY* 3.1 13.9 + - - -
214A LEU 4.0 7.3 + - - +
215A THR* 4.1 9.2 - - - +
216A THR* 4.1 31.6 - - - +
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Residues in contact with ARG 211 (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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4A PRO* 4.5 9.2 - - - +
207A GLN 2.9 11.0 + - - +
208A HIS* 2.8 33.5 + - - +
209A LEU 2.7 0.8 + - - -
210A LEU* 1.3 78.4 - - - +
212A TRP* 1.3 91.6 + - + +
213A GLY 3.1 3.7 + - - -
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Residues in contact with TRP 212 (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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3A SER* 2.7 29.5 + - - -
4A PRO* 3.9 32.3 - - + -
5A ILE* 4.0 22.8 - - + +
167A ILE* 3.6 46.6 - - + +
170A PRO* 6.0 3.1 - - + -
208A HIS* 2.9 56.7 + + - -
209A LEU* 2.6 13.5 + - - +
211A ARG* 1.3 99.6 - - - +
213A GLY* 1.3 48.9 + - - +
214A LEU* 3.1 10.3 + - + +
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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
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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