Contacts of the helix formed by residues 193 - 206 (chain A) in PDB entry 1C3D
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 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A GLN 3.7 3.2 + - - -
192A ARG* 1.3 72.1 - - - +
194A TYR* 1.3 57.0 + - - +
196A VAL* 3.4 1.6 + - - +
197A ALA* 2.9 31.8 + - - +
220A THR* 3.3 32.9 + - - +
227A TRP* 3.9 8.0 - - - +
228A GLU 2.9 43.4 + - - -
229A ASP* 2.8 10.4 + - - -
239A ALA* 4.7 2.0 - - - -
297A GOL 4.5 4.5 + - - -
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Residues in contact with TYR 194 (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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137A ILE 4.3 0.5 + - - -
139A GLY* 3.4 31.1 + - - -
140A LEU* 3.4 32.0 + - + +
149A ALA* 4.5 4.7 - - + -
153A PHE* 5.8 0.3 - - - -
192A ARG* 3.5 29.8 - - - +
193A SER* 1.3 76.9 - - - +
195A THR* 1.3 62.5 + - - +
197A ALA* 3.2 4.5 + - - +
198A ILE* 2.9 48.8 + - + +
229A ASP* 2.9 17.5 + - - +
235A TYR* 3.9 21.8 - - + +
238A GLU* 2.8 39.5 + - + -
239A ALA* 3.8 16.9 - - + +
242A TYR* 4.9 2.5 - + - -
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Residues in contact with THR 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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145A GLU* 2.7 27.6 + - + +
148A MET* 3.7 20.6 - - + -
149A ALA* 3.9 15.2 - - - +
190A LEU* 3.6 26.5 - - + -
192A ARG* 3.3 24.4 + - - +
194A TYR* 1.3 75.1 - - - +
196A VAL* 1.3 61.8 + - - +
198A ILE* 3.7 7.0 - - + -
199A ALA* 2.9 37.3 + - + +
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Residues in contact with VAL 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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187A TYR* 2.8 37.8 + - + +
190A LEU* 3.8 26.2 - - + -
192A ARG 3.0 21.1 + - - +
193A SER* 3.6 7.4 - - - +
194A TYR 3.3 0.2 - - - -
195A THR* 1.3 75.5 - - - +
197A ALA* 1.3 54.0 + - - +
200A GLY* 2.8 21.8 + - - -
216A LYS* 4.2 7.4 - - - +
217A PHE* 3.8 18.6 - - + -
220A THR* 3.6 22.2 - - + +
227A TRP* 4.3 2.0 - - - +
297A GOL 3.8 21.8 - - - -
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Residues in contact with ALA 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 SER 2.9 18.5 + - - +
194A TYR 3.5 4.0 - - - +
196A VAL* 1.3 74.1 - - - +
198A ILE* 1.3 60.1 + - - +
200A GLY* 3.3 1.0 + - - -
201A TYR* 3.0 28.9 + - - +
217A PHE* 4.1 11.4 - - - -
227A TRP* 4.2 6.5 - - + -
239A ALA* 3.2 33.7 - - - +
242A TYR* 3.9 7.3 - - + +
243A ALA* 4.1 11.7 - - + +
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Residues in contact with ILE 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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140A LEU* 4.3 3.6 - - + -
149A ALA* 4.0 23.6 - - - +
152A ALA* 4.0 11.4 - - + -
153A PHE* 4.0 17.5 - - + -
156A ILE* 3.5 19.8 - - + +
194A TYR* 2.9 45.2 + - + +
195A THR* 3.5 13.0 - - - +
197A ALA* 1.3 72.7 - - - +
199A ALA* 1.3 62.4 + - + +
201A TYR* 3.2 5.0 + - - +
202A ALA* 3.1 22.2 + - - +
242A TYR* 3.8 42.6 - - + +
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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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148A MET* 4.6 1.3 - - + -
152A ALA* 3.7 18.2 - - + -
183A LEU* 4.1 18.6 - - + +
187A TYR* 3.8 19.1 - - + -
190A LEU* 4.3 5.8 - - + -
195A THR* 2.9 26.3 + - + +
198A ILE* 1.3 72.5 - - + +
200A GLY* 1.3 64.9 + - - +
202A ALA* 3.8 0.7 - - - +
203A LEU* 3.0 29.5 + - - +
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Residues in contact with GLY 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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187A TYR* 3.6 15.2 - - - -
196A VAL 2.8 22.2 + - - -
197A ALA 3.7 1.1 - - - -
198A ILE 3.2 0.4 - - - -
199A ALA* 1.3 78.4 - - - +
201A TYR* 1.3 55.4 + - - +
203A LEU* 3.8 0.3 - - - +
204A ALA* 2.9 31.5 + - - +
209A LEU* 3.5 19.0 - - - +
217A PHE* 4.2 3.6 - - - -
246A ALA* 4.2 3.6 - - - -
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Residues in contact with TYR 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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156A ILE* 3.6 39.9 - - + -
160A GLU* 3.5 15.9 + - - -
197A ALA 3.0 13.6 + - - +
198A ILE 3.5 7.6 - - - +
200A GLY* 1.3 74.5 - - - +
202A ALA* 1.3 65.6 + - - +
204A ALA* 3.2 1.0 + - - -
205A GLN* 3.0 43.6 + - + +
242A TYR* 3.7 27.1 - + + +
245A LEU* 3.7 45.3 - - + +
246A ALA* 3.7 23.2 - - - +
249A GLN* 4.3 11.9 + - + -
281A MET* 5.4 0.2 - - + -
284A GLN* 4.4 2.2 + - - -
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Residues in contact with ALA 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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152A ALA* 4.0 7.0 - - - +
155A LEU* 3.9 13.2 - - + -
156A ILE* 3.9 14.3 - - + +
159A GLN* 3.0 17.9 + - - -
183A LEU* 3.6 26.2 - - + -
198A ILE 3.1 12.7 + - - +
199A ALA 3.8 2.2 - - - +
201A TYR* 1.3 77.8 - - - +
203A LEU* 1.3 63.4 - - - +
205A GLN* 3.2 17.8 - - - +
206A MET* 3.6 6.9 + - - +
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Residues in contact with LEU 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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180A GLY* 3.7 30.1 - - - +
183A LEU* 3.9 13.9 - - + -
184A GLU* 4.0 14.1 - - + +
187A TYR* 3.7 32.1 - - + -
199A ALA 3.0 15.9 + - - +
200A GLY 3.8 2.7 - - - +
202A ALA* 1.3 77.1 - - - +
204A ALA* 1.3 61.5 + - - +
206A MET* 2.9 14.2 + - - +
208A ARG* 2.9 40.4 + - + +
209A LEU* 4.1 16.6 - - + -
213A LEU* 4.0 21.1 - - + -
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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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200A GLY 2.9 21.9 + - - +
201A TYR 3.2 4.5 + - - +
203A LEU* 1.3 73.4 - - - +
205A GLN* 1.3 58.3 + - - +
207A GLY* 2.9 18.8 + - - +
209A LEU* 3.8 18.6 - - + +
246A ALA* 4.1 17.5 - - + +
249A GLN* 3.2 26.7 + - + +
250A LEU* 4.1 14.6 - - + +
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Residues in contact with GLN 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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156A ILE* 3.5 24.6 + - - +
159A GLN* 2.6 51.6 + - + +
160A GLU* 4.0 13.5 + - - +
201A TYR* 3.0 59.1 + - + +
202A ALA* 3.2 9.6 - - - +
203A LEU 3.1 0.2 - - - -
204A ALA* 1.3 76.6 - - - +
206A MET* 1.3 55.8 + - - +
207A GLY 3.4 0.4 + - - -
249A GLN* 3.8 20.6 + - - +
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Residues in contact with MET 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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155A LEU* 3.2 39.7 - - + -
159A GLN* 3.2 17.3 - - - +
176A ILE* 3.0 39.9 - - + +
177A THR* 4.9 0.9 - - - -
180A GLY* 3.5 16.4 - - - -
202A ALA 3.8 7.2 - - - +
203A LEU* 2.9 12.3 + - - +
205A GLN* 1.3 75.7 - - - +
207A GLY* 1.3 63.8 + - - +
208A ARG* 3.2 30.4 + - - +
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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