Contacts of the helix formed by residues 181 - 200 (chain A) in PDB entry 1CF5
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 LEU 181 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLU* 5.3 10.3 - - + +
179A PRO 3.4 3.6 + - - +
180A ASN* 1.3 84.6 - - - +
182A ALA* 1.3 60.0 + - - +
183A ILE 3.5 1.2 - - - +
184A ILE* 3.8 16.1 - - + +
185A SER* 3.1 27.4 + - - -
214A ILE* 3.3 35.3 - - + +
215A LYS 3.5 6.7 - - - +
216A PRO 4.2 2.7 - - - +
217A THR 4.4 0.9 - - - -
218A GLY* 3.4 22.2 - - - +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TYR* 3.6 22.4 - - + -
180A ASN* 2.6 21.1 + - - +
181A LEU* 1.3 72.2 - - - +
183A ILE* 1.3 56.2 + - - +
185A SER* 3.2 3.6 + - - -
186A LEU* 2.9 38.1 + - + +
213A LEU* 4.9 0.8 - - - +
214A ILE 3.2 17.9 - - - +
215A LYS* 4.7 0.4 - - - -
216A PRO* 4.0 15.9 - - + +
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Residues in contact with ILE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 5.0 3.4 - - + -
164A TYR* 4.5 6.1 - - + -
165A ILE* 3.8 30.9 - - + +
168A HIS* 3.6 28.9 - - + -
177A PHE* 3.6 31.9 - - + -
179A PRO* 4.5 14.4 - - + -
180A ASN* 3.3 25.8 + - - +
182A ALA* 1.3 76.2 - - - +
184A ILE* 1.3 60.8 + - - +
186A LEU* 3.5 8.7 + - - +
187A GLU* 3.0 44.9 + - - +
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ARG* 3.8 30.1 - - + +
121A GLU* 3.4 37.9 - - + +
179A PRO* 3.4 28.7 - - + +
181A LEU* 3.8 19.9 + - + +
182A ALA 3.3 0.8 - - - -
183A ILE* 1.3 77.4 - - - +
185A SER* 1.3 54.1 + - - +
187A GLU* 3.1 15.3 - - - +
188A ASN* 2.7 53.4 + - - +
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU 3.1 16.9 + - - -
182A ALA 3.2 4.7 + - - -
184A ILE* 1.3 76.3 - - - +
186A LEU* 1.3 67.1 + - - +
188A ASN* 4.4 5.2 - - - +
189A GLN* 2.9 41.4 + - - +
213A LEU* 3.3 32.7 - - - +
214A ILE* 3.4 21.7 + - - +
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PHE* 3.1 44.7 - - + -
164A TYR* 3.3 39.9 - - + -
165A ILE* 4.3 5.8 - - + -
182A ALA* 2.9 29.2 + - + +
183A ILE* 3.8 7.0 - - - +
185A SER* 1.3 70.2 - - - +
187A GLU* 1.3 65.0 + - - +
189A GLN* 3.0 2.6 + - - -
190A TRP 3.0 22.2 + - - -
193A LEU* 4.8 1.1 - - + -
213A LEU* 3.6 21.1 - - + -
230A VAL* 4.4 16.4 - - + -
234A ASN* 3.9 14.4 - - - +
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Residues in contact with GLU 187 (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 TYR* 4.1 10.8 - - + -
120A ARG* 2.8 33.6 + - - +
154A GLN* 2.5 35.1 - - - +
158A GLU* 3.7 33.7 - - - +
161A ARG* 5.5 1.9 + - - -
162A PHE* 4.2 1.1 - - - -
165A ILE* 4.0 8.2 - - + +
183A ILE* 3.0 37.3 + - - +
184A ILE* 3.1 11.5 - - - +
186A LEU* 1.3 76.1 - - - +
188A ASN* 1.3 55.1 + - - +
189A GLN 2.7 12.8 + - - -
190A TRP* 3.6 11.4 + - - +
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Residues in contact with ASN 188 (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 TYR* 4.8 4.2 - - - +
120A ARG* 2.5 31.4 + - - +
184A ILE* 2.7 36.7 + - - +
185A SER* 3.6 6.8 + - - +
187A GLU* 1.3 70.9 - - - +
189A GLN* 1.3 69.8 + - - +
190A TRP 5.5 0.4 - - - -
191A SER* 6.0 0.9 - - - -
192A ALA* 5.9 0.2 - - - +
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Residues in contact with GLN 189 (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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185A SER* 2.9 30.7 + - - +
186A LEU* 3.0 4.1 + - - +
187A GLU 2.7 8.1 + - - -
188A ASN* 1.3 87.9 - - - +
190A TRP* 1.3 59.4 + - - +
191A SER* 3.0 9.0 + - - -
192A ALA* 3.2 15.2 + - + +
193A LEU* 3.0 27.0 + - + +
211A VAL* 3.3 28.0 - - + -
212A ASP 2.9 27.7 + - - -
213A LEU* 4.4 4.9 - - + +
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Residues in contact with TRP 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 4.5 0.7 - - + -
68A ASN* 3.6 21.8 - - - -
69A VAL* 4.1 8.5 - - + -
70A TYR* 4.5 8.3 - + - -
158A GLU* 5.2 0.9 - - - +
161A ARG* 3.2 65.3 - - + +
162A PHE* 3.3 30.7 - + + -
186A LEU 3.0 6.9 + - - +
187A GLU 3.6 7.6 + - - +
188A ASN 5.5 0.2 - - - -
189A GLN* 1.3 71.6 - - - +
191A SER* 1.3 69.6 + - - +
193A LEU* 4.4 4.7 - - + -
194A SER* 4.2 6.6 + - - -
235A ILE* 4.4 7.9 - - + -
237A LEU 2.6 27.3 + - - -
238A LEU 4.2 2.7 - - - -
239A LEU* 3.5 49.1 - - + -
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Residues in contact with SER 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ASN 6.0 0.4 - - - -
189A GLN 3.0 2.1 + - - -
190A TRP* 1.3 77.9 - - - +
192A ALA* 1.3 56.1 + - - +
194A SER* 3.4 20.3 + - - +
195A LYS* 2.6 37.2 + - - +
239A LEU* 3.4 23.8 - - - +
244A SER* 3.9 2.4 - - - -
247A ASP* 4.0 12.3 + - - -
249A ASN* 3.3 11.4 + - - +
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Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLN* 3.2 20.7 + - + +
191A SER* 1.3 77.2 - - - +
193A LEU* 1.3 58.6 + - - +
195A LYS 3.3 0.3 + - - -
196A GLN* 2.9 36.0 + - - +
211A VAL* 4.1 17.3 - - + -
249A ASN* 3.0 36.0 + - + +
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PHE* 3.7 22.0 - - + -
186A LEU* 4.8 4.7 - - + -
189A GLN* 3.0 18.3 + - + +
190A TRP* 4.4 3.6 - - + -
191A SER 4.4 2.2 - - - +
192A ALA* 1.3 77.8 - - - +
194A SER* 1.3 55.1 + - - +
196A GLN* 4.0 1.2 - - - +
197A ILE* 3.0 39.0 + - + +
207A PHE* 4.3 10.3 - - + -
211A VAL* 3.5 35.9 - - + -
213A LEU* 4.8 2.5 - - + -
223A VAL* 4.3 13.9 - - + -
230A VAL* 3.7 15.5 - - + -
231A VAL* 5.1 0.7 - - + -
235A ILE* 3.4 34.8 - - + -
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Residues in contact with SER 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A TRP* 4.2 9.9 + - - -
191A SER* 3.1 17.4 + - - +
193A LEU* 1.3 75.1 - - - +
195A LYS* 1.3 65.0 + - - +
197A ILE* 4.1 1.0 - - - +
198A PHE* 3.1 25.5 + - - +
235A ILE* 6.0 0.3 - - - +
238A LEU* 4.0 18.1 - - - +
239A LEU* 3.0 51.1 + - - +
244A SER* 4.0 5.1 + - - -
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Residues in contact with LYS 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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191A SER 2.6 16.8 + - - +
192A ALA* 3.6 4.9 - - - +
194A SER* 1.3 74.0 - - - +
196A GLN* 1.3 70.2 + - - +
198A PHE* 3.6 1.7 + - - +
199A LEU* 3.1 41.4 + - + +
208A ARG* 2.9 38.9 - - - +
244A SER* 3.2 35.6 - - - +
245A THR* 3.9 19.6 + - - +
247A ASP 3.1 4.6 + - - -
248A GLU* 3.1 16.6 + - - +
249A ASN* 2.9 35.4 - - - +
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Residues in contact with GLN 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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192A ALA 2.9 18.0 + - - +
193A LEU 4.2 0.7 - - - +
195A LYS* 1.3 85.3 - - - +
197A ILE* 1.3 55.7 + - - +
198A PHE 3.2 0.9 - - - -
199A LEU* 3.7 6.0 - - - +
200A ALA* 2.7 38.0 + - - +
207A PHE* 3.5 33.5 - - + -
208A ARG* 3.5 18.5 - - + +
209A ASN* 2.7 51.8 + - - +
211A VAL* 4.7 3.3 - - + +
249A ASN* 2.5 33.6 + - - +
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Residues in contact with ILE 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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31A VAL* 3.8 13.1 - - + +
32A TYR* 3.6 37.3 - - + -
34A ILE* 4.0 20.2 - - + -
193A LEU* 3.0 19.0 + - + +
194A SER 4.3 0.2 - - - +
196A GLN* 1.3 74.4 - - - +
198A PHE* 1.3 62.8 + - - +
200A ALA* 3.4 11.8 + - - -
201A GLN 3.8 0.5 + - - -
207A PHE* 4.2 16.4 - - + -
226A VAL* 5.2 1.1 - - + -
231A VAL* 3.7 22.7 - - + -
235A ILE* 3.7 29.8 - - + -
238A LEU* 4.0 16.2 - - + -
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Residues in contact with PHE 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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29A HIS* 6.3 1.3 - + - -
31A VAL* 4.6 6.7 - - + +
36A LEU* 4.6 20.9 - - + -
194A SER 3.1 19.9 + - - +
195A LYS* 3.6 4.9 - - - +
197A ILE* 1.3 74.3 - - - +
199A LEU* 1.3 86.1 + - + +
201A GLN* 2.8 46.3 + - - +
202A ASN* 4.7 9.0 + - - -
238A LEU* 5.0 4.6 - - + +
239A LEU 6.0 0.2 - - - +
241A SER* 4.2 28.7 - - - -
244A SER* 4.8 6.3 - - - +
245A THR* 6.0 5.8 - - + -
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Residues in contact with LEU 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 LYS* 3.1 31.2 + - + +
196A GLN* 3.7 13.0 - - - +
198A PHE* 1.3 90.9 - - + +
200A ALA* 1.3 51.6 + - - +
201A GLN 2.5 19.1 + - - -
202A ASN* 2.7 33.5 + - - +
203A GLN* 3.6 15.4 - - - +
208A ARG* 3.4 53.6 - - + +
245A THR* 5.6 6.3 - - - +
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Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 2.5 29.7 + - + -
196A GLN 2.7 24.2 + - - +
197A ILE* 3.8 9.4 - - - +
198A PHE 3.3 1.0 - - - -
199A LEU* 1.3 69.1 - - - +
201A GLN* 1.3 52.0 + - - +
202A ASN 3.4 0.2 - - - -
203A GLN* 4.3 3.4 - - - -
205A GLY 2.8 32.6 + - - +
206A LYS 3.3 28.0 + - - +
207A PHE* 4.2 4.9 - - + -
226A VAL* 4.8 0.9 - - + -
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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