Contacts of the helix formed by residues 205 - 221 (chain A) in PDB entry 1CM8
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 GLN 205 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A HIS* 3.1 70.1 + - + +
148A GLY* 3.8 12.5 - - - -
149A ILE 3.1 23.2 + - - +
150A ILE* 3.8 11.9 - - + -
178A ALA* 3.9 21.4 - - + +
204A THR* 1.3 77.6 - - - +
206A THR* 1.3 61.4 + - + +
207A VAL 3.1 1.8 + - - -
208A ASP* 3.2 8.5 + - - +
209A ILE* 3.9 1.3 + - - -
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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
----------------------------------------------------------
195A GLU* 4.5 0.7 + - - -
204A THR* 2.7 24.4 + - - +
205A GLN* 1.3 77.7 - - - +
207A VAL* 1.3 60.5 + - - +
209A ILE* 2.8 26.0 + - + +
210A TRP 3.1 8.3 + - - -
296A ALA* 3.6 35.2 + - - +
299A ARG* 3.8 31.1 + - + +
300A VAL 4.3 8.7 - - - +
301A THR* 5.1 9.6 - - + -
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Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 4.2 10.8 - - + -
152A ARG* 4.8 2.0 - - + -
187A VAL* 4.4 18.5 - - + +
191A TYR 4.7 0.7 - - - +
193A ALA* 4.4 6.5 + - + +
195A GLU* 3.4 23.1 - - - +
196A VAL* 4.4 10.5 - - + -
203A TYR* 3.4 31.0 - - + -
204A THR 3.0 19.2 + - - +
206A THR* 1.3 77.1 - - - +
208A ASP* 1.3 74.8 + - - +
210A TRP* 3.1 8.9 + - - +
211A SER* 3.1 28.5 + - - -
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Residues in contact with ASP 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.8 9.8 - - + +
145A HIS* 2.9 29.4 + - + +
150A ILE* 3.7 4.3 - - - +
151A HIS* 2.9 32.3 + - - +
152A ARG* 2.9 27.3 + - - -
153A ASP 4.3 2.3 + - - -
154A LEU* 3.9 9.5 + - + +
187A VAL* 5.7 0.2 - - - +
205A GLN 3.2 8.7 + - - +
206A THR 3.1 0.4 - - - -
207A VAL* 1.3 87.6 - - - +
209A ILE* 1.3 59.1 + - - +
211A SER* 3.6 7.1 + - - -
212A VAL* 3.1 32.4 + - - +
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Residues in contact with ILE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 4.1 10.5 - - + -
141A LEU* 3.7 22.0 - - + -
145A HIS* 4.9 2.7 - - + -
205A GLN 4.5 3.1 - - - +
206A THR* 2.8 20.5 + - + +
208A ASP* 1.3 75.5 - - - +
210A TRP* 1.3 65.8 + - - +
212A VAL* 3.3 4.4 + - + +
213A GLY* 3.0 18.9 + - - -
291A MET* 3.8 36.5 - - + +
299A ARG* 4.3 2.9 - - + -
300A VAL* 3.5 28.5 - - + +
301A THR* 4.0 2.9 - - - -
302A ALA* 3.6 29.6 - - + +
305A ALA* 5.0 1.3 - - + -
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Residues in contact with TRP 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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191A TYR 3.3 20.2 - - - -
192A ARG 3.3 10.3 + - - -
193A ALA* 3.3 23.6 - - + -
194A PRO* 3.7 20.0 - - + -
206A THR 3.1 8.2 + - - +
207A VAL 3.2 11.0 - - - +
209A ILE* 1.3 76.7 - - - +
211A SER* 1.3 54.0 + - - +
213A GLY* 2.7 24.3 + - - -
214A CYS* 3.1 26.8 + - - -
226A PHE* 3.5 25.5 - + - -
234A GLN* 6.0 0.2 - - - +
238A ILE* 3.7 24.5 - - + -
242A THR* 4.1 6.1 - - + -
291A MET 4.3 3.1 + - - -
292A LEU* 3.3 51.9 - - + +
293A VAL 3.5 11.9 - - - -
294A LEU* 4.6 0.9 - - + -
299A ARG* 3.4 23.6 - - - +
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Residues in contact with SER 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 3.3 36.7 + - - -
187A VAL* 3.7 12.8 - - - +
191A TYR* 2.8 28.1 + - - -
207A VAL 3.1 11.1 + - - -
208A ASP* 3.8 10.4 + - - -
210A TRP* 1.3 78.0 - - - +
212A VAL* 1.3 57.2 + - - +
214A CYS* 3.2 4.0 + - - +
215A ILE* 2.8 35.8 + - - +
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 4.3 14.4 - - + -
137A MET* 4.5 20.0 - - + -
138A LEU* 4.1 21.5 - - + -
141A LEU* 3.9 19.3 - - + -
154A LEU* 4.0 13.5 - - + -
208A ASP 3.1 20.6 + - - +
209A ILE* 3.6 7.2 - - - +
210A TRP 3.2 0.2 - - - -
211A SER* 1.3 75.1 - - - +
213A GLY* 1.3 57.6 + - - +
215A ILE* 3.7 8.8 - - + +
216A MET* 2.8 27.0 + - - +
291A MET* 4.1 16.4 - - - -
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Residues in contact with GLY 213 (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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209A ILE 3.0 9.9 + - - -
210A TRP 2.7 15.1 + - - -
212A VAL* 1.3 70.4 - - - +
214A CYS* 1.3 53.7 + - - -
216A MET 3.3 0.2 + - - -
217A ALA* 2.8 36.2 + - - +
288A LEU* 3.4 20.1 - - - +
291A MET* 4.2 9.1 - - - -
292A LEU* 4.1 15.5 - - - -
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Residues in contact with CYS 214 (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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190A TRP 3.8 16.6 - - - +
191A TYR* 3.7 21.3 - - + -
210A TRP* 3.1 44.4 + - - -
211A SER 3.6 5.6 - - - +
213A GLY* 1.3 74.6 - - - +
215A ILE* 1.3 59.5 + - - +
217A ALA* 3.4 6.4 + - - +
218A GLU* 2.9 30.1 + - - +
225A LEU* 4.4 13.8 + - + +
226A PHE* 4.1 18.2 - - - -
292A LEU* 4.3 1.8 - - - +
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Residues in contact with ILE 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.9 27.6 - - + -
120A MET* 4.8 0.2 - - + -
137A MET* 4.4 8.1 - - - -
154A LEU* 3.4 37.7 - - + -
155A LYS* 3.5 10.8 - - - +
156A PRO* 4.2 10.8 - - + -
159A LEU* 4.1 13.9 - - + -
191A TYR* 3.7 19.1 - - + -
211A SER 2.8 30.2 + - - +
212A VAL* 3.7 8.7 - - + +
214A CYS* 1.3 74.3 - - - +
216A MET* 1.3 64.7 + - - +
218A GLU* 3.1 7.5 + - - +
219A MET* 3.0 24.5 + - + +
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Residues in contact with MET 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ILE* 4.7 3.1 - - + -
134A VAL* 3.5 28.7 - - + -
137A MET* 5.5 0.8 - - - -
212A VAL 2.8 20.4 + - - +
213A GLY 3.8 3.1 - - - +
215A ILE* 1.3 73.6 - - - +
217A ALA* 1.3 62.3 + - - +
219A MET* 3.3 12.5 + - - +
220A ILE* 3.2 37.2 + - + +
284A ALA* 4.1 20.4 - - + +
287A LEU* 4.1 7.0 - - + -
288A LEU* 3.8 14.6 - - + -
291A MET* 3.6 23.6 - - + -
310A TYR* 3.3 45.8 - - + +
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Residues in contact with ALA 217 (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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213A GLY 2.8 18.8 + - - +
214A CYS 3.6 4.3 - - - +
216A MET* 1.3 76.9 - - - +
218A GLU* 1.3 56.8 + - - +
220A ILE* 3.3 3.9 + - - +
221A THR* 3.1 36.0 + - - +
225A LEU* 3.7 31.6 - - + -
277A LEU* 4.7 7.2 - - + -
288A LEU* 4.1 20.8 - - + +
292A LEU* 5.0 0.4 - - + -
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Residues in contact with GLU 218 (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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120A MET* 4.4 16.8 - - + +
156A PRO* 4.0 12.0 - - - +
191A TYR* 2.5 37.0 + - - -
214A CYS 2.9 15.9 + - - +
215A ILE* 3.1 6.0 + - - +
217A ALA* 1.3 73.9 - - - +
219A MET* 1.3 61.4 + - - +
221A THR* 4.0 0.2 - - - -
222A GLY* 2.8 35.7 + - - +
223A LYS 3.3 26.5 - - - +
224A THR* 4.1 21.3 + - - +
225A LEU* 5.0 1.0 + - - +
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Residues in contact with MET 219 (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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116A LEU* 3.9 11.7 - - + -
120A MET* 3.8 28.3 - - + +
124A LYS* 4.4 11.4 - - - +
125A LEU* 3.5 22.5 + - + +
130A ILE* 3.9 27.4 - - + +
133A LEU* 3.4 47.3 - - + -
134A VAL* 3.8 20.0 - - - -
137A MET* 3.9 11.9 - - + -
215A ILE 3.0 20.0 + - - +
216A MET* 3.3 8.9 + - - +
218A GLU* 1.3 78.2 - - - +
220A ILE* 1.3 62.3 + - - +
222A GLY* 4.3 2.3 + - - -
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Residues in contact with ILE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LYS* 3.7 10.9 - - - -
130A ILE* 4.1 25.0 - - + +
216A MET* 3.2 32.5 + - + +
217A ALA* 3.7 4.5 - - - +
218A GLU 3.2 0.8 - - - -
219A MET* 1.3 78.0 - - - +
221A THR* 1.3 69.4 + - + +
277A LEU* 5.0 3.1 - - + -
279A ASN* 4.0 17.5 + - - +
280A ALA* 3.6 39.3 - - + +
284A ALA* 4.5 6.7 - - + -
288A LEU* 3.9 25.8 - - + -
310A TYR* 5.6 0.4 - - - +
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Residues in contact with THR 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LYS* 3.6 15.4 + - - -
217A ALA* 3.1 16.3 + - + +
220A ILE* 1.3 77.4 - - + +
222A GLY* 1.3 69.3 + - - +
223A LYS* 3.0 31.2 + - - +
225A LEU* 5.9 4.7 - - + -
276A ILE* 4.7 8.7 - - + +
277A LEU* 3.9 33.9 - - + -
278A THR* 5.4 6.3 - - - +
279A ASN* 5.3 3.6 - - - +
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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
------------------------------------------------------------
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