Contacts of the helix formed by residues 215 - 234 (chain A) in PDB entry 2CVP
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 THR 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ILE* 3.8 23.1 - - + -
210A SER* 4.1 4.0 + - - -
212A THR* 3.5 6.8 + - - -
213A PHE 3.8 1.0 - - - -
214A THR* 1.3 75.7 + - - +
216A GLN* 1.3 70.3 + - - +
217A GLU* 3.6 19.5 - - - +
218A THR* 3.3 7.4 + - - +
219A ILE* 3.0 23.6 + - - +
519A LYS* 5.0 11.3 + - - +
801A ACT 2.6 33.5 + - + +
389B HIS* 4.0 11.2 - - + +
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Residues in contact with GLN 216 (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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214A THR 3.1 7.0 + - - +
215A THR* 1.3 72.9 - - - +
217A GLU* 1.3 68.4 + - - +
219A ILE* 5.2 2.0 - - - -
220A THR* 2.8 42.0 + - - +
522A ALA* 5.6 1.4 - - - +
523A LYS* 3.5 27.2 - - - +
526A GLU* 3.0 40.3 + - - +
424B ILE* 3.6 28.9 - - + +
428B ASN* 4.5 4.9 + - - -
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Residues in contact with GLU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE* 4.1 10.5 - - + -
185A SER 4.1 12.8 - - - +
187A ILE* 3.4 38.2 - - + +
215A THR* 3.3 6.1 - - - +
216A GLN* 1.3 81.5 + - - +
218A THR* 1.3 59.5 + - - +
220A THR* 3.8 1.2 - - - -
221A ASN* 2.9 35.9 + - - -
385B THR* 3.1 26.4 + - - +
388B GLN* 4.2 4.2 - - - +
389B HIS* 2.7 39.7 + - - -
424B ILE* 5.6 1.8 - - + -
428B ASN* 4.5 7.6 - - - +
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Residues in contact with THR 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ILE* 3.5 33.8 - - + +
156A GLY* 3.6 17.3 - - - +
157A ILE* 3.6 16.8 + - - +
185A SER 5.9 0.4 - - - -
208A ILE* 4.0 14.8 - - + -
209A ALA 3.6 14.2 + - - +
210A SER* 4.2 7.9 - - - -
215A THR* 3.3 16.4 + - - +
217A GLU* 1.3 77.6 - - - +
219A ILE* 1.3 61.0 + - + +
221A ASN* 3.5 3.0 + - - +
222A ALA* 2.8 29.3 + - - +
801A ACT 4.8 1.4 + - - -
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Residues in contact with ILE 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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208A ILE* 4.4 8.7 - - + -
210A SER* 5.6 0.2 - - - +
213A PHE* 3.6 63.0 - - + +
214A THR* 4.3 4.5 - - - +
215A THR 3.0 16.6 + - - +
216A GLN* 4.4 2.5 - - - +
218A THR* 1.3 79.3 - - + +
220A THR* 1.3 60.5 + - - +
222A ALA* 3.2 4.1 + - + +
223A GLU* 2.8 57.3 + - + +
256A PHE* 4.6 9.4 - - + -
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Residues in contact with THR 220 (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 ILE* 3.6 23.1 - - + -
216A GLN* 2.8 36.4 + - - +
219A ILE* 1.3 76.2 - - - +
221A ASN* 1.3 63.1 + - - +
223A GLU* 3.2 10.3 + - - +
224A THR* 2.9 25.2 + - - -
417B ARG* 3.7 2.6 + - - +
420B LEU* 3.9 25.4 - - + -
421B HIS* 3.9 13.7 - - + +
424B ILE* 3.9 9.6 - - + +
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Residues in contact with ASN 221 (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 ILE* 3.5 21.0 - - + +
184A VAL* 3.8 14.8 - - + +
185A SER* 3.7 12.7 + - - +
186A ASN 3.0 27.3 + - - +
187A ILE* 4.2 1.4 - - - +
188A ASP 5.3 0.3 - - - +
192A ILE* 3.0 28.1 + - + +
217A GLU 2.9 22.8 + - - +
218A THR* 4.9 0.6 - - - +
220A THR* 1.3 75.8 - - - +
222A ALA* 1.3 57.7 + - - +
224A THR 3.3 1.0 + - - -
225A ALA* 2.9 25.3 + - - +
421B HIS* 3.1 25.8 + - - -
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Residues in contact with ALA 222 (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 ILE* 4.1 10.9 - - - +
208A ILE* 3.7 33.2 - - + -
218A THR 2.8 21.2 + - - +
219A ILE* 3.5 7.4 - - - +
220A THR 3.2 0.2 - - - -
221A ASN* 1.3 72.9 - - - +
223A GLU* 1.3 58.0 + - - +
225A ALA* 3.3 3.5 + - - +
226A LYS* 2.8 29.5 + - - +
243A PHE* 4.2 1.6 - - - -
256A PHE* 3.8 19.6 - - + -
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Residues in contact with GLU 223 (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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219A ILE* 2.8 38.3 + - + +
220A THR* 3.2 7.8 + - - +
222A ALA* 1.3 72.3 - - - +
224A THR* 1.3 56.4 + - - +
226A LYS* 3.4 9.8 + - - +
227A GLU* 2.9 29.8 + - - +
256A PHE* 3.7 22.4 - - + -
417B ARG* 4.0 19.8 + - - +
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Residues in contact with THR 224 (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 ILE* 4.0 21.5 - - + -
196A LEU* 4.8 6.1 - - + -
220A THR 2.9 8.6 + - - -
221A ASN 3.5 8.5 - - - -
222A ALA 3.3 0.2 - - - -
223A GLU* 1.3 73.3 - - - +
225A ALA* 1.3 63.1 + - - +
227A GLU* 3.3 5.1 + - - +
228A TRP* 3.0 23.7 + - + +
416B ILE* 4.1 8.5 - - + -
417B ARG* 2.8 37.6 + - + +
421B HIS* 2.7 31.0 + - - +
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Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ILE* 3.9 20.4 - - + -
192A ILE* 3.9 7.6 - - + +
196A LEU* 4.5 4.3 - - + -
206A PHE* 3.9 22.4 - - + -
221A ASN 2.9 14.0 + - - +
222A ALA 3.4 8.3 - - - +
224A THR* 1.3 76.3 - - - +
226A LYS* 1.3 57.0 + - - +
228A TRP* 3.3 10.3 + - - +
229A PHE* 2.9 29.3 + - - +
243A PHE* 3.9 8.0 - - + -
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Residues in contact with LYS 226 (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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222A ALA 2.8 19.7 + - - +
223A GLU* 3.7 9.6 - - - +
224A THR 3.3 0.2 - - - -
225A ALA* 1.3 72.6 - - - +
227A GLU* 1.3 53.2 + - - +
229A PHE* 3.3 0.5 + - - +
230A LEU* 2.8 56.6 + - + +
239A VAL* 4.3 23.1 - - + +
243A PHE* 3.6 17.4 - - + -
256A PHE* 3.1 49.4 + - + +
257A GLY* 5.1 2.0 + - - -
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Residues in contact with GLU 227 (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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223A GLU 2.9 18.1 + - - +
224A THR* 3.7 5.7 - - - +
225A ALA 3.3 0.2 - - - -
226A LYS* 1.3 76.3 - - - +
228A TRP* 1.3 58.5 + - - +
230A LEU* 3.3 5.9 + - - +
231A GLU* 3.0 50.8 + - - +
417B ARG* 3.2 35.2 + - - +
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Residues in contact with TRP 228 (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 LEU* 3.6 52.7 + - + +
199A LEU* 3.6 29.6 - - + -
200A SER 3.7 5.8 - - - -
201A PRO* 3.4 45.6 - - + +
204A SER* 4.6 0.9 - - - -
206A PHE* 3.6 25.6 - + - -
224A THR* 3.0 14.1 + - + +
225A ALA 3.4 11.7 - - - +
227A GLU* 1.3 77.8 - - - +
229A PHE* 1.3 79.5 + - + +
231A GLU* 3.5 13.7 + - - +
232A ALA* 3.6 10.6 + - - +
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Residues in contact with PHE 229 (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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144A TYR* 3.7 10.5 - + - -
201A PRO* 3.6 26.5 - - + -
206A PHE* 5.0 3.1 - + + -
225A ALA 2.9 18.2 + - - +
226A LYS 3.6 3.1 - - - +
228A TRP* 1.3 88.1 - + + +
230A LEU* 1.3 68.9 + - + +
232A ALA* 3.1 8.0 + - - +
233A ALA* 2.9 45.0 + - + +
238A ALA* 3.6 26.9 - - + -
239A VAL* 3.8 11.9 - - + -
242A HIS* 3.3 44.6 - + + -
243A PHE* 4.0 22.0 - + + -
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Residues in contact with LEU 230 (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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226A LYS* 2.8 45.5 + - + +
227A GLU* 4.1 5.6 - - - +
229A PHE* 1.3 80.9 - - + +
231A GLU* 1.3 61.6 + - - +
233A ALA* 4.8 0.2 - - + -
234A LYS* 2.8 32.2 + - - +
235A ASP 3.6 39.3 - - - +
236A PRO* 3.9 9.2 - - + -
239A VAL* 4.0 16.4 - - + -
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Residues in contact with GLU 231 (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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227A GLU* 3.0 44.3 + - - +
228A TRP* 3.6 10.0 + - - +
229A PHE 3.3 0.2 - - - -
230A LEU* 1.3 76.8 - - - +
232A ALA* 1.3 56.6 + - - +
234A LYS* 3.1 25.3 + - - -
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Residues in contact with ALA 232 (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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144A TYR* 3.6 17.9 + - - +
201A PRO* 3.6 28.7 - - + -
228A TRP 3.6 3.5 + - - +
229A PHE 3.1 8.5 + - - +
231A GLU* 1.3 80.0 - - - +
233A ALA* 1.3 62.6 + - - +
234A LYS* 3.4 16.6 + - - +
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Residues in contact with ALA 233 (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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144A TYR* 3.6 32.6 - - + -
229A PHE* 2.9 48.9 + - + +
230A LEU* 4.5 0.7 - - - -
232A ALA* 1.3 72.1 - - - +
234A LYS* 1.3 70.8 + - - +
235A ASP* 3.2 10.0 + - - +
238A ALA* 4.1 7.6 - - + -
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Residues in contact with LYS 234 (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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230A LEU* 2.8 28.5 + - - +
231A GLU 3.1 22.9 + - - +
232A ALA* 3.4 13.5 + - - +
233A ALA* 1.3 72.6 - - - +
235A ASP* 1.3 58.7 + - - +
236A PRO* 4.4 3.0 - - - +
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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