Contacts of the helix formed by residues 221 - 235 (chain A) in PDB entry 6EVO
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 HIS 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A ASP* 2.9 25.6 + - - -
214A LEU* 4.0 14.4 - - + -
215A LEU* 3.9 5.5 - - - +
218A ASP* 3.0 40.9 + - + +
219A PRO 3.2 1.8 - - - +
220A SER* 1.3 72.9 - - - +
222A GLU* 1.3 66.2 + - - +
223A ARG* 3.4 35.1 + - + -
224A ALA* 3.1 34.4 + - + +
225A GLY* 3.0 17.8 + - - -
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Residues in contact with GLU 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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220A SER 3.0 15.6 + - - +
221A HIS* 1.3 72.5 + - - +
223A ARG* 1.3 63.8 + - - +
225A GLY* 3.1 3.9 + - - +
226A GLY* 3.0 19.4 + - - -
229A ARG* 4.7 3.6 + - - -
5C ARG* 5.2 1.3 - - - +
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Residues in contact with ARG 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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192A ASP* 2.8 43.4 + - - -
221A HIS* 3.3 20.1 + - + -
222A GLU* 1.3 79.4 - - - +
224A ALA* 1.3 56.9 + - - +
226A GLY* 3.2 3.0 + - - +
227A ASN* 2.9 35.2 + - - +
302A SO4 5.3 3.0 + - - -
5C ARG* 3.1 76.9 + - + +
6C GLY 3.3 21.4 + - - -
7C PRO* 3.8 10.9 - - - +
8C PRO* 4.3 12.5 - - - +
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Residues in contact with ALA 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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211A THR* 3.6 6.2 - - + +
214A LEU* 3.6 29.4 - - + -
215A LEU* 4.3 11.4 - - + +
221A HIS* 3.1 35.6 + - + +
223A ARG* 1.3 75.9 - - - +
225A GLY* 1.3 57.7 + - - +
227A ASN* 3.3 12.2 + - - +
228A LEU* 2.9 28.4 + - - +
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Residues in contact with GLY 225 (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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215A LEU* 4.0 16.7 - - - +
221A HIS 3.0 14.2 + - - -
222A GLU* 3.1 4.4 + - - -
224A ALA* 1.3 75.2 - - - +
226A GLY* 1.3 57.5 + - - +
228A LEU* 3.3 6.8 + - - +
229A ARG* 3.0 46.3 + - - +
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Residues in contact with GLY 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 GLU 3.0 13.3 + - - -
223A ARG* 3.2 3.8 + - - -
225A GLY* 1.3 73.1 - - - +
227A ASN* 1.3 66.3 + - - +
229A ARG* 3.3 23.0 + - - +
230A TYR* 3.0 22.7 + - - +
4C PRO* 5.9 0.2 - - - -
5C ARG* 6.1 1.1 - - - -
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Residues in contact with ASN 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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192A ASP* 5.3 1.8 + - - -
195A SER* 5.3 6.7 + - - -
196A TYR* 5.4 3.4 - - - +
211A THR* 4.0 11.8 + - + -
214A LEU* 5.9 2.4 - - - +
223A ARG* 2.9 24.3 + - - +
224A ALA* 3.5 10.8 - - - +
226A GLY* 1.3 77.6 - - - +
228A LEU* 1.3 54.9 + - - +
230A TYR* 3.2 7.0 + - - +
231A PHE* 2.9 46.8 + - + -
3C GLY 4.7 0.3 - - - +
4C PRO* 3.2 13.2 - - - +
5C ARG* 2.8 49.9 + - - +
6C GLY* 5.1 0.4 - - - -
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Residues in contact with LEU 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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208A LEU* 3.6 17.0 - - + -
211A THR* 3.6 14.1 - - + +
212A ARG* 3.5 32.8 - - + +
215A LEU* 3.7 29.6 - - + -
224A ALA 2.9 16.9 + - - +
225A GLY* 3.6 7.2 - - - +
226A GLY 3.3 0.2 - - - -
227A ASN* 1.3 72.3 - - - +
229A ARG* 1.3 62.1 + - + +
231A PHE* 3.3 2.3 + - - +
232A GLU* 2.9 55.5 + - - +
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Residues in contact with ARG 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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222A GLU 4.7 3.8 + - - -
225A GLY* 3.0 28.1 + - - +
226A GLY* 3.6 25.2 - - - +
228A LEU* 1.3 77.5 - - + +
230A TYR* 1.3 61.5 + - - +
232A GLU* 4.0 6.5 - - - +
233A GLN* 3.0 27.3 + - - +
238A GLU* 4.5 1.9 - - - +
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Residues in contact with TYR 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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199A PHE* 4.0 10.4 - + - -
226A GLY 3.0 14.6 + - - +
227A ASN* 3.2 8.9 + - - +
229A ARG* 1.3 77.0 - - - +
231A PHE* 1.3 77.0 + + - +
233A GLN* 3.3 8.6 + - + +
234A LEU* 2.8 67.4 + - + +
2C PRO* 3.6 20.3 + - + -
3C GLY* 3.5 37.6 - - - +
4C PRO* 3.7 19.1 - - + -
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Residues in contact with PHE 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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195A SER* 5.0 3.8 - - - -
196A TYR* 5.9 1.3 - - - -
199A PHE* 3.3 41.3 - + + -
204A LEU* 5.2 3.4 - - + -
207A ALA* 4.0 19.5 - - + -
208A LEU* 3.9 25.3 - - + +
211A THR* 3.3 30.7 - - + -
227A ASN* 2.9 37.1 + - + +
228A LEU* 4.1 0.9 - - - +
230A TYR* 1.3 91.1 - + - +
232A GLU* 1.3 59.4 + - - +
234A LEU* 4.2 7.4 - - + -
235A LEU* 2.9 37.1 + - + +
4C PRO* 3.7 20.9 - - + -
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Residues in contact with GLU 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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208A LEU* 3.8 8.7 - - + -
212A ARG* 3.1 25.6 + - - +
228A LEU* 2.9 45.4 + - + +
229A ARG* 4.0 5.5 - - - +
231A PHE* 1.3 75.9 - - - +
233A GLN* 1.3 58.1 + - - +
236A GLU* 2.9 9.0 + - - -
237A GLU* 2.8 45.0 + - - +
238A GLU* 3.6 27.4 - - + +
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Residues in contact with GLN 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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229A ARG 3.0 16.4 + - - +
230A TYR* 3.8 7.1 - - + +
232A GLU* 1.3 76.3 - - - +
234A LEU* 1.3 65.3 + - - +
235A LEU 3.4 0.5 + - - -
236A GLU* 3.4 22.4 + - - +
238A GLU* 3.1 23.4 + - - +
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Residues in contact with LEU 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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199A PHE* 4.2 15.5 - - + -
204A LEU* 4.5 11.0 - - + -
230A TYR* 2.8 54.4 + - + +
231A PHE* 3.7 9.0 - - + +
233A GLN* 1.3 80.3 - - - +
235A LEU* 1.3 77.6 + - + +
236A GLU* 3.7 3.1 + - - +
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Residues in contact with LEU 235 (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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204A LEU* 3.7 52.5 - - + +
205A HIS* 3.9 29.1 + - + +
208A LEU* 4.0 18.6 - - + -
231A PHE* 2.9 20.7 + - + +
234A LEU* 1.3 92.8 - - + +
236A GLU* 1.3 71.8 + - - +
237A GLU* 3.2 20.0 + - + +
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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