Contacts of the helix formed by residues 210 - 223 (chain A) in PDB entry 1EG4
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A LYS 3.7 0.2 + - - -
209A ALA* 1.4 77.5 - - - +
211A LEU* 1.3 65.8 + - - +
212A GLU* 4.3 6.3 - - + +
213A ASP* 3.0 34.6 + - - +
214A LYS* 3.2 8.8 + - - +
299A HIS* 4.4 2.7 - - - -
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Residues in contact with LEU 211 (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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210A HIS* 1.3 71.5 - - - +
212A GLU* 1.3 62.6 + - - +
214A LYS* 3.2 8.0 + - - +
215A TYR* 3.0 66.4 + - + +
295A LEU* 4.0 14.8 - - + -
296A PRO* 3.8 24.5 - - + -
299A HIS* 3.4 43.6 + - + +
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Residues in contact with GLU 212 (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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210A HIS* 3.3 3.8 - - + +
211A LEU* 1.3 78.8 - - - +
213A ASP* 1.3 60.1 + - - +
215A TYR* 3.6 12.8 - - + +
216A ARG* 2.8 70.7 + - - +
282A LEU* 4.0 12.3 - - + +
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Residues in contact with ASP 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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126A LEU* 3.8 22.5 - - + +
209A ALA* 4.4 7.1 - - + +
210A HIS* 3.0 32.4 + - - +
212A GLU* 1.3 83.4 - - - +
214A LYS* 1.4 58.8 + - - +
216A ARG* 3.8 10.2 - - - +
217A TYR* 2.8 31.5 + - - +
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Residues in contact with LYS 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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116A GLN* 5.1 0.8 - - - +
126A LEU* 5.3 0.4 - - - -
204A ILE* 3.2 31.4 - - + +
205A SER* 2.8 30.8 + - - +
206A LEU 4.3 0.2 - - - -
207A CYS* 2.9 23.9 + - - -
209A ALA* 3.6 28.9 - - + +
210A HIS 3.2 4.9 + - - +
211A LEU* 3.4 7.4 - - - +
213A ASP* 1.4 73.1 - - - +
215A TYR* 1.3 60.1 + - - +
217A TYR* 3.3 1.6 + - - +
218A LEU* 2.8 38.9 + - + +
295A LEU* 3.8 18.8 - - + +
298A LEU* 4.9 3.0 - - - +
299A HIS* 2.8 33.4 + - + +
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Residues in contact with TYR 215 (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 LEU* 3.0 49.5 + - + +
212A GLU* 3.6 8.7 - - + +
214A LYS* 1.3 75.8 - - - +
216A ARG* 1.4 64.9 + - - +
218A LEU* 3.9 5.7 - - + -
219A PHE* 2.9 26.9 + - - +
281A PHE* 3.9 15.0 - + + -
282A LEU* 3.4 28.7 - - + -
285A MET* 3.6 50.0 + - + +
292A MET* 5.0 5.2 - - + -
295A LEU* 3.8 27.1 - - + -
296A PRO* 3.5 23.0 - - - +
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Residues in contact with ARG 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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212A GLU* 2.8 50.4 + - - +
213A ASP* 3.8 11.2 - - - +
215A TYR* 1.4 77.7 - - - +
217A TYR* 1.3 64.8 - - - +
219A PHE* 3.8 5.2 - - - +
220A LYS* 3.0 26.2 + - - +
278A ALA* 4.2 23.1 - - + +
279A ALA* 5.2 3.6 - - - +
282A LEU* 3.3 27.9 - - + +
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Residues in contact with TYR 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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126A LEU* 4.0 17.5 - - + -
130A CYS* 3.5 27.9 - - - -
133A LEU* 3.4 11.4 - - - +
200A LYS* 3.3 31.7 + - + -
204A ILE* 3.4 37.9 - - + -
213A ASP 2.8 18.2 + - - +
214A LYS* 3.6 4.3 - - - +
216A ARG* 1.3 79.4 - - - +
218A LEU* 1.3 68.1 + - + +
220A LYS* 3.2 15.2 + - - +
221A GLN* 3.1 57.3 + - + +
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Residues in contact with LEU 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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197A LEU* 5.9 0.9 - - + -
200A LYS* 4.1 3.8 - - + +
201A THR* 3.9 33.0 - - + +
204A ILE* 4.0 15.3 - - + -
205A SER* 3.8 22.9 - - - +
214A LYS* 2.8 28.4 + - + +
215A TYR* 4.1 5.8 - - + +
217A TYR* 1.3 89.6 - - + +
219A PHE* 1.3 63.6 + - - +
221A GLN* 3.1 21.6 + - + +
222A VAL* 3.6 5.2 + - - +
237A LEU* 3.7 33.9 - - + +
241A SER* 4.9 2.7 - - - +
281A PHE* 5.9 0.4 - - + -
292A MET* 5.8 4.3 - - + -
295A LEU* 5.2 7.9 - - + -
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Residues in contact with PHE 219 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A TYR 2.9 18.4 + - - +
216A ARG* 3.8 5.6 - - - +
218A LEU* 1.3 75.7 - - - +
220A LYS* 1.3 61.1 + - - +
222A VAL* 3.1 6.1 + - + +
223A ALA* 2.8 39.5 + - + +
227A GLY* 3.6 15.9 - - - -
229A CYS* 3.3 39.5 - - + -
234A LEU* 5.5 0.7 - - + -
237A LEU* 4.0 9.5 - - + +
276A ILE* 3.6 11.7 - - + -
277A GLU 3.5 15.5 - - - -
278A ALA* 3.3 31.2 - - + -
281A PHE* 3.5 44.6 - + + -
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Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A ARG 3.0 14.9 + - - +
217A TYR* 3.4 19.5 - - - +
219A PHE* 1.3 82.9 - - - +
221A GLN* 1.3 75.5 + - - +
222A VAL 3.2 1.0 + - - -
223A ALA* 3.5 20.2 + - + +
224A SER 5.2 0.2 - - - +
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Residues in contact with GLN 221 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A ASN* 2.8 35.3 + - - +
197A LEU* 3.7 16.4 - - + -
200A LYS* 2.8 31.0 + - + -
217A TYR* 3.1 66.7 + - + +
218A LEU* 3.1 15.5 + - + +
220A LYS* 1.3 91.4 - - - +
222A VAL* 1.3 61.5 + - - +
223A ALA 4.7 1.1 - - - +
233A ARG* 5.6 0.3 + - - -
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Residues in contact with VAL 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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197A LEU* 3.7 32.5 - - + -
218A LEU 3.9 8.1 - - - +
219A PHE* 3.4 15.3 - - + +
221A GLN* 1.3 79.5 - - - +
223A ALA* 1.3 63.2 + - - +
229A CYS* 4.0 13.2 - - - -
233A ARG* 3.0 65.3 + - + +
234A LEU* 4.8 0.4 - - - -
236A LEU* 4.0 7.1 - - + +
237A LEU* 3.9 26.5 - - + +
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Residues in contact with ALA 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 PHE* 2.8 40.8 + - + +
220A LYS* 3.5 14.9 + - + +
221A GLN 4.7 1.2 - - - +
222A VAL* 1.3 82.2 - - - +
224A SER* 1.3 71.7 + - - +
227A GLY* 3.9 7.4 - - - -
228A PHE 3.4 17.5 - - - +
229A CYS* 4.6 3.6 - - - -
233A ARG* 3.6 5.2 + - - +
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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