Contacts of the helix formed by residues 209 - 226 (chain A) in PDB entry 2YEV
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 209 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ILE* 6.4 0.2 - - + -
164A GLY* 3.9 24.0 - - - +
167A SER* 4.7 7.6 - - - +
168A LEU* 3.6 38.8 - - + -
205A ASN* 3.2 21.6 + - - +
206A LEU 4.8 1.1 - - - +
207A PHE 3.5 1.0 - - - -
208A SER* 1.3 76.1 + - - +
210A ALA* 1.3 64.2 + - - +
212A LEU* 2.9 25.4 + - + +
213A THR* 2.9 24.8 + - - +
248A TYR* 3.3 41.1 - - + +
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Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU 5.1 1.2 + - - -
207A PHE 3.9 11.1 + - - +
208A SER* 2.9 0.6 + - - +
209A LEU* 1.3 76.3 - - - +
211A GLY* 1.3 57.4 + - - +
213A THR* 3.2 9.2 + - - -
214A ALA* 2.8 33.8 + - - +
247A PHE* 5.4 2.7 - - + -
627A SER 4.8 2.2 + - - +
630A GLY 3.2 37.7 - - - +
631A LEU* 3.3 13.5 - - + +
634A ILE* 3.8 8.6 - - + +
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Residues in contact with GLY 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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208A SER 3.1 11.7 + - - -
210A ALA* 1.3 77.5 - - - +
212A LEU* 1.3 57.1 + - - +
214A ALA* 3.7 0.4 - - - +
215A ALA* 3.0 21.8 + - - +
244A PHE* 3.1 37.1 - - - +
247A PHE* 4.3 11.1 - - - -
248A TYR 4.2 4.3 - - - -
634A ILE* 4.2 9.5 - - - +
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Residues in contact with LEU 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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79A PHE* 3.8 29.2 - - + -
141A PHE* 4.2 8.5 - - + -
160A ILE* 3.9 17.3 - - + -
209A LEU* 2.9 16.6 + - + +
211A GLY* 1.3 73.3 - - - +
213A THR* 1.3 66.1 + - - +
215A ALA* 4.4 2.0 - - + +
216A THR* 2.6 52.2 + - - +
244A PHE 4.8 0.4 - - - -
245A PHE* 4.0 33.7 - - + +
248A TYR* 3.5 38.2 - - + +
249A SER* 5.0 2.0 - - - +
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Residues in contact with THR 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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160A ILE* 5.8 1.6 - - - -
161A LEU* 4.3 18.4 - - + +
164A GLY* 5.9 0.5 - - - -
168A LEU* 5.6 2.1 - - - +
209A LEU* 2.9 30.2 + - - +
210A ALA* 3.6 11.3 - - - -
212A LEU* 1.3 76.7 - - - +
214A ALA* 1.3 53.6 + - - +
216A THR* 3.8 3.2 - - - -
217A LEU* 2.8 45.5 + - + +
631A LEU* 4.1 22.7 - - + -
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Residues in contact with ALA 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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210A ALA 2.8 17.3 + - - +
211A GLY 3.7 4.3 - - - +
213A THR* 1.3 75.3 - - - +
215A ALA* 1.3 65.8 + - - +
217A LEU* 4.0 4.7 - - - +
218A LEU* 3.0 32.5 + - - +
244A PHE* 4.2 12.3 - - + -
631A LEU* 4.5 4.4 - - + +
634A ILE* 4.1 13.2 - - + -
635A LEU* 3.9 29.2 - - + -
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Residues in contact with ALA 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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141A PHE* 4.4 4.0 - - + -
211A GLY 3.0 18.1 + - - +
212A LEU* 3.3 4.0 + - - +
214A ALA* 1.3 75.4 - - - +
216A THR* 1.3 60.7 + - - +
218A LEU* 3.6 3.0 + - - +
219A VAL* 3.1 30.7 + - - +
230A PHE* 5.1 0.2 - - - -
241A PHE* 3.6 28.6 - - + -
244A PHE* 4.0 8.9 - - + +
245A PHE* 3.8 23.8 - - + +
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Residues in contact with THR 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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141A PHE* 3.7 12.7 - - - -
157A LEU* 3.4 46.4 - - + +
160A ILE* 3.4 17.6 - - + +
161A LEU* 3.9 13.0 - - + -
212A LEU* 2.6 39.4 + - - +
213A THR 3.8 2.2 - - - -
215A ALA* 1.3 74.7 - - - +
217A LEU* 1.3 65.5 + - - +
219A VAL 3.4 1.2 + - - -
220A LEU* 3.1 22.6 + - - +
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Residues in contact with LEU 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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161A LEU* 4.5 23.3 - - + +
213A THR* 2.8 28.9 + - + +
214A ALA* 4.0 4.9 - - - +
216A THR* 1.3 72.8 - - - +
218A LEU* 1.3 59.6 + - + +
220A LEU* 3.3 8.7 + - + +
221A LEU* 2.8 62.0 + - + +
631A LEU* 6.1 1.3 - - + -
635A LEU* 5.6 4.3 - - + -
731A THR* 5.4 8.7 - - + -
735A LEU* 4.5 28.5 - - + -
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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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214A ALA* 3.0 19.3 + - - +
215A ALA 4.0 0.4 - - - +
217A LEU* 1.3 78.6 - - + +
219A VAL* 1.3 63.7 + - - +
221A LEU* 3.7 11.6 + - + +
222A GLU* 3.1 24.4 + - - +
227A LEU* 4.0 7.0 - - + +
228A SER* 5.4 0.3 - - - -
229A TRP* 3.7 44.1 + - + +
230A PHE* 3.7 34.6 - - + -
244A PHE* 3.7 21.3 - - + -
635A LEU* 4.4 8.5 - - + -
731A THR* 3.7 21.8 - - + +
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Residues in contact with VAL 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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141A PHE* 4.1 5.4 - - + -
143A TYR* 4.6 8.5 - - + -
146A SER* 3.8 28.0 - - - +
147A ALA* 4.5 5.4 - - + +
153A VAL* 4.9 0.2 - - + -
157A LEU* 3.8 19.5 - - + -
215A ALA 3.1 18.8 + - - +
217A LEU 3.4 0.2 - - - -
218A LEU* 1.3 76.2 - - - +
220A LEU* 1.3 58.0 + - - +
222A GLU* 3.3 8.0 + - - +
223A ARG* 3.0 40.5 + - + +
230A PHE* 4.3 6.7 - - + -
241A PHE* 3.5 28.3 - - + -
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Residues in contact with LEU 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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154A ASP* 4.0 27.1 - - + +
157A LEU* 3.6 25.2 - - + +
158A ALA* 5.0 5.8 - - + +
161A LEU* 3.9 26.2 - - + -
216A THR 3.1 17.7 + - - +
217A LEU* 3.6 9.6 - - + +
219A VAL* 1.3 73.8 - - - +
221A LEU* 1.3 66.6 + - + +
223A ARG* 3.2 3.3 + - - +
224A LYS* 2.9 48.6 + - + +
569A PHE* 5.9 1.6 - - + -
572A VAL* 4.3 21.5 - - + -
573A ALA* 5.8 0.4 - - - -
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Residues in contact with LEU 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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217A LEU* 2.8 49.9 + - + +
218A LEU* 3.9 19.1 - - + +
220A LEU* 1.3 74.6 - - + +
222A GLU* 1.3 58.1 + - - +
224A LYS* 4.8 2.9 - - + -
225A ILE* 2.8 56.5 + - + +
226A GLY 3.3 1.4 + - - -
227A LEU* 3.6 21.5 + - + +
731A THR* 4.7 14.8 - - + +
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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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143A TYR* 2.6 42.1 + - - -
147A ALA* 4.2 12.1 - - + +
218A LEU 3.1 14.8 + - - +
219A VAL* 3.5 6.5 - - - +
220A LEU 3.2 0.4 - - - -
221A LEU* 1.3 78.9 - - - +
223A ARG* 1.3 62.6 + - - +
226A GLY* 3.0 22.2 + - - -
227A LEU 3.2 16.1 + - - +
228A SER* 2.5 35.5 + - - -
230A PHE* 4.4 6.2 - - - -
231A ASN* 4.7 1.7 - - - +
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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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146A SER 2.7 34.9 + - - -
147A ALA* 3.3 33.1 + - + +
148A GLN 4.2 0.2 - - - -
149A SER 3.0 29.3 + - - +
150A GLU* 5.0 1.2 - - - +
151A SER 4.0 11.5 + - - -
153A VAL* 3.8 20.2 - - - +
154A ASP* 2.8 40.9 + - - +
157A LEU* 4.5 3.4 - - - -
219A VAL* 3.0 25.1 + - - +
220A LEU* 3.8 4.3 - - - +
222A GLU* 1.3 76.9 - - - +
224A LYS* 1.3 63.9 + - + +
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Residues in contact with LYS 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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154A ASP* 3.3 29.6 + - - -
220A LEU* 2.9 33.3 + - + +
221A LEU* 4.3 3.1 - - + +
223A ARG* 1.3 84.3 - - + +
225A ILE* 1.3 70.8 + - + +
226A GLY 3.8 0.4 - - - -
572A VAL* 2.9 20.3 + - + -
573A ALA 2.9 24.7 + - - -
574A ALA 4.6 0.4 - - - -
575A LEU 3.0 16.3 + - - +
576A PRO* 4.9 2.8 - - + +
577A VAL* 4.0 35.6 + - + +
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Residues in contact with ILE 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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221A LEU* 2.8 42.6 + - + +
224A LYS* 1.3 84.9 - - + +
226A GLY* 1.3 59.0 + - - +
227A LEU* 4.0 17.7 - - + +
577A VAL* 4.0 25.6 - - + +
578A PRO* 5.7 1.6 - - + -
720A TRP* 2.9 47.3 + - + -
721A GLN* 4.5 4.9 - - - +
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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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221A LEU 3.3 0.2 + - - -
222A GLU* 3.0 24.4 + - - -
223A ARG 4.8 0.2 - - - -
224A LYS 3.8 0.2 - - - -
225A ILE* 1.3 77.4 - - - +
227A LEU* 1.3 62.2 + - - +
228A SER* 3.5 5.4 + - - -
720A TRP* 3.8 3.0 - - - -
721A GLN* 3.2 32.4 - - - +
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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