Contacts of the helix formed by residues 203 - 220 (chain A) in PDB entry 2YG9
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 TYR 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.8 28.7 - - + -
31A GLY* 4.2 7.6 - - - -
32A ALA* 3.6 36.6 - - + -
35A HIS* 3.6 41.3 - + + -
36A LEU* 3.7 10.9 - - + +
170A PRO* 3.3 5.8 - - + -
200A TRP 2.9 15.8 + - - +
201A ALA 3.4 0.2 - - - -
202A PRO* 1.3 102.1 - - + +
204A ARG* 1.3 64.7 + - - +
205A SER 3.2 2.4 + - - -
206A LEU* 3.5 4.5 + - + +
207A ALA* 3.2 21.3 + - - +
1229A NI 4.4 3.8 - - + -
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Residues in contact with ARG 204 (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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170A PRO 3.3 0.6 + - - -
171A ASP* 2.8 56.4 + - - +
172A VAL 3.5 9.0 - - - +
173A PHE* 3.9 22.6 - - + +
197A THR* 3.2 31.3 + - - +
198A ALA* 4.6 10.9 - - - +
200A TRP* 3.8 7.4 - - + -
201A ALA* 3.7 20.5 - - - +
203A TYR* 1.3 76.6 - - - +
205A SER* 1.3 58.0 + - - +
207A ALA* 3.7 5.1 - - - +
208A SER* 2.9 34.0 + - - -
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Residues in contact with SER 205 (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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164A LEU* 3.7 15.6 - - - +
169A ARG 2.6 29.8 + - - -
170A PRO* 3.0 14.6 + - - -
172A VAL* 3.0 30.3 + - - +
204A ARG* 1.3 76.7 - - - +
206A LEU* 1.3 57.7 + - - +
208A SER* 3.2 4.3 + - - -
209A ARG* 2.9 32.7 + - - +
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Residues in contact with LEU 206 (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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26A LEU* 4.8 8.3 - - + +
29A HIS* 3.6 46.2 - - + +
32A ALA* 3.5 32.1 - - + -
33A VAL* 3.9 15.7 - - + -
36A LEU* 4.2 9.4 - - + -
52A LEU* 4.0 13.7 - - + -
170A PRO 4.3 0.8 + - - -
203A TYR* 3.5 5.5 + - + +
204A ARG 3.5 0.2 - - - -
205A SER* 1.3 76.2 - - - +
207A ALA* 1.3 59.8 + - - +
209A ARG* 3.2 14.8 + - + +
210A TYR* 2.8 52.3 + - + -
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Residues in contact with ALA 207 (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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36A LEU* 3.7 18.7 - - + +
42A LEU* 3.8 9.5 - - + +
200A TRP* 3.3 38.1 - - + -
203A TYR 3.2 17.7 + - - +
204A ARG 3.7 2.5 - - - +
206A LEU* 1.3 76.7 - - - +
208A SER* 1.3 62.7 + - - +
210A TYR* 3.1 6.2 + - - +
211A LEU* 2.9 26.6 + - - +
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Residues in contact with SER 208 (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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164A LEU* 4.2 3.6 - - - -
172A VAL 3.3 14.5 + - - -
173A PHE* 3.5 20.1 - - - -
180A LEU* 3.4 31.5 - - - +
200A TRP* 5.0 0.4 - - - -
204A ARG 2.9 23.3 + - - -
205A SER 3.3 6.1 - - - -
207A ALA* 1.3 75.2 - - - +
209A ARG* 1.3 62.4 + - - +
211A LEU* 3.1 5.2 + - - -
212A TRP* 3.0 32.9 + - - -
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Residues in contact with ARG 209 (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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29A HIS* 3.7 17.6 + - - -
52A LEU* 3.7 23.6 - - + +
53A PRO* 2.9 50.9 + - - +
55A LEU* 3.6 31.9 - - - +
164A LEU* 3.9 26.9 - - + -
165A PHE* 4.5 9.6 - - + -
205A SER* 2.9 17.8 + - - +
206A LEU* 3.2 15.3 + - - +
208A SER* 1.3 74.6 - - - +
210A TYR* 1.3 57.3 + - - +
212A TRP* 3.4 17.1 + - + +
213A ALA* 2.8 27.9 + - - +
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Residues in contact with TYR 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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29A HIS* 5.3 0.9 + - - -
33A VAL* 4.1 13.4 - - + +
36A LEU* 4.7 3.8 - - + -
42A LEU* 5.1 5.2 - - + -
45A VAL* 3.7 15.8 - - + +
46A THR* 3.7 42.1 - - + -
49A CYS* 3.9 21.1 - - + -
50A GLY 2.6 30.6 + - - -
51A GLU* 3.8 5.0 + - - -
52A LEU* 3.7 26.7 + - + -
206A LEU* 2.8 53.4 + - + +
207A ALA* 3.1 9.2 + - - +
209A ARG* 1.3 73.7 - - - +
211A LEU* 1.3 60.3 + - - +
213A ALA* 3.7 2.6 - - + +
214A ASN* 2.9 30.3 + - - +
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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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42A LEU* 4.6 14.8 - - + -
45A VAL* 5.6 2.0 - - + -
173A PHE* 4.2 3.4 - - + -
179A ALA 5.5 2.5 - - - +
180A LEU* 3.8 29.6 - - + +
183A GLY* 4.7 13.4 - - - -
184A VAL* 3.8 27.6 - - + -
187A LEU* 4.0 26.9 - - + -
188A TYR* 5.2 2.2 - - + -
200A TRP* 3.8 22.7 - - + -
207A ALA 2.9 14.8 + - - +
208A SER* 3.1 7.2 + - - +
210A TYR* 1.3 77.5 - - - +
212A TRP* 1.3 62.7 + - - +
214A ASN* 3.3 4.4 + - + +
215A SER* 3.0 22.5 + - - -
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Residues in contact with TRP 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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161A MET* 3.7 30.5 - - + -
164A LEU* 4.0 16.6 - - + -
165A PHE* 3.5 29.8 - + - -
177A ASP* 3.0 38.4 + - - -
179A ALA* 3.9 19.4 - - + +
180A LEU* 3.5 28.4 - - + +
208A SER* 3.0 25.8 + - - -
209A ARG* 3.7 13.9 - - + +
211A LEU* 1.3 76.2 - - - +
213A ALA* 1.3 64.0 + - - +
215A SER* 3.2 7.2 + - - -
216A ALA* 3.1 22.7 + - - +
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Residues in contact with ALA 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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49A CYS* 3.8 20.9 - - + -
52A LEU* 4.2 17.5 - - + -
209A ARG 2.8 18.7 + - - +
210A TYR* 3.7 8.5 - - - +
211A LEU 3.2 0.4 - - - -
212A TRP* 1.3 78.1 - - - +
214A ASN* 1.3 55.6 + - - +
216A ALA* 3.3 8.2 + - - +
217A ARG* 2.9 27.5 + - - +
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Residues in contact with ASN 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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45A VAL* 3.9 32.1 - - + +
48A LEU* 5.0 0.2 - - - +
49A CYS* 3.6 9.4 - - - -
187A LEU* 4.2 17.5 - - + +
210A TYR 2.9 16.8 + - - +
211A LEU* 3.7 7.2 - - + +
212A TRP 3.2 0.2 - - - -
213A ALA* 1.3 73.6 - - - +
215A SER* 1.3 61.4 + - - +
217A ARG* 2.9 45.9 + - - +
218A MET* 2.9 35.3 + - - +
225A LEU* 4.6 3.0 - - - +
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Residues in contact with SER 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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179A ALA* 5.4 12.6 - - - +
211A LEU 3.0 14.0 + - - -
212A TRP* 3.5 11.9 - - - -
213A ALA 3.2 0.2 - - - -
214A ASN* 1.3 79.2 - - - +
216A ALA* 1.3 51.6 + - - +
218A MET* 3.3 7.7 + - - +
219A GLN* 2.8 55.2 + - - +
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Residues in contact with ALA 216 (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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212A TRP 3.1 11.6 + - - +
213A ALA* 3.5 11.7 - - - +
215A SER* 1.3 76.6 + - - +
217A ARG* 1.3 56.1 + - - +
219A GLN* 3.2 10.5 + - - +
220A ALA* 2.9 30.8 + - - +
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Residues in contact with ARG 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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48A LEU* 3.7 54.7 - - - +
49A CYS* 4.0 9.2 - - - +
213A ALA 2.9 14.9 + - - +
214A ASN* 2.9 39.9 + - - +
216A ALA* 1.3 76.1 - - - +
218A MET* 1.3 72.1 + - - +
220A ALA* 3.3 13.4 + - - +
221A GLY 3.4 0.5 + - - -
222A GLY* 3.0 26.3 + - - -
223A ALA 2.8 42.4 + - - +
224A PRO* 4.4 0.6 - - - +
225A LEU* 4.1 6.7 - - - +
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Residues in contact with MET 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 ASN* 2.9 23.9 + - - +
215A SER* 3.6 9.6 - - - +
217A ARG* 1.3 96.9 - - - +
219A GLN* 1.3 64.0 + - + +
220A ALA 3.1 1.6 - - - -
221A GLY* 2.9 19.8 + - - -
222A GLY 3.4 20.7 + - - +
223A ALA 3.6 8.3 - - - +
224A PRO* 3.5 31.2 - - + -
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Residues in contact with GLN 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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215A SER* 2.8 43.1 + - - +
216A ALA* 3.2 9.9 + - - +
218A MET* 1.3 73.0 - - + +
220A ALA* 1.3 58.4 + - - +
221A GLY 3.7 0.2 + - - -
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Residues in contact with ALA 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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216A ALA 2.9 16.3 + - - +
217A ARG* 3.5 8.3 - - - +
218A MET 3.1 0.6 - - - -
219A GLN* 1.3 77.3 - - - +
221A GLY* 1.3 56.2 + - - +
222A GLY 3.5 1.3 - - - -
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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