Contacts of the helix formed by residues 206 - 219 (chain A) in PDB entry 2Y92
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 PHE 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A ALA* 3.9 14.8 - - + -
102A ASP* 3.9 12.8 - - + -
103A LEU* 3.7 44.2 - - + -
106A TYR* 3.3 50.3 - + + -
146A LEU* 5.2 3.6 - - + -
178A LEU* 4.0 18.2 - - + -
203A ASP 3.3 17.8 + - - +
204A GLY* 3.7 13.7 - - - -
205A GLY* 1.3 74.5 - - - +
207A ARG* 1.3 63.3 - - - +
209A VAL* 3.3 8.9 - - - +
210A LYS* 3.3 17.0 + - - +
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Residues in contact with ARG 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 3.7 12.6 + - - +
202A PRO* 3.7 35.2 + - - +
203A ASP* 3.0 35.4 + - - +
205A GLY 3.3 0.8 - - - -
206A PHE* 1.3 77.6 - - - +
208A GLN* 1.4 59.9 + - - +
210A LYS* 3.4 5.1 + - - +
211A GLU* 3.1 48.0 + - + +
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Residues in contact with GLN 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A TYR* 4.1 7.5 + - - +
197A VAL* 3.6 22.1 - - + +
198A ASP* 3.9 14.1 + - - +
201A GLY* 3.7 11.9 - - - -
202A PRO* 3.1 47.5 - - + +
205A GLY* 3.6 7.3 + - - -
206A PHE 3.5 0.2 - - - -
207A ARG* 1.4 74.5 - - + +
209A VAL* 1.4 60.3 + - - +
211A GLU* 3.5 15.9 + - - +
212A ALA* 3.1 27.4 + - - +
215A ARG* 4.2 3.2 + - - +
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 3.7 28.3 - - + -
107A LEU* 4.6 5.2 - - + -
144A VAL* 4.7 12.1 - - + -
176A ILE* 3.8 23.6 - - + +
178A LEU* 4.0 19.7 - - + -
197A VAL* 3.8 15.0 - - + -
205A GLY 3.3 17.7 + - - +
206A PHE* 3.3 17.0 - - - +
208A GLN* 1.4 72.8 - - - +
210A LYS* 1.4 59.4 + - - +
212A ALA* 3.4 8.8 + - - +
213A VAL* 3.1 32.7 + - - +
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Residues in contact with LYS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 3.4 35.8 + - + +
107A LEU* 3.4 40.6 - - + -
109A GLY 3.8 5.3 + - - -
110A SER* 3.1 27.2 + - - +
129A ILE* 3.9 13.5 - - + -
206A PHE 3.3 17.0 + - - +
207A ARG* 3.6 5.8 - - - +
208A GLN 3.4 0.2 - - - -
209A VAL* 1.4 75.3 - - - +
211A GLU* 1.4 59.0 + - - +
213A VAL* 3.3 4.1 + - - +
214A MET* 3.0 49.4 + - + +
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Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ARG* 3.1 37.4 + - + +
208A GLN* 3.8 18.4 - - - +
209A VAL 3.4 0.2 - - - -
210A LYS* 1.4 73.3 - - - +
212A ALA* 1.4 56.9 + - - +
214A MET* 3.4 19.4 + - + +
215A ARG* 2.9 51.8 + - - +
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Residues in contact with ALA 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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174A CYS* 4.7 1.4 - - - -
176A ILE* 3.9 24.0 - - + +
195A TYR* 4.1 19.7 - - + +
208A GLN 3.1 18.0 + - - +
209A VAL* 3.5 8.1 - - - +
210A LYS 3.3 0.2 - - - -
211A GLU* 1.4 74.5 - - - +
213A VAL* 1.4 62.3 + - - +
215A ARG* 3.6 18.9 + - - +
216A TYR* 3.4 21.0 + - - +
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Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP* 4.9 2.7 - - + +
88A VAL* 3.7 44.0 - - + -
107A LEU* 4.3 6.5 - - + -
129A ILE* 4.2 11.7 - - + -
142A CYS* 4.1 16.3 - - + -
144A VAL* 4.9 1.1 - - + -
176A ILE* 3.8 15.5 - - + -
209A VAL 3.1 18.6 + - - +
210A LYS* 3.5 8.5 - - - +
211A GLU 3.3 0.2 - - - -
212A ALA* 1.4 74.8 - - - +
214A MET* 1.4 62.4 + - - +
216A TYR* 3.2 5.5 + - - +
217A LEU* 3.1 40.8 + - + +
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Residues in contact with MET 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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129A ILE* 3.8 21.1 - - + -
210A LYS* 3.0 48.1 + - + +
211A GLU* 3.4 20.8 + - + +
213A VAL* 1.4 76.4 - - - +
215A ARG* 1.4 59.5 + - + +
217A LEU* 3.6 12.8 + - + +
218A GLN* 3.3 29.6 + - - +
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Residues in contact with ARG 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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195A TYR* 3.7 30.1 + - - -
208A GLN* 4.2 4.9 + - - +
211A GLU* 2.9 38.9 + - + +
212A ALA* 3.6 22.9 - - - +
214A MET* 1.4 75.5 - - - +
216A TYR* 1.4 60.5 + - - +
218A GLN* 3.6 20.6 + - - +
219A THR* 3.7 7.3 + - - -
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Residues in contact with TYR 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 HIS* 3.8 29.3 + - + -
142A CYS* 3.7 13.9 - - - -
173A GLY* 3.6 35.3 + - - -
174A CYS* 3.6 26.2 + - + -
212A ALA 3.4 9.3 + - - +
213A VAL 3.2 9.2 + - - +
215A ARG* 1.4 76.7 - - - +
217A LEU* 1.3 64.1 + - + +
218A GLN 3.2 0.7 - - - -
219A THR* 3.2 29.7 + - + -
220A LEU* 3.8 28.2 + - + +
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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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81A ARG* 3.6 38.8 - - + +
87A ASP* 3.5 29.8 - - + +
125A PRO* 6.0 0.9 - - - +
129A ILE* 4.2 12.3 - - + -
141A HIS* 4.5 7.9 - - + -
142A CYS* 5.9 0.9 - - - -
213A VAL* 3.1 40.3 + - + +
214A MET* 3.9 11.2 - - + +
215A ARG 3.4 0.4 - - - -
216A TYR* 1.3 75.9 - - + +
218A GLN* 1.4 64.6 + - - +
219A THR 3.3 0.2 - - - -
220A LEU* 3.5 41.1 + - + +
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Residues in contact with GLN 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 MET* 3.3 26.9 + - - +
215A ARG* 3.6 11.7 - - - +
216A TYR 3.2 0.6 - - - -
217A LEU* 1.4 81.0 - - - +
219A THR* 1.3 62.2 + - - +
220A LEU 3.5 5.2 + - - +
221A SER 5.5 1.4 - - - -
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Residues in contact with THR 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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79A SER* 5.3 1.2 - - - +
215A ARG 3.7 9.4 + - - -
216A TYR* 3.2 24.5 + - + -
218A GLN* 1.3 77.4 - - - +
220A LEU* 1.3 60.8 + - - +
221A SER 3.8 3.9 + - - +
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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