Contacts of the helix formed by residues 192 - 209 (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 PRO 192 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A MET* 3.8 46.9 - - + +
99A LEU* 5.0 0.2 - - + -
186A MET* 4.8 5.2 - - + -
190A LYS 3.8 3.1 - - - +
191A MET* 1.3 91.5 - - + +
193A ILE* 1.3 65.5 + - - +
195A VAL* 3.0 22.8 + - + +
196A TRP* 3.4 7.6 + - - -
266A GLU* 3.2 16.4 - - - +
276A LEU* 5.8 0.2 - - + -
503A THR* 3.9 25.4 - - + -
504A LEU 5.6 0.2 - - - +
528A GLU* 4.6 10.1 - - + +
530A PRO* 6.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A MET 3.6 1.6 + - - -
192A PRO* 1.3 69.3 - - - +
194A TYR* 1.3 65.8 + - - +
196A TRP* 3.2 11.1 + - + +
197A SER* 3.0 19.6 + - - -
262A GLY* 3.7 8.3 - - - +
265A ALA* 3.5 25.6 - - + -
266A GLU* 3.0 17.4 + - - +
276A LEU* 3.7 22.5 - - + +
279A TYR* 4.4 10.0 - - + +
282A MET* 3.8 32.8 - - + -
283A VAL* 4.0 23.1 - - + -
286A GLN* 3.7 20.9 - - - +
328A LYS* 4.2 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLY 2.6 27.8 + - - -
90A PHE* 3.7 3.3 - - - +
91A GLY* 3.2 24.9 + - - -
94A VAL* 4.4 6.5 - - + -
95A VAL* 4.1 13.5 - - + -
98A MET* 3.8 20.2 - - - -
193A ILE* 1.3 78.6 - - - +
195A VAL* 1.3 56.7 + - - +
197A SER* 2.7 27.1 + - - -
198A VAL* 2.9 34.2 + - + +
259A PRO 3.7 14.4 - - - -
262A GLY* 4.2 3.1 - - - +
263A ILE* 3.6 24.2 - - + -
266A GLU* 2.9 30.1 + - + +
405A TRP* 4.0 21.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL* 4.4 15.3 - - + -
98A MET* 3.8 36.6 - - + -
99A LEU* 3.9 11.0 - - + -
178A ILE* 3.7 29.0 - - + +
191A MET* 3.7 24.2 - - + -
192A PRO* 3.0 17.1 + - + +
194A TYR* 1.3 74.2 - - - +
196A TRP* 1.3 61.3 + - - +
198A VAL* 3.3 7.1 + - - +
199A PHE* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 3.1 47.2 + - + -
189A TRP* 3.9 27.6 - + - -
191A MET* 3.7 10.5 - - + -
192A PRO 3.4 10.6 + - - -
193A ILE* 3.2 14.2 + - + +
195A VAL* 1.3 77.8 - - - +
197A SER* 1.3 58.1 + - - +
199A PHE* 3.1 40.3 - + - +
200A ALA* 2.8 31.0 + - + +
279A TYR* 2.9 34.0 + + - -
283A VAL* 3.7 37.4 - - + +
286A GLN* 3.5 13.5 + - - +
287A MET* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ILE 3.0 7.7 + - - -
194A TYR* 2.7 26.3 + - - -
196A TRP* 1.3 78.1 - - - +
198A VAL* 1.3 55.8 + - - +
200A ALA* 3.8 3.0 - - - +
201A ALA* 2.9 31.4 + - - +
258A LEU* 3.3 27.4 - - - +
259A PRO* 3.5 14.9 - - - +
262A GLY* 3.6 6.6 - - - -
286A GLN* 3.4 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLY 4.7 0.2 - - - +
87A LEU* 3.9 24.9 - - + -
91A GLY* 4.8 1.8 - - - -
95A VAL* 4.2 13.5 - - + -
174A PHE* 3.9 36.1 - - + -
178A ILE* 4.6 4.5 - - + -
194A TYR* 2.9 54.6 + - + +
195A VAL 3.7 5.2 - - - +
197A SER* 1.3 77.5 - - - +
199A PHE* 1.3 58.2 + - - +
201A ALA* 3.9 0.9 - - - +
202A SER* 2.9 36.1 + - - +
259A PRO* 4.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL* 3.8 25.8 - - + -
178A ILE* 3.9 23.6 - - + -
179A TYR* 3.6 31.4 - + - -
188A LEU* 4.5 9.9 - - + -
191A MET* 5.0 2.7 - - + -
195A VAL 2.9 14.6 + - - +
196A TRP* 3.1 42.6 - + - +
198A VAL* 1.3 78.1 - - - +
200A ALA* 1.3 62.6 + - - +
202A SER* 3.3 4.6 + - - -
203A VAL* 3.0 42.9 + - + +
623A TRP* 4.5 3.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A TRP* 2.8 18.0 + - + +
197A SER* 3.8 4.5 - - - +
199A PHE* 1.3 72.6 - - - +
201A ALA* 1.3 65.0 + - - +
203A VAL* 3.4 5.5 + - - +
204A LEU* 3.1 25.5 + - - +
258A LEU* 4.0 9.0 - - + -
286A GLN* 4.3 19.7 - - + +
287A MET* 5.4 1.8 - - + +
290A VAL* 3.6 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.3 8.3 - - + -
197A SER 2.9 18.5 + - - +
198A VAL 3.9 3.4 - - - +
200A ALA* 1.3 75.9 - - - +
202A SER* 1.3 57.5 + - - +
204A LEU* 3.7 3.5 - - - +
205A ASN* 2.9 31.7 + - - +
255A VAL* 3.8 18.5 - - + +
258A LEU* 4.1 10.7 - - + +
259A PRO* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.5 2.8 - - - +
171A ASN* 3.7 27.4 + - - +
174A PHE* 3.6 22.5 - - - +
175A VAL* 3.8 20.9 - - - -
198A VAL* 2.9 22.4 + - - +
199A PHE 3.6 4.0 - - - -
201A ALA* 1.3 77.2 - - - +
203A VAL* 1.3 56.9 + - - +
205A ASN* 3.4 1.4 + - - +
206A LEU* 2.9 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL* 4.4 3.1 - - + -
199A PHE* 3.0 44.5 + - + +
200A ALA* 3.9 5.6 - - - +
202A SER* 1.3 72.6 - - - +
204A LEU* 1.3 68.3 + - - +
206A LEU* 3.2 9.2 + - - +
207A PHE* 3.2 24.2 + - + +
290A VAL* 4.9 11.7 - - + -
623A TRP* 3.7 27.8 - - + -
626A VAL* 4.8 4.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ALA 3.1 18.1 + - - +
201A ALA 3.7 3.6 - - - +
203A VAL* 1.3 78.3 - - - +
205A ASN* 1.3 61.1 + - - +
207A PHE* 3.4 4.1 + - + +
208A SER* 2.9 28.2 + - - +
251A PRO* 3.6 36.1 - - + +
254A TYR* 3.9 19.5 - - + -
255A VAL* 3.7 13.2 - - + +
258A LEU* 4.6 5.2 - - + -
289A ILE 5.0 1.1 - - - +
290A VAL* 3.9 31.0 - - + +
293A GLY* 5.0 1.8 - - - -
294A THR* 3.5 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ILE* 4.3 3.1 - - - +
87A LEU* 5.9 0.6 - - - +
167A SER* 3.8 16.1 + - - -
168A LEU* 4.3 1.4 - - - +
171A ASN* 2.8 29.8 + - - +
201A ALA 2.9 18.8 + - - +
202A SER 3.8 1.3 - - - +
203A VAL 3.2 0.2 - - - -
204A LEU* 1.3 77.2 - - - +
206A LEU* 1.3 61.6 + - - +
208A SER* 4.1 1.8 - - - -
209A LEU* 3.2 33.1 + - - +
248A TYR* 2.7 40.2 + - - -
255A VAL* 3.7 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 3.7 41.8 - - + +
171A ASN* 3.6 15.9 - - + -
172A ALA 4.1 8.3 - - - +
175A VAL* 4.5 3.4 - - + -
202A SER 2.9 29.2 + - - +
203A VAL* 3.2 9.8 + - - +
205A ASN* 1.3 76.9 - - - +
207A PHE* 1.3 62.2 + - - +
209A LEU* 4.4 2.4 + - - +
210A ALA 5.1 1.2 + - - -
623A TRP* 3.7 42.2 - - + +
624A PHE* 4.3 5.4 - - - -
626A VAL* 3.9 11.4 - - + -
627A SER* 3.1 34.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A VAL* 3.2 13.5 + - + +
204A LEU* 4.1 3.6 - - + +
206A LEU* 1.3 81.4 - - - +
208A SER* 1.3 66.7 + - - +
209A LEU 3.8 0.2 + - - -
210A ALA* 3.9 5.9 - - - +
247A PHE* 4.3 25.6 - + - -
294A THR* 4.6 20.2 - - + -
626A VAL* 4.1 17.3 - - + -
629A VAL* 4.5 6.7 - - + -
630A GLY* 3.7 37.0 - - - -
633A ALA* 5.5 1.3 - - + -
14C VAL* 4.7 8.7 - - + -
18C PHE* 4.0 33.4 - + + -
49C ALA* 4.2 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 2.9 25.7 + - - +
205A ASN* 4.1 0.2 - - - -
207A PHE* 1.3 82.8 - - - +
209A LEU* 1.3 64.0 + - - +
210A ALA 2.9 7.8 + - - -
211A GLY* 3.1 11.6 + - - -
247A PHE* 4.0 14.6 - - - -
248A TYR* 3.2 24.0 + - - +
251A PRO* 3.3 38.1 - - - +
294A THR* 4.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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