Contacts of the helix formed by residues 197 - 211 (chain A) in PDB entry 3T79
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 CYS 197 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLN* 2.9 3.5 - - - +
189A PRO* 3.7 2.2 - - - -
190A ASN* 3.2 44.9 - - + +
193A SER 3.2 3.4 + - - +
194A PRO* 2.8 20.1 + - + +
196A THR* 1.3 75.3 - - - +
198A PRO* 1.3 63.2 - - - +
199A ILE* 3.1 36.6 - - - -
200A PHE* 3.7 9.0 - - + -
201A THR* 2.8 30.3 + - - -
344A VAL* 4.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.0 19.0 - - + +
144A GLN* 2.8 35.1 - - + +
145A TRP* 4.5 2.7 - - - +
148A ASN* 3.9 27.1 - - - +
187A LEU* 4.4 26.5 - - + -
188A VAL 4.7 8.1 - - - +
190A ASN* 5.5 1.3 - - + +
196A THR 3.6 8.3 - - - +
197A CYS* 1.3 87.8 - - - +
199A ILE* 1.3 62.8 + - + +
201A THR* 3.2 2.0 - - - -
202A MET* 2.9 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 2.9 37.0 - - + -
187A LEU* 4.8 8.1 - - + +
188A VAL* 3.3 12.3 - - - +
189A PRO* 3.0 46.0 - - + -
197A CYS* 3.1 17.7 - - - -
198A PRO* 1.3 76.6 - - + +
200A PHE* 1.3 60.1 + - - +
201A THR 2.9 1.3 - - - -
202A MET* 2.4 38.5 + - + +
203A ALA* 2.8 11.8 + - - -
340A LEU* 5.3 5.6 - - + -
341A LEU* 5.5 3.4 - - + -
344A VAL* 4.4 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TRP* 3.9 24.2 - + - -
190A ASN 5.8 0.2 - - - +
194A PRO* 3.4 42.2 - - + +
195A PHE* 4.8 7.4 - + - -
197A CYS* 3.7 6.8 - - + +
198A PRO 3.6 0.2 - - - -
199A ILE* 1.3 79.6 - - - +
201A THR* 1.3 55.0 + - - +
203A ALA* 3.2 5.6 + - - +
204A VAL* 3.0 48.0 + - + +
344A VAL* 3.7 18.4 - - + +
345A LEU* 4.0 27.8 - - + -
348A SER* 3.6 36.6 - - - +
349A LEU* 4.3 2.2 - - + -
352A LEU* 4.1 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TRP* 3.0 25.1 - - + -
137A LEU* 3.8 10.9 - - + +
140A LEU* 3.6 21.0 - - + +
141A LEU* 3.7 33.2 - - + +
144A GLN* 3.3 8.0 + - - -
197A CYS 2.8 17.4 + - - -
198A PRO* 3.2 12.6 - - - -
200A PHE* 1.3 80.3 - - - +
202A MET* 1.3 55.9 + - - +
204A VAL* 3.4 1.9 + - - +
205A TYR* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.4 25.8 - - + -
161A LEU* 6.4 0.4 - - - -
164A LEU* 5.3 9.4 - - - -
177A LEU* 3.4 16.4 - - + -
187A LEU* 5.9 3.6 - - + -
198A PRO 2.9 6.1 + - - +
199A ILE* 2.4 48.9 + - + +
201A THR* 1.3 67.0 - - - +
203A ALA* 1.3 56.1 + - - -
205A TYR* 4.2 4.9 - - - -
206A TYR* 2.9 74.8 + - + +
233A ILE* 5.2 7.4 - - - -
337A VAL* 6.0 0.7 - - - -
341A LEU* 4.0 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ILE 2.8 13.5 + - - +
200A PHE* 3.4 14.1 - - - +
202A MET* 1.3 70.1 - - - +
204A VAL* 1.3 67.1 + - - +
206A TYR 3.3 0.5 + - - -
207A TYR* 2.9 20.4 + - - +
326A PHE* 3.4 10.1 - - + -
341A LEU* 3.6 43.0 - - + +
344A VAL* 5.1 0.4 - - + -
345A LEU* 3.6 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TRP* 4.0 14.6 - - + -
137A LEU* 3.3 26.2 - - + -
200A PHE* 3.0 29.0 + - + +
201A THR 3.9 0.9 - - - +
203A ALA* 1.3 74.0 - - - +
205A TYR* 1.3 63.9 + - - +
207A TYR* 2.8 16.3 + - - +
208A LEU* 2.8 30.2 + - + +
345A LEU* 3.5 19.7 - - + -
349A LEU* 4.8 0.2 - - + -
352A LEU* 4.5 5.6 - - + -
359A HIS* 4.0 11.9 - - + -
361A ILE* 4.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLN* 3.5 43.2 + - + -
137A LEU* 3.9 19.0 - - + +
138A LYS* 3.5 32.2 - - + +
141A LEU* 4.6 11.9 - - + -
201A THR* 2.9 19.5 + - + +
202A MET* 4.0 2.9 - - - +
204A VAL* 1.3 76.5 - - - +
206A TYR* 1.3 90.3 + + - +
208A LEU* 3.6 7.9 + - - +
209A ARG* 2.9 36.3 + - - +
233A ILE 3.7 10.8 - - - -
234A ILE* 4.1 7.9 - - + -
235A ARG* 3.3 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 3.3 28.9 - - + +
202A MET* 2.9 39.6 + - + +
203A ALA 3.8 3.1 - - - +
205A TYR* 1.3 92.6 - + - +
207A TYR* 1.3 62.0 + - - +
209A ARG* 3.0 30.6 + - - -
210A PHE* 2.9 46.9 + + + +
233A ILE* 2.7 40.5 + - - +
326A PHE* 4.1 13.3 - - + -
337A VAL* 6.0 2.2 - - + -
338A PHE* 4.8 5.4 - + - -
341A LEU* 3.4 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ALA 2.9 11.9 + - - +
204A VAL* 2.8 11.9 + - - +
206A TYR* 1.3 76.9 - - - +
208A LEU* 1.3 66.6 + - + +
211A HIS* 2.7 70.5 + + + +
212A GLY 3.0 20.8 + - - -
213A VAL* 5.7 2.0 - - + -
222A TYR* 4.5 2.2 - - - -
325A LEU* 3.7 36.2 - - + +
326A PHE* 3.6 15.8 - + + -
345A LEU* 4.7 4.5 - - + -
361A ILE* 3.8 27.4 - - + -
364A ASP* 2.8 13.9 + - + -
366A SER* 3.7 5.4 + - - -
367A LEU* 3.6 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A CYS* 4.7 4.0 - - + -
134A GLN* 3.9 39.9 + - + +
137A LEU* 4.4 4.0 - - + -
204A VAL* 2.8 57.3 + - + +
205A TYR* 4.0 7.9 - - - +
207A TYR* 1.3 78.9 - - + +
209A ARG* 1.3 60.4 + - - +
212A GLY* 3.3 23.4 - - - +
213A VAL* 4.6 15.7 - - + +
217A TYR* 5.5 6.5 - - + +
218A LYS 4.6 2.8 - - - +
219A GLY* 4.4 1.0 - - - -
359A HIS* 4.8 3.4 - - + -
360A ASP* 4.1 27.4 - - + +
361A ILE* 4.8 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLN* 3.2 17.9 - - - +
161A LEU* 5.2 1.8 - - - +
205A TYR* 2.9 38.4 + - + +
206A TYR* 3.0 21.2 + - - +
207A TYR 3.2 0.2 - - - -
208A LEU* 1.3 79.2 - - - +
210A PHE* 1.3 85.8 + - + +
218A LYS 4.6 0.2 - - - +
219A GLY 3.6 0.2 - - - -
220A ASP* 2.8 44.9 + - - +
231A ILE* 4.5 5.3 + - - +
232A PRO 2.7 23.4 + - - -
233A ILE 2.8 30.1 + - - -
234A ILE* 4.0 0.8 - - - +
235A ARG* 2.4 48.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 5.4 5.4 - - + -
206A TYR* 2.9 48.2 + + + +
209A ARG* 1.3 117.2 - - + +
211A HIS* 1.3 61.7 + - - +
212A GLY 3.2 1.1 - - - -
219A GLY* 2.9 19.6 - - - -
220A ASP* 3.8 5.8 - - + +
221A GLY* 3.1 32.4 + - - +
222A TYR* 3.6 27.2 - + + -
224A ILE* 3.6 11.2 - - + -
225A LEU* 3.3 32.1 - - + -
231A ILE* 6.2 2.5 - - + -
235A ARG* 4.8 2.5 - - - -
338A PHE* 4.7 15.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A TYR* 2.8 48.2 + + + +
210A PHE* 1.3 78.1 - - - +
212A GLY* 1.3 88.6 + - - +
214A LYS* 3.0 34.5 + - - +
219A GLY* 3.7 5.5 + - - -
222A TYR* 3.2 25.4 + - + +
325A LEU 4.4 5.1 + - - -
364A ASP* 2.2 27.2 + - - -
366A SER* 4.1 11.7 - - - -
----------------------------------------------------------
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