Contacts of the helix formed by residues 179 - 199 (chain A) in PDB entry 2Z98
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 GLY 179 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ILE 4.4 2.3 + - - -
177A ALA 3.3 6.7 + - - -
178A TYR* 1.2 80.5 - - - +
180A PRO* 1.4 67.5 - - - +
181A GLU 3.4 2.2 - - - -
182A MET 3.1 4.5 + - - -
183A ALA* 2.8 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLY* 1.4 80.9 - - - +
181A GLU* 1.3 71.7 + - - +
183A ALA* 4.5 5.8 - - + +
184A ALA* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLY 3.4 1.2 + - - -
180A PRO* 1.3 83.7 - - - +
182A MET* 1.3 61.1 + - + +
184A ALA* 3.7 4.6 - - - +
185A LYS* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 3.8 29.2 - - + -
174A GLU 4.3 2.4 - - - +
175A GLY* 3.5 19.4 - - - +
178A TYR* 3.8 31.4 + - + +
179A GLY 3.1 8.1 + - - +
181A GLU* 1.3 76.8 - - + +
183A ALA* 1.2 67.8 + - - +
185A LYS* 3.3 19.6 + - - +
186A ALA* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLN* 5.8 1.1 - - - +
175A GLY 4.0 4.4 + - - -
176A ILE* 3.9 24.9 - - + +
179A GLY 2.8 21.8 + - - +
180A PRO* 4.2 5.4 - - + +
182A MET* 1.2 72.8 - - - +
184A ALA* 1.3 62.8 + - - +
186A ALA* 3.2 8.1 + - - +
187A GLN* 3.0 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A PRO 3.0 19.8 + - - +
181A GLU* 3.8 4.7 - - - +
183A ALA* 1.3 77.6 - - - +
185A LYS* 1.3 62.9 + - - +
187A GLN* 3.4 12.8 + - - +
188A SER* 3.0 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLU 2.9 19.2 + - - +
182A MET* 3.7 21.1 - - - +
184A ALA* 1.3 71.5 - - - +
186A ALA* 1.3 62.8 + - - +
188A SER* 3.2 5.0 + - - -
189A ASP* 2.5 65.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PHE 4.3 0.4 - - - +
173A ALA* 4.1 8.6 - - - +
174A GLU 3.2 34.3 - - - +
176A ILE* 3.8 20.2 - - + -
182A MET 3.0 10.2 + - - +
183A ALA 3.2 8.5 + - - +
185A LYS* 1.3 77.4 - - - +
187A GLN* 1.3 56.9 + - - +
189A ASP* 3.9 4.2 - - - +
190A ALA* 3.0 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLN* 3.0 36.0 + - - +
19A GLN* 5.3 7.7 - - - +
20A LEU* 4.8 9.2 - - + -
176A ILE* 5.1 2.7 - - + +
183A ALA* 3.0 30.7 + - - +
184A ALA* 3.4 10.5 + - - +
186A ALA* 1.3 71.1 - - - +
188A SER* 1.3 59.4 + - - +
190A ALA* 3.4 4.6 + - - +
191A LYS* 2.9 58.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ALA 3.0 17.8 + - - -
185A LYS* 3.8 4.9 - - - -
187A GLN* 1.3 77.2 - - - +
189A ASP* 1.3 66.4 + - - +
191A LYS* 3.8 5.7 - - - +
192A ALA* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PHE 5.2 1.1 - - - +
185A LYS* 2.5 57.5 + - - +
186A ALA* 4.1 4.3 - - - +
188A SER* 1.3 82.9 + - - +
190A ALA* 1.3 56.6 + - - +
192A ALA* 3.5 6.7 + - - +
193A ALA* 3.0 28.1 + - - +
203A EDO 3.6 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.8 28.9 - - + -
171A VAL* 3.7 18.5 - - + +
172A PHE 3.7 16.1 + - - +
173A ALA* 4.2 1.8 - - + -
186A ALA 3.0 19.3 + - - +
187A GLN 3.9 0.2 - - - +
189A ASP* 1.3 74.2 - - - +
191A LYS* 1.3 58.5 + - - +
193A ALA* 3.3 2.9 + - - +
194A ILE* 2.9 34.3 + - - +
203A EDO 4.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN* 5.3 14.6 + - - +
20A LEU* 3.8 16.2 - - + +
23A TYR* 3.8 53.7 - - + +
187A GLN* 2.9 48.3 + - + +
188A SER* 3.9 5.2 - - - +
190A ALA* 1.3 69.8 - - - +
192A ALA* 1.2 59.3 + - - +
194A ILE* 3.3 4.3 + - - +
195A ASP* 2.8 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A SER* 3.0 19.0 + - - +
189A ASP* 3.8 7.2 - - - +
190A ALA 3.3 0.2 - - - -
191A LYS* 1.2 74.3 - - - +
193A ALA* 1.3 62.8 + - - +
195A ASP* 3.3 12.2 + - - +
196A SER* 3.0 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PHE 5.4 0.7 - - - +
171A VAL* 4.2 12.1 - - + -
189A ASP 3.0 17.2 + - - +
190A ALA 3.3 4.5 + - - +
192A ALA* 1.3 75.4 - - - +
194A ILE* 1.3 60.7 + - - +
196A SER* 2.7 24.5 + - - +
197A ILE* 3.1 16.7 + - + +
203A EDO 3.9 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.8 40.4 - - + +
23A TYR* 3.9 17.0 - - + -
24A PHE* 3.6 39.5 - - + -
27A GLN* 5.1 0.9 - - + -
137A ILE* 4.2 14.8 - - + -
171A VAL* 4.1 18.6 - - + -
190A ALA 2.9 17.9 + - - +
191A LYS* 3.5 7.6 - - - +
193A ALA* 1.3 68.8 - - - +
195A ASP* 1.3 68.9 + - - +
197A ILE* 3.0 9.9 + - - +
198A VAL* 2.9 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 2.5 33.7 + - - -
27A GLN* 4.2 9.9 - - - +
31A LYS* 5.9 0.2 - - - +
191A LYS* 2.8 18.2 + - - +
192A ALA* 3.3 14.1 + - - +
194A ILE* 1.3 75.0 - - - +
196A SER* 1.3 63.9 + - - +
198A VAL* 3.4 6.6 + - - +
199A SER* 2.9 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ALA 3.0 13.1 + - - -
193A ALA* 2.7 24.3 + - - -
195A ASP* 1.3 74.9 - - - +
197A ILE* 1.3 62.4 + - - +
199A SER* 3.7 6.0 - - - -
200A ALA* 3.2 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 4.2 13.5 - - + -
28A TRP* 4.6 7.6 - - + -
135A ILE* 3.9 34.1 - - + -
169A LYS* 3.9 34.3 - - + +
170A PHE 5.6 0.7 - - - +
171A VAL* 3.5 31.6 - - + -
193A ALA* 3.1 13.1 + - + +
194A ILE* 3.0 8.6 + - - +
196A SER* 1.3 81.1 - - - +
198A VAL* 1.3 63.7 + - - +
199A SER 3.2 0.9 + - - -
200A ALA* 3.5 18.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
24A PHE* 4.1 11.9 - - + +
27A GLN* 3.7 30.5 - - + +
28A TRP* 3.9 27.9 - - + +
31A LYS* 3.4 31.3 + - + -
32A HIS* 2.8 33.0 + - - +
194A ILE* 2.9 36.7 + - + +
195A ASP* 4.0 4.7 - - - +
197A ILE* 1.3 74.8 - - - +
199A SER* 1.3 57.4 + - - +
200A ALA 3.7 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS* 3.5 26.9 - - - +
32A HIS* 5.6 0.2 - - - -
195A ASP* 2.9 22.4 + - - +
196A SER* 3.7 6.8 + - - -
198A VAL* 1.3 79.0 - - - +
200A ALA* 1.3 60.4 + - - +
----------------------------------------------------------
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