Contacts of the strand formed by residues 195 - 209 (chain A) in PDB entry 2PBH
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 MET 195 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 4.2 13.0 + - - -
46A LEU* 5.0 7.0 - - + -
175A SER* 3.3 36.6 - - - +
176A VAL 3.3 16.6 - - - +
177A TYR* 3.6 27.8 - - + +
194A GLU* 1.3 73.5 - - - +
196A MET* 1.3 62.3 + - - +
197A GLY* 3.9 24.0 - - - +
198A GLY 4.6 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 5.9 0.2 - - - -
35A MET* 3.6 27.1 - - + -
38A LEU 4.2 6.7 - - - +
39A LYS* 3.7 44.5 - - - +
42A CYS* 3.7 18.1 - - - +
176A VAL* 2.7 29.6 + - + -
178A SER* 3.8 28.9 - - - +
181A LEU* 3.9 21.1 - - + -
194A GLU* 3.2 31.6 + - - +
195A MET* 1.3 75.6 - - - +
197A GLY* 1.3 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A CYS* 3.9 6.7 - - - -
175A SER* 3.7 1.7 - - - -
176A VAL* 2.7 35.4 + - - +
195A MET* 3.1 21.5 - - - +
196A MET* 1.3 83.1 - - - +
198A GLY* 1.3 58.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A CYS* 3.1 15.8 + - - +
44A THR* 2.9 41.3 + - - -
46A LEU* 3.5 24.5 - - - +
174A PHE 3.9 2.7 - - - -
195A MET* 4.6 0.4 - - - +
197A GLY* 1.3 73.0 - - - -
199A HIS* 1.3 60.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLN* 4.3 0.4 - - - -
29A CYS* 3.4 33.3 - - + +
41A LEU 3.5 7.9 + - - -
42A CYS* 4.1 3.5 - - - -
44A THR* 4.0 5.1 - - - +
46A LEU* 5.4 0.2 - - - +
174A PHE* 3.1 48.3 + + + +
176A VAL* 3.3 24.5 - - + -
197A GLY 4.0 0.4 + - - -
198A GLY* 1.3 74.3 - - - +
200A ALA* 1.3 74.3 + - - +
201A ILE* 3.8 11.4 - - + +
219A ASN* 2.7 32.7 + - - -
220A SER* 3.8 6.2 + - - -
221A TRP* 3.7 31.8 - + - -
----------------------------------------------------------
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
----------------------------------------------------------
29A CYS* 3.6 18.5 - - - +
30A TRP* 3.9 1.8 - - - -
44A THR* 3.1 29.5 + - + +
76A PRO* 4.3 1.8 - - + -
171A GLU* 3.6 20.6 - - - +
172A GLY 3.4 18.8 - - - +
173A ALA* 4.2 0.9 - - - +
199A HIS* 1.3 89.0 + - - +
201A ILE* 1.3 70.7 + - - +
220A SER* 4.7 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY* 4.5 7.9 - - - -
171A GLU* 3.2 9.2 - - - +
172A GLY* 2.8 43.2 + - - +
173A ALA 4.0 1.1 - - - +
174A PHE* 3.7 19.3 - - + -
199A HIS* 3.8 20.6 - - + +
200A ALA* 1.3 84.4 - - - +
202A ARG* 1.3 60.3 + - - +
203A ILE* 4.0 5.2 - - + -
217A VAL* 3.3 22.0 - - + -
218A ALA 3.9 13.5 - - - +
219A ASN* 4.1 3.8 - - - -
220A SER* 5.6 0.2 - - - +
231A PHE* 4.0 14.4 - - + -
242A ILE* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR 4.2 4.5 + - - -
17A ILE* 2.9 33.7 + - - +
19A GLU 2.9 28.1 + - - -
33A GLY* 4.7 9.2 - - - -
36A GLU* 4.1 24.1 + - + +
37A ALA* 4.0 18.8 - - + +
40A ASP* 2.9 23.2 + - - -
169A PRO* 3.4 25.3 - - + +
170A VAL 3.3 11.4 - - - +
201A ILE* 1.3 78.2 - - - +
203A ILE* 1.3 60.1 + - - +
204A LEU* 3.1 17.6 - - - +
217A VAL* 3.6 2.2 - - - -
218A ALA* 2.8 56.1 + - - +
230A PHE* 5.0 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ILE* 5.2 4.7 - - + -
164A ILE* 3.8 11.5 - - + +
169A PRO* 3.4 3.5 - - - +
170A VAL* 2.9 47.2 + - + +
172A GLY* 4.9 7.0 - - - +
201A ILE* 4.0 12.6 - - + -
202A ARG* 1.3 72.1 - - - +
204A LEU* 1.3 62.6 + - - +
205A GLY 4.0 2.5 - - - +
215A TRP* 3.7 39.9 - - + -
216A LEU 3.7 10.3 - - - +
217A VAL* 3.7 14.1 - - + -
242A ILE* 3.9 35.0 - - + +
246A VAL* 4.9 5.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
6A ASP* 4.3 3.5 - - - +
7A ALA* 2.8 30.6 + - + +
8A ARG* 3.7 31.0 - - + +
17A ILE* 3.9 3.1 - - + -
164A ILE* 3.9 11.0 - - - +
169A PRO* 3.7 24.2 - - + -
202A ARG* 3.1 35.7 - - - +
203A ILE* 1.3 74.4 - - - +
205A GLY* 1.3 59.5 + - - +
216A LEU* 2.9 24.7 + - + +
217A VAL 4.0 0.4 - - - -
218A ALA* 3.6 20.9 - - + +
230A PHE* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 3.3 14.8 - - - -
164A ILE* 4.3 2.2 - - - +
203A ILE* 3.8 3.2 - - - +
204A LEU* 1.3 81.2 - - - +
206A TRP* 1.3 78.3 + - - +
215A TRP* 3.3 12.0 - - - -
216A LEU* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 4.2 2.0 - - + -
2A PRO* 2.8 40.0 + - + -
3A ALA 4.0 2.2 - - - -
4A SER* 3.6 10.3 - - - +
5A PHE* 2.6 70.6 + + + +
161A MET* 3.2 59.2 - - + +
164A ILE* 4.3 10.3 - - + -
165A TYR* 4.1 10.5 - - + -
205A GLY* 1.3 82.2 - - - +
207A GLY* 1.3 58.2 + - - +
214A TYR* 3.3 23.7 + - - +
215A TRP* 3.9 17.5 - + + -
216A LEU* 4.2 4.8 - - - +
235A ARG* 3.7 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA 3.9 2.0 - - - -
4A SER* 3.8 20.4 - - - -
206A TRP* 1.3 80.4 - - - +
208A VAL* 1.3 63.3 + - - -
213A PRO* 3.4 2.4 - - - +
214A TYR* 2.9 44.2 + - - +
235A ARG* 3.5 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA 4.4 9.9 + - - +
4A SER* 5.0 1.4 - - - -
207A GLY* 1.3 73.9 - - - +
209A GLU* 1.3 58.1 + - - +
210A ASN 3.9 1.2 + - - -
211A GLY* 3.5 33.2 - - - +
212A THR 3.7 5.8 - - - +
213A PRO* 3.6 25.4 - - + -
214A TYR* 3.7 2.8 + - - -
235A ARG* 4.0 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR 5.2 0.2 - - - +
186A GLY* 3.2 34.9 - - - -
187A VAL* 3.8 7.8 + - + +
208A VAL* 1.3 69.8 - - - +
210A ASN* 1.3 80.3 + - + +
212A THR* 3.1 20.8 + - - -
214A TYR* 3.2 22.8 - - + -
232A LYS* 2.5 28.6 + - - -
----------------------------------------------------------
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