Contacts of the strand formed by residues 170 - 177 (chain A) in PDB entry 1PBH
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 VAL 170 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA* 4.4 6.1 - - - -
41A ARG* 3.1 26.7 - - - +
80A TRP* 5.3 0.7 - - - -
153A VAL* 4.5 2.0 - - + -
160A ILE* 4.5 4.5 - - + -
163A GLU* 3.9 17.7 - - + -
164A ILE* 3.8 23.8 - - + -
168A GLY 3.8 3.1 - - - +
169A PRO* 1.3 72.5 - - - +
171A GLU* 1.3 62.3 + - - +
202A ARG* 3.2 8.0 - - - +
203A ILE* 2.9 31.0 + - + +
246A VAL* 3.9 24.9 - - + -
247A VAL 3.9 7.4 - - - +
248A ALA* 3.6 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP 2.8 27.1 - - - +
33A GLY* 3.4 15.0 + - - +
34A ALA* 2.9 14.2 + - - -
76A PRO* 3.5 21.3 - - - +
80A TRP* 2.7 46.5 + - + +
170A VAL* 1.3 76.6 - - - +
172A GLY* 1.3 62.8 + - - +
200A ALA* 3.8 7.7 - - - +
201A ILE 2.9 19.1 - - - +
202A ARG* 4.4 0.2 - - - +
245A GLU 3.1 2.6 - - - +
246A VAL* 3.2 4.4 - - - -
247A VAL* 2.8 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PRO* 5.4 1.4 - - - +
170A VAL 4.2 0.8 + - - -
171A GLU* 1.3 76.8 - - - +
173A ALA* 1.3 63.8 + - - +
200A ALA* 3.4 5.2 - - - +
201A ILE* 2.8 42.2 + - - +
203A ILE* 4.9 2.2 - - - +
242A ILE 4.8 3.1 - - - -
245A GLU 3.5 15.3 - - - -
246A VAL* 4.2 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 4.3 13.9 - - + -
46A LEU* 4.0 19.1 - - + -
76A PRO* 5.0 2.2 - - + -
172A GLY* 1.3 76.2 - - - +
174A PHE* 1.3 68.7 + - - +
199A HIS 3.4 12.3 - - - +
200A ALA* 4.1 5.8 - - + -
201A ILE* 3.4 4.6 - - - +
241A GLY 3.1 20.8 - - - +
242A ILE* 3.6 6.1 + - - -
245A GLU* 4.1 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.2 10.0 - - - +
173A ALA* 1.3 80.2 - - - +
175A SER* 1.3 69.6 + - - +
176A VAL* 3.5 8.2 + - + +
180A PHE* 3.5 48.7 - + - -
188A TYR* 5.2 2.0 - + - -
198A GLY* 4.6 0.2 - - - -
199A HIS* 2.9 61.9 + + - +
201A ILE* 3.7 22.0 - - + -
231A PHE* 3.9 11.0 - + - -
233A ILE* 3.9 19.7 - - + -
240A CYS* 3.2 23.3 - - + +
242A ILE* 3.8 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.2 12.0 - - - +
174A PHE* 1.3 75.4 - - - +
176A VAL* 1.3 62.2 + - - +
177A TYR* 3.5 31.1 + - - -
188A TYR* 5.2 1.7 + - - -
195A MET* 3.6 24.7 - - - +
197A GLY 3.4 7.1 + - - -
198A GLY* 4.5 0.7 - - - -
240A CYS* 3.1 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A CYS* 3.8 24.5 - - - -
174A PHE* 3.9 14.6 - - + +
175A SER* 1.3 72.7 - - - +
177A TYR* 1.3 71.3 + - - +
180A PHE* 3.5 29.6 - - + -
181A LEU* 4.4 12.6 - - + -
195A MET* 3.6 2.1 - - - +
196A MET* 2.8 27.7 + - + +
197A GLY 2.8 13.7 + - - +
199A HIS* 3.3 37.0 - - + -
221A TRP* 4.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A SER* 3.5 31.1 + - - -
176A VAL* 1.3 80.9 - - - +
178A SER* 1.3 67.8 + - - +
179A ASP* 2.9 19.0 + - - +
180A PHE* 3.0 18.4 + - - +
181A LEU* 4.0 1.2 + - - +
188A TYR* 4.3 1.5 + - - +
190A HIS* 3.2 44.3 - + + -
192A THR 4.1 1.6 - - - +
193A GLY 3.4 15.5 - - - -
194A GLU 2.9 11.7 - - - -
195A MET* 3.9 24.6 - - + +
196A MET* 3.9 2.8 - - - +
240A CYS* 4.3 11.2 - - - -
----------------------------------------------------------
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