Contacts of the helix formed by residues 169 - 177 (chain A) in PDB entry 4L87
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 SER 169 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 1.3 77.3 - - - +
170A HIS* 1.3 79.3 + - - +
171A VAL* 3.1 14.4 + - - +
172A ASP* 3.2 14.9 + - - -
173A LEU* 3.1 21.5 + - - +
385A GLY* 4.2 12.4 + - - -
386A SER* 3.3 19.4 + - - -
442A GLU* 3.6 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A SER* 1.3 76.7 + - - +
171A VAL* 1.3 77.4 + - + +
173A LEU* 3.8 7.6 - - - +
174A VAL* 3.1 32.2 + - - +
311A ASP* 4.6 10.6 + - + -
314A GLY* 4.3 11.8 - - - -
316A PHE* 3.6 30.0 - - + +
383A PHE* 4.3 11.7 - + - -
386A SER* 3.6 12.0 + - - -
390A ARG* 5.5 4.4 + - + -
438A CYS* 3.7 35.1 - - + +
441A LEU* 4.8 3.6 - - + +
442A GLU* 2.8 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A SER* 3.1 10.1 - - - +
170A HIS* 1.3 101.1 - - + +
172A ASP* 1.3 67.9 + - - +
174A VAL* 3.3 21.7 - - - +
175A VAL* 3.5 11.1 - - + +
313A ARG* 3.6 31.2 - - + -
314A GLY* 3.8 16.2 - - - +
475A PRO* 4.6 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 3.9 21.3 - - + -
169A SER* 3.2 17.7 + - - +
171A VAL* 1.3 82.4 - - - +
173A LEU* 1.3 60.7 + - - +
175A VAL* 3.3 4.0 + - - +
176A MET* 3.0 45.8 + - + +
474A ALA* 4.5 4.5 - - + -
475A PRO* 3.4 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 3.4 21.5 - - + +
169A SER 3.1 23.6 + - - +
170A HIS* 4.0 4.9 - - - +
172A ASP* 1.3 77.7 - - - +
174A VAL* 1.3 61.0 + - - +
175A VAL 3.4 0.5 + - - -
176A MET* 3.8 10.5 - - + -
177A VAL* 3.2 28.6 + - - +
441A LEU* 3.4 42.0 - - + +
442A GLU* 3.8 5.6 - - + -
445A GLN* 3.8 21.3 - - + +
450A ILE* 3.8 12.8 - - + -
470A PHE* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A HIS 3.1 15.5 + - - +
171A VAL* 3.3 20.4 - - - +
173A LEU* 1.3 76.5 - - - +
175A VAL* 1.3 60.2 + - + +
177A VAL 4.6 0.6 - - - -
178A ASP 4.3 0.9 + - - -
179A GLY* 3.5 17.3 + - - +
180A PHE* 3.4 43.3 - - + +
196A LEU* 5.0 0.4 - - + -
200A LEU* 3.6 25.5 - - + +
314A GLY* 4.9 8.5 - - - -
315A ILE* 4.1 26.5 - - + -
438A CYS* 6.3 0.2 - - - -
441A LEU* 4.2 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A VAL* 3.5 18.6 - - + +
172A ASP 3.3 5.5 + - - +
173A LEU 3.2 0.2 - - - -
174A VAL* 1.3 85.5 - - + +
176A MET* 1.3 59.9 + - - +
177A VAL 3.2 2.0 - - - -
178A ASP* 2.9 21.4 + - - +
180A PHE* 3.9 26.5 - - + +
472A LYS* 3.9 28.1 - - - +
473A PRO 5.2 2.5 - - - +
475A PRO* 4.0 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 3.6 39.9 - - + -
172A ASP* 3.0 32.0 + - + +
173A LEU* 3.6 19.3 + - + +
175A VAL* 1.3 77.4 - - - +
177A VAL* 1.3 57.4 + - - +
178A ASP 3.2 0.4 - - - -
470A PHE* 3.6 27.2 - - + -
471A VAL 3.1 6.8 + - - -
472A LYS* 2.8 47.8 + - - +
473A PRO* 3.7 0.9 - - - -
474A ALA* 3.6 33.9 - - - +
475A PRO* 4.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU 3.2 19.6 + - - +
174A VAL 5.2 1.1 - - - +
175A VAL 3.2 0.6 - - - -
176A MET* 1.3 75.0 - - - +
178A ASP* 1.3 71.3 + - - +
179A GLY 5.2 1.1 - - - +
199A VAL* 3.6 20.1 - - + +
200A LEU* 5.7 6.1 - - + -
441A LEU* 5.1 5.2 - - + -
450A ILE* 3.8 25.8 - - + -
468A ILE* 3.5 28.0 - - + +
469A PRO 3.3 23.1 - - - +
470A PHE* 3.8 11.2 - - + -
471A VAL* 3.6 10.1 - - - +
----------------------------------------------------------
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