Contacts of the helix formed by residues 178 - 183 (chain D) in PDB entry 3K75
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 178 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D MET* 5.6 0.2 - - - +
176D THR* 3.2 27.4 - - - -
177D VAL* 1.3 79.5 - - - +
179D GLY* 1.3 72.3 + - - +
181D PHE* 3.7 10.0 - - - +
182D ARG* 3.6 14.3 + - - -
190D ASP 5.6 0.9 - - - +
192D ASP* 2.7 24.4 + - + +
194D LEU* 3.7 24.9 - - + -
269D VAL* 4.1 9.0 - - - -
272D PHE* 3.7 15.9 - - + +
273D THR* 3.7 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D CYS* 1.3 76.0 - - - +
180D SER* 1.3 57.1 + - - -
181D PHE 2.9 3.4 - - - -
182D ARG* 2.6 34.5 + - - +
183D ARG* 3.5 10.2 + - - +
190D ASP 6.1 0.9 - - - -
192D ASP* 4.6 8.1 - - - +
272D PHE 3.1 17.9 + - - -
273D THR* 3.8 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D ARG* 4.5 4.1 + - - -
179D GLY* 1.3 69.8 - - - -
181D PHE* 1.3 64.0 + - - +
183D ARG* 3.0 42.8 + - - +
184D GLY 3.2 0.3 + - - -
185D ALA* 3.0 32.6 + - - +
187D SER 3.6 15.3 + - - -
188D SER* 3.7 14.2 + - - -
189D GLY 4.7 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D ARG* 3.0 52.3 + - + +
155D MET* 3.6 40.2 - - + -
156D LEU* 4.2 17.0 - - + -
159D GLN* 3.7 39.5 - - + -
177D VAL* 3.3 29.2 - - + -
178D CYS 3.7 7.4 - - - +
179D GLY 2.7 4.2 + - - -
180D SER* 1.3 79.3 + - - +
182D ARG* 1.3 64.5 + - - +
184D GLY* 2.8 17.2 + - - -
185D ALA 4.4 2.7 - - - +
188D SER* 3.6 17.7 + - - +
190D ASP 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D ARG* 5.5 0.3 + - - -
176D THR* 3.9 17.7 - - - +
177D VAL 3.7 22.4 - - - +
178D CYS* 3.6 4.4 + - - +
179D GLY 2.6 15.2 + - - +
181D PHE* 1.3 83.1 - - - +
183D ARG* 1.3 56.4 + - - +
184D GLY 3.3 3.1 + - - -
269D VAL* 3.5 9.2 - - - +
273D THR* 2.7 52.0 + - + +
316D GLU* 2.8 43.1 + - - +
327D TYR* 4.7 1.8 + - - -
330D PRO* 3.1 35.4 - - + +
331D LYS 4.5 0.7 + - - -
333D ARG* 3.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D GLY* 3.5 1.2 + - - +
180D SER* 3.0 41.2 + - - +
182D ARG* 1.3 75.1 - - - +
184D GLY* 1.3 63.1 + - - +
185D ALA* 3.5 2.1 + - + +
273D THR* 2.8 24.1 + - + +
274D GLY 2.7 36.5 + - - +
275D SER* 4.0 11.3 - - - +
330D PRO 3.3 21.8 - - - +
331D LYS* 3.4 22.3 - - - +
333D ARG* 3.2 28.6 + - - -
334D SER* 5.3 1.6 - - - +
----------------------------------------------------------
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