Contacts of the helix formed by residues 183 - 193 (chain B) in PDB entry 4CCN
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 183 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B MET* 1.3 76.1 - - - +
184B PRO* 1.3 64.4 - - - +
185B LEU 3.6 1.2 + - - -
186B ARG* 3.0 24.7 + - - +
187B ARG* 2.8 35.3 + - - +
236B THR* 3.7 4.3 - - - -
239B GLN* 2.8 52.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B MET 4.5 0.2 - - - +
183B SER* 1.3 82.0 - - - +
185B LEU* 1.3 55.4 + - - +
187B ARG* 3.3 28.6 + - - +
188B VAL* 3.0 30.0 + - - +
208B TRP* 3.4 9.6 + - - +
234B ASP* 3.9 20.2 - - - +
236B THR* 3.4 27.4 - - - +
237B TYR* 3.7 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B SER 3.1 0.6 - - - -
184B PRO* 1.3 79.6 - - - +
186B ARG* 1.3 58.7 + - + +
188B VAL* 3.0 8.6 - - + +
189B LEU* 2.9 53.2 + - + +
208B TRP* 3.4 23.3 - - + -
237B TYR 3.2 17.4 + - - +
238B TYR* 3.5 6.3 - - - +
239B GLN 3.5 12.1 - - - +
240B GLY* 3.7 3.8 - - - +
241B LEU* 3.4 49.6 - - + +
307B THR* 6.1 0.7 - - - -
311B PHE* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B MET* 3.3 33.8 - - + +
183B SER* 3.0 32.2 + - - +
185B LEU* 1.3 79.0 - - + +
187B ARG* 1.3 58.2 + - - +
189B LEU* 3.9 11.7 - - + +
190B ALA* 3.1 23.2 + - - +
239B GLN* 4.0 13.9 + - - +
240B GLY* 3.7 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B MET* 3.1 50.1 + - + +
183B SER 2.8 13.0 + - - +
184B PRO* 3.7 33.9 - - - +
186B ARG* 1.3 75.5 - - - +
188B VAL* 1.3 63.2 + - - +
190B ALA* 3.4 5.3 + - - +
191B GLU* 3.1 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PRO 3.0 12.5 + - - +
185B LEU* 3.0 22.7 - - + +
187B ARG* 1.3 74.4 - - - +
189B LEU* 1.3 72.2 + - - +
191B GLU* 3.0 9.3 + - + +
192B LEU* 3.0 33.4 + - + +
204B ARG* 4.3 22.2 - - + +
205B LEU* 4.5 10.8 - - + -
208B TRP* 3.6 52.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 2.9 50.6 + - + +
186B ARG* 3.9 11.7 - - + +
188B VAL* 1.3 78.6 - - + +
190B ALA* 1.3 64.3 + - - +
192B LEU* 3.2 26.7 + - + +
193B ASN* 3.4 11.1 + - - +
205B LEU* 5.1 2.9 - - + -
240B GLY 5.9 1.1 - - - +
307B THR* 5.7 12.8 - - + +
310B GLN* 4.0 42.8 + - + +
311B PHE* 5.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B MET* 4.4 16.4 - - + -
186B ARG 3.1 19.5 + - - +
187B ARG 3.5 6.5 - - - +
189B LEU* 1.3 78.0 - - - +
191B GLU* 1.3 62.1 + - - +
193B ASN* 3.3 19.7 + - - +
194B ARG* 3.6 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ARG 3.1 13.6 + - - +
188B VAL* 3.0 13.0 + - - +
190B ALA* 1.3 74.9 - - - +
192B LEU* 1.3 56.8 + - + +
194B ARG* 2.7 42.1 + - + +
195B ILE* 3.5 15.0 - - + +
200B ARG* 5.4 0.3 + - - -
204B ARG* 2.8 51.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B VAL* 3.0 24.8 + - + +
189B LEU* 3.2 26.7 + - + +
191B GLU* 1.3 76.2 - - - +
193B ASN* 1.3 63.9 + - - +
195B ILE* 3.0 12.5 + - + +
201B ARG* 3.0 61.9 - - + +
204B ARG* 3.8 24.0 - - + -
205B LEU* 4.3 24.2 - - + +
310B GLN* 5.0 5.8 - - - +
314B VAL* 4.5 16.8 - - + -
515B THR* 4.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU 3.4 6.8 + - - +
190B ALA* 3.3 14.0 + - - +
191B GLU 3.1 1.0 + - - -
192B LEU* 1.3 80.1 - - - +
194B ARG* 1.3 61.7 + - + +
195B ILE 3.2 2.6 + - - +
310B GLN* 5.4 5.2 + - - -
514B LEU 4.4 3.1 - - - +
515B THR* 3.7 29.3 - - - +
516B ASP* 2.6 53.2 + - - +
517B ARG* 5.5 4.2 + - - +
----------------------------------------------------------
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