Contacts of the helix formed by residues 174 - 184 (chain C) in PDB entry 4GKH
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 PRO 174 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C ALA* 5.8 0.9 - - + -
172C GLY 3.5 6.9 - - - +
173C TRP* 1.3 87.2 - - - +
175C VAL* 1.3 66.5 + - - +
176C GLU* 3.6 16.2 - - + +
177C GLN* 2.9 42.2 + - + +
178C VAL* 3.4 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C MSE 3.7 22.7 - - + +
161C VAL* 4.0 25.8 - - + -
163C ALA* 5.1 7.3 - - + +
166C PHE* 4.2 19.1 - - + -
173C TRP 3.7 1.6 + - - -
174C PRO* 1.3 70.3 - - - +
176C GLU* 1.3 78.5 + - - +
178C VAL* 3.2 5.1 + - - +
179C TRP* 3.0 25.1 + - - +
270C PHE* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C MSE 4.1 20.9 - - - +
174C PRO* 3.6 19.3 - - + +
175C VAL* 1.3 92.8 + - - +
177C GLN* 1.3 57.9 + - - +
179C TRP* 3.4 2.8 + - - +
180C LYS* 3.0 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C TRP* 3.7 36.0 - - + +
174C PRO* 2.9 39.3 + - + +
176C GLU* 1.3 77.2 - - - +
178C VAL* 1.3 60.6 + - - +
180C LYS* 4.1 4.9 - - - +
181C GLU* 2.9 59.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C PHE* 3.9 25.6 - - + -
170C ARG* 4.1 17.7 - - - -
173C TRP* 3.9 20.6 - - + -
174C PRO 3.9 10.1 - - - +
175C VAL* 3.2 7.9 + - - +
177C GLN* 1.3 74.5 - - - +
179C TRP* 1.3 59.4 + - - +
182C MSE 2.9 34.0 + - - +
266C MSE 3.6 28.5 - - + +
269C GLU* 4.4 6.1 - - + -
270C PHE* 3.7 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LEU* 3.5 33.0 - - + -
152C ALA* 4.1 3.6 - - + -
153C GLN* 3.6 41.2 - - + +
156C MSE 3.7 30.5 - - + +
175C VAL 3.0 13.8 + - - +
176C GLU* 3.5 8.7 - - + +
178C VAL* 1.3 78.6 - - - +
180C LYS* 1.3 71.0 + - + +
182C MSE 3.5 26.6 - - + +
183C HIS* 2.7 64.1 + + - -
270C PHE* 3.6 20.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLU* 3.0 28.1 + - + +
177C GLN* 4.1 5.2 - - - +
179C TRP* 1.3 86.1 - - + +
181C GLU* 1.3 65.1 + - + +
183C HIS* 3.2 19.4 + - - +
184C LYS* 3.7 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C TRP* 3.9 17.5 - - + -
177C GLN* 2.9 46.9 + - + +
180C LYS* 1.3 74.6 - - + +
182C MSE 1.3 65.8 + - - +
184C LYS* 3.3 51.7 + - - +
185C LEU* 4.1 8.5 + - - +
262C GLN* 5.8 0.2 + - - -
266C MSE 3.7 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LEU* 3.5 20.0 - - + -
178C VAL 2.9 19.5 + - - +
179C TRP* 3.5 33.0 - - + +
180C LYS 3.3 0.2 - - - -
181C GLU* 1.3 78.1 - - - +
183C HIS* 1.3 65.4 + - + +
185C LEU* 3.1 21.3 + - - +
186C LEU* 4.1 2.3 + - - +
263C PHE* 3.6 28.2 - - + -
266C MSE 3.5 24.8 - - + +
267C LEU* 3.5 42.0 - - + -
270C PHE* 3.6 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LEU* 4.2 11.9 - - + +
179C TRP* 2.7 72.8 + + - -
180C LYS* 3.2 12.7 + - - +
182C MSE 1.3 86.4 - - + +
184C LYS* 1.3 61.2 + - - +
186C LEU* 3.3 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C LYS 3.8 10.1 - - - +
181C GLU* 3.3 41.8 + - - +
182C MSE 3.2 0.8 - - - -
183C HIS* 1.3 75.8 - - - +
185C LEU* 1.3 65.6 + - + +
186C LEU 3.5 6.9 + - - +
----------------------------------------------------------
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