Contacts of the helix formed by residues 179 - 188 (chain B) in PDB entry 4CEV
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 GLU 179 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU 3.9 1.1 + - - +
178B ASP* 1.3 72.4 - - - +
180B GLY* 1.3 64.3 + - - +
182B LYS* 3.2 36.5 + - - +
183B LYS* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL 5.7 0.4 - - - -
128B ASN* 5.0 0.2 - - - -
132B THR* 4.1 32.3 + - - +
178B ASP* 3.2 3.0 - - - +
179B GLU* 1.3 77.9 - - - +
181B GLU* 1.3 56.1 + - - +
183B LYS* 3.2 13.2 + - - +
184B PHE* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ORN 3.3 9.7 + - - -
125B GLY* 3.6 2.7 + - - -
126B ASP* 3.0 14.6 + - - -
127B VAL* 3.0 44.0 + - + +
128B ASN* 3.2 30.6 + - - +
140B GLY 4.3 0.5 - - - +
176B SER 4.5 0.7 - - - +
177B LEU* 3.8 14.3 - - + -
178B ASP* 2.9 43.1 + - + +
180B GLY* 1.3 74.3 - - - +
182B LYS* 1.3 60.1 + - - +
184B PHE* 3.4 4.5 - - - +
185B ILE* 2.9 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LYS* 3.1 21.8 + - - +
298A LEU 3.4 24.0 - - - -
299A MET* 3.1 40.5 + - - +
177B LEU* 3.7 30.0 + - + +
178B ASP 2.8 13.8 + - - +
179B GLU* 3.2 37.3 + - - +
181B GLU* 1.3 75.7 - - - +
183B LYS* 1.3 57.4 + - - +
186B ARG* 3.1 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B GLU 3.1 9.7 + - - +
180B GLY* 3.3 13.5 - - - +
181B GLU 3.1 0.2 - - - -
182B LYS* 1.3 77.0 - - - +
184B PHE* 1.3 59.5 + - - +
186B ARG* 3.2 28.4 - - - +
187B GLU* 2.8 68.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 3.6 30.1 - - + +
129B THR* 5.5 5.8 - - + -
144B ALA* 4.1 12.8 - - + -
147B LEU* 3.6 19.5 - - + -
149B PHE* 3.8 30.1 - + + -
180B GLY 2.9 14.1 + - - +
181B GLU* 3.4 12.8 - - - +
183B LYS* 1.3 74.0 - - - +
185B ILE* 1.3 61.4 + - - +
187B GLU* 4.9 3.6 - - - -
188B LYS* 2.8 74.6 + - + +
190B ILE* 3.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A MET* 3.5 19.5 - - + -
127B VAL* 4.1 13.9 - - + -
171B LEU* 3.8 23.3 - - + -
177B LEU* 3.5 43.3 - - + -
181B GLU 2.9 16.9 + - - +
184B PHE* 1.3 77.3 - - - +
186B ARG* 1.3 62.9 + - - +
189B GLY* 3.0 19.9 + - - -
190B ILE* 3.1 42.8 + - + +
192B ILE* 3.9 16.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
299A MET* 3.7 17.0 - - + -
182B LYS* 3.1 20.2 + - - +
183B LYS* 3.2 43.7 - - - +
185B ILE* 1.3 78.3 - - - +
187B GLU* 1.3 86.5 + - - +
189B GLY* 3.5 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LYS* 2.8 62.1 + - - +
184B PHE* 4.2 3.4 + - - +
186B ARG* 1.3 97.4 + - - +
188B LYS* 1.3 69.4 + - + +
189B GLY* 3.0 6.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B PHE* 3.2 32.5 - - + -
166B PRO* 3.3 27.7 - - + +
184B PHE* 2.8 73.3 + - + +
187B GLU* 1.3 82.3 + - + +
189B GLY* 1.3 63.4 + - - +
190B ILE* 4.0 15.5 - - + -
59D GLU* 3.3 20.9 + - - +
----------------------------------------------------------
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