Contacts of the helix formed by residues 181 - 186 (chain L) in PDB entry 3CX5
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 THR 181 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64L PRO 5.0 1.0 + - - +
67L ASN* 3.2 20.4 - - - +
148L VAL* 4.8 1.3 - - - -
152L GLU* 5.9 0.4 - - - -
177L PRO* 3.7 12.1 - - + -
180L GLY* 1.3 75.5 - - - -
182L LEU* 1.3 58.2 + - - +
183L GLU* 3.8 6.9 + - - +
184L SER* 3.0 28.6 + - - -
185L LEU* 2.9 34.2 + - - +
32P SER* 3.8 24.3 + - - +
34P TYR* 4.0 16.8 - - + -
35P ARG* 4.6 7.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145L LEU* 3.7 35.6 - - + +
148L VAL* 3.7 23.8 - - + +
149L GLN* 3.8 25.4 - - + +
152L GLU* 5.3 12.1 - - + -
181L THR* 1.3 71.7 - - - +
183L GLU* 1.3 73.5 + - - +
185L LEU* 3.7 4.2 - - - +
186L GLU* 3.1 38.5 + - - +
306O LYS* 5.8 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 183 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181L THR* 3.2 3.9 + - - +
182L LEU* 1.3 93.0 + - - +
184L SER* 1.3 61.1 + - - +
186L GLU* 3.5 20.8 - - - +
187L ASN* 3.7 11.3 + - - +
31P LYS* 4.2 7.6 + - - +
32P SER* 3.3 43.9 + - - +
35P ARG* 4.4 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64L PRO 3.5 18.2 - - - -
65L TYR 3.4 21.3 - - - +
67L ASN* 2.6 29.3 + - - +
181L THR* 3.0 20.4 + - - -
183L GLU* 1.3 77.4 - - - +
185L LEU* 1.3 64.8 + - - +
187L ASN* 3.3 11.5 + - - +
188L LEU* 3.1 24.6 + - - +
35P ARG* 3.9 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L ASN 3.9 0.2 - - - +
68L GLY* 3.6 40.2 - - - +
71L ASN* 5.2 0.9 - - + +
72L LEU* 4.0 11.3 - - + +
141L LYS* 3.4 10.9 - - + +
144L VAL* 4.5 12.6 - - + +
145L LEU* 3.6 22.4 - - + -
148L VAL* 3.7 24.7 - - + -
179L ARG 3.5 19.5 - - - +
180L GLY 4.3 0.2 - - - -
181L THR 2.9 25.0 + - - +
182L LEU 3.7 0.7 - - - +
184L SER* 1.3 77.0 + - - +
186L GLU* 1.3 56.9 + - - +
187L ASN 3.2 0.2 - - - -
188L LEU* 3.1 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 186 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141L LYS* 2.9 26.3 + - - +
145L LEU* 4.1 21.8 - - + +
182L LEU* 3.1 29.6 + - - +
183L GLU* 3.5 13.7 - - - +
185L LEU* 1.3 75.7 - - - +
187L ASN* 1.3 55.9 + - + +
188L LEU 3.3 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