Contacts of the helix formed by residues 183 - 188 (chain C) in PDB entry 3NJ4
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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ASN 3.9 3.5 + - - -
180C VAL 3.1 16.7 + - - -
181C ASN 3.1 0.2 + - - -
182C ASP* 1.3 76.7 - - - +
184C VAL* 1.3 56.9 + - - +
186C LYS* 2.6 31.4 + - - +
187C SER* 3.2 5.1 + - - -
364C ASN* 3.5 28.2 + - - -
385C PHE* 5.8 1.9 - - - +
386C LEU* 3.7 25.8 + - - +
391C ASP* 3.3 15.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C ASP 3.7 2.8 + - - -
183C SER* 1.3 69.4 - - - +
185C THR* 1.3 53.4 + - - +
186C LYS 2.8 10.7 + - - -
187C SER* 4.1 5.6 - - - -
188C LYS* 3.3 21.0 + - + +
189C PHE* 3.2 15.2 - - + -
388C LYS* 4.5 4.9 - - - +
391C ASP* 2.8 21.0 + - - +
432C TYR* 3.6 37.0 - - + -
247D ILE* 3.6 30.1 - - + -
431D ARG* 3.2 36.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C VAL* 1.3 69.3 - - - +
186C LYS* 1.3 56.7 + - - +
189C PHE* 3.4 19.0 - - + +
360C ASN* 2.9 37.5 + - - +
364C ASN* 2.9 26.6 + - - -
391C ASP* 2.7 50.4 + - - +
394C VAL* 3.6 7.3 - - - +
395C ALA* 3.9 24.0 - - + +
247D ILE* 4.0 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C GLU* 3.1 31.5 + - - +
180C VAL* 3.5 20.4 - - + +
181C ASN* 3.0 25.1 - - - +
183C SER* 2.6 20.2 + - - +
184C VAL 2.8 0.8 + - - -
185C THR* 1.3 74.5 - - - +
187C SER* 1.3 66.5 + - - +
188C LYS 3.2 0.7 - - - -
189C PHE 2.8 0.9 + - - -
190C ASP* 2.5 49.9 + - + +
191C ASN* 2.9 18.6 - - - +
361C SER* 3.5 18.2 - - - -
364C ASN* 4.2 4.7 - - - +
603C AFX 2.7 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ASN* 3.0 25.4 + - - -
182C ASP* 4.2 9.1 - - - -
183C SER 3.4 13.9 + - - -
184C VAL* 3.9 2.8 + - - -
186C LYS* 1.3 78.8 - - - +
188C LYS* 1.3 71.4 + - - +
189C PHE 3.2 3.8 + - - -
191C ASN* 3.0 40.5 + - - +
192C LEU 3.6 2.3 + - - -
223C ASP* 3.9 16.0 - - - +
431D ARG* 4.3 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C VAL* 3.3 26.5 + - + +
186C LYS 3.2 0.8 - - - -
187C SER* 1.3 84.7 + - - +
189C PHE* 1.3 71.7 + - + +
192C LEU* 3.8 28.5 - - - +
193C TYR* 3.6 14.7 + - - -
223C ASP* 3.0 25.1 + - - +
226C LYS* 4.7 6.5 - - - +
431C ARG 4.6 4.9 - - - +
432C TYR* 4.3 17.9 - - + -
188D LYS* 6.1 1.2 - - - +
251D GLN* 4.7 8.5 - - - +
431D ARG* 4.4 20.0 - - + -
432D TYR* 2.7 30.8 + - - +
----------------------------------------------------------
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