Contacts of the helix formed by residues 239 - 248 (chain C) in PDB entry 3RN5
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 239 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ASN* 3.7 23.8 - - + +
288B THR* 4.9 14.1 - - + +
184C GLU* 3.0 30.7 - - + +
237C ASN* 3.7 9.9 - - - +
238C VAL* 1.3 91.7 - - + +
240C LEU* 1.3 69.2 + - - +
241C ASN* 3.0 3.0 + - - +
242C ILE* 3.0 29.9 + - + -
243C ILE* 3.5 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ASN* 4.0 32.5 - - + +
238C VAL 3.7 2.1 + - - +
239C PRO* 1.3 72.2 - - - +
241C ASN* 1.3 61.1 + - - +
243C ILE* 3.8 13.8 + - + +
244C ARG* 3.5 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LYS* 3.7 21.9 - - + +
253B ASN* 2.9 43.2 + - - +
254B THR* 3.9 10.3 + - - -
288B THR* 4.6 5.9 - - + +
239C PRO* 4.0 1.9 - - - +
240C LEU* 1.3 78.0 - - - +
242C ILE* 1.3 72.6 + - - +
243C ILE 3.4 0.2 - - - -
244C ARG* 3.8 31.4 + - - +
245C LYS* 3.1 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ASN* 4.4 5.8 - - - +
182C ALA* 4.4 0.9 - - + -
184C GLU 3.8 1.3 - - - +
185C LYS 3.5 10.1 - - - +
186C GLU* 3.5 33.7 - - - +
187C PHE* 3.7 29.9 - - + -
238C VAL* 3.6 21.8 - - + -
239C PRO* 3.0 20.7 + - + +
241C ASN* 1.3 90.3 + - - +
243C ILE* 1.3 61.2 + - - +
245C LYS* 4.5 3.8 - - - -
246C ALA* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C MET* 4.9 12.1 - - + -
159C LEU* 3.9 29.4 - - + +
238C VAL* 3.7 37.5 - - + +
239C PRO 3.5 6.2 + - - +
240C LEU* 4.0 14.8 - - + +
242C ILE* 1.3 77.4 - - - +
244C ARG* 1.3 62.9 + - - +
246C ALA* 3.5 2.9 + - - +
247C GLY* 3.2 17.3 + - - -
14M A 6.1 1.1 - - - -
15M A 4.2 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LYS* 5.6 5.9 - - - +
240C LEU 3.5 10.1 + - - +
241C ASN* 3.8 36.0 + - - +
242C ILE 3.2 0.6 - - - -
243C ILE* 1.3 77.3 - - - +
245C LYS* 1.3 68.4 + - - +
247C GLY* 2.9 4.0 + - - -
248C GLU* 2.7 61.8 + - + +
15M A 4.8 6.0 + - - +
16M A 5.6 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LYS* 5.5 6.9 - - - +
187C PHE* 3.4 27.6 - - + -
189C PHE* 6.0 0.2 - - - -
241C ASN 3.1 16.0 + - - +
242C ILE* 3.9 3.8 - - - +
244C ARG* 1.3 89.7 - - - +
246C ALA* 1.3 64.2 + - - +
247C GLY 3.0 1.2 + - - -
248C GLU* 3.0 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LEU* 3.3 34.8 - - + -
180C THR* 3.9 12.6 + - + +
187C PHE* 3.4 31.4 - - + -
189C PHE* 4.1 16.3 - - - -
242C ILE 2.9 14.3 + - - +
243C ILE 3.6 0.7 - - - +
244C ARG 3.3 0.2 - - - -
245C LYS* 1.3 76.6 - - - +
247C GLY* 1.3 58.8 + - - +
248C GLU 4.4 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C LYS* 6.6 0.2 - - - -
243C ILE 3.2 3.4 + - - -
244C ARG 2.9 6.8 + - - -
246C ALA* 1.3 78.3 - - - +
248C GLU* 1.3 66.4 + - - +
249C THR* 3.5 3.6 + - - -
15M A 2.9 45.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ARG* 2.7 51.1 + - + +
245C LYS* 3.0 42.3 + - + +
246C ALA 4.4 2.6 - - - +
247C GLY* 1.3 76.8 - - - +
249C THR* 1.3 68.1 + - - +
250C PRO* 3.8 13.5 - - + +
265C ASN 4.8 2.6 - - - +
16M A 4.0 17.0 - - - +
----------------------------------------------------------
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