Contacts of the helix formed by residues 334 - 342 (chain C) in PDB entry 2O2C
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 GLY 334 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C MET* 3.9 6.5 - - - -
329C MET* 3.3 22.5 + - - -
331C SER 2.9 10.3 + - - -
333C ILE* 1.3 77.8 - - - +
335C LEU* 1.3 62.0 + - - +
336C PRO* 3.4 1.8 - - - -
337C ILE* 3.0 20.1 + - - +
338C MET* 3.0 18.7 + - - +
346C PHE* 3.4 7.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C MET* 3.8 43.0 - - + +
180C PHE* 3.9 36.6 - - + -
181C SER* 4.7 2.0 - - - -
255C ILE* 4.4 6.3 - - + -
297C VAL* 4.2 8.3 - - + -
299C LEU* 3.7 20.9 - - + -
317C PHE* 4.0 13.5 - - + -
332C ALA 3.0 17.8 + - - +
334C GLY* 1.3 75.6 - - - +
336C PRO* 1.4 65.1 - - + +
338C MET* 3.1 4.3 + - + +
339C ILE* 2.9 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C VAL* 4.8 7.2 - - + -
202C ASN* 3.6 30.1 - - + +
212C PRO* 3.9 18.8 - - + -
216C THR* 4.0 4.1 - - - +
229C LEU* 4.6 7.0 - - + +
231C PHE* 4.6 10.8 - - + -
255C ILE* 4.2 17.9 - - + -
299C LEU* 4.2 5.2 - - + -
333C ILE 3.3 15.3 - - - +
335C LEU* 1.4 91.5 - - + +
337C ILE* 1.3 60.9 - - - +
339C ILE* 3.5 8.2 + - + +
340C SER* 3.1 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C GLY 4.1 2.0 - - - +
212C PRO* 4.0 26.5 - - + -
215C ALA* 3.6 36.6 - - + +
216C THR* 3.9 13.9 - - + -
219C LEU* 5.0 0.4 - - + -
329C MET* 4.0 22.4 - - + +
334C GLY* 3.0 25.3 + - - +
336C PRO* 1.3 75.8 - - - +
338C MET* 1.3 57.7 + - - +
340C SER* 3.2 3.6 + - - -
341C ILE* 2.9 54.6 + - + +
346C PHE* 4.0 11.2 - - + -
349C LEU* 4.2 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C LEU* 4.2 7.0 - - + +
177C MET* 3.5 55.0 - - + +
178C ARG* 3.7 5.2 - - - -
181C SER* 3.5 12.6 - - - +
185C ARG* 4.1 2.6 - - - -
334C GLY 3.0 11.8 + - - +
335C LEU* 3.1 9.6 + - - +
337C ILE* 1.3 74.8 - - - +
339C ILE* 1.3 60.2 + - - +
342C GLY* 2.8 37.1 + - - +
343C TYR* 3.8 35.9 - - + +
346C PHE* 3.6 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C PHE* 4.2 6.7 - - + -
181C SER* 4.0 24.5 - - - -
184C VAL* 3.9 23.8 - - + -
185C ARG* 3.0 28.1 + - + +
200C VAL* 3.9 19.7 - - + -
227C LEU* 3.6 13.5 - - + +
229C LEU* 5.2 2.2 - - + -
253C LEU* 4.2 18.6 - - + -
255C ILE* 3.9 28.9 - - + -
335C LEU* 2.9 29.2 + - + +
336C PRO* 3.8 4.9 - - + +
338C MET* 1.3 75.2 - - - +
340C SER* 1.3 58.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C ARG* 2.9 8.9 + - - -
216C THR* 4.1 11.5 + - - +
223C SER* 3.3 19.1 - - - -
224C GLN* 2.9 30.7 + - - +
227C LEU* 5.1 3.1 - - - -
229C LEU* 3.4 31.3 - - - +
336C PRO 3.1 18.4 + - - -
337C ILE 3.5 4.0 - - - -
339C ILE* 1.3 78.9 - - - +
341C ILE* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C ARG* 3.7 7.4 + - - -
215C ALA 5.6 0.4 - - - +
216C THR* 5.7 2.7 - - - -
219C LEU* 3.6 56.1 - - + +
222C PHE* 3.5 18.0 - - + +
223C SER* 4.2 1.1 - - - +
337C ILE* 2.9 38.3 + - + +
338C MET* 4.5 0.7 - - - -
340C SER* 1.3 82.5 - - - +
342C GLY* 1.3 64.0 + - - +
345C ASN* 3.1 53.8 + - + +
346C PHE* 3.9 5.4 - - + +
349C LEU* 5.0 1.6 - - + -
536C PRO* 4.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C GLU* 5.0 1.1 - - - -
185C ARG* 3.3 24.3 - - - +
338C MET* 2.8 26.1 + - - +
341C ILE* 1.3 76.7 - - - +
343C TYR* 1.3 65.6 + - - -
344C GLU 3.5 2.0 - - - -
345C ASN 3.5 0.9 + - - -
346C PHE* 3.1 22.2 + - - +
----------------------------------------------------------
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