Contacts of the helix formed by residues 312 - 317 (chain C) in PDB entry 5IXM
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 TYR 312 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C GLU 5.3 0.3 + - - -
286C ARG* 5.1 8.1 - - - +
311C ASP* 1.3 79.3 + - - +
313C SER* 1.3 68.4 + - - +
315C LEU* 3.3 30.4 - - + +
316C PHE* 3.7 20.0 - + - -
336C GLY* 3.5 20.6 - - - -
337C LEU 3.5 3.8 + - - -
338C THR* 3.3 16.2 + - - -
353C SER* 3.7 26.5 - - - -
354C VAL 3.5 7.4 - - - -
355C GLY* 3.5 35.0 - - - -
383C ALA* 3.9 9.3 - - - +
384C GLY* 4.7 10.2 + - - +
385C ASP* 3.7 25.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 313 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C ARG* 5.6 2.0 + - - +
311C ASP* 3.1 18.2 + - - -
312C TYR* 1.3 81.9 - - - +
314C GLY* 1.3 57.2 + - - +
315C LEU 2.9 10.3 + - - -
316C PHE* 2.9 24.2 + - - +
317C ARG* 3.8 3.2 + - - +
104D ARG* 3.9 20.6 + - - -
126D GLU* 5.1 4.9 - - - -
130D GLN* 4.4 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C SER* 4.0 11.2 - - - -
311C ASP* 2.7 30.8 + - - -
313C SER* 1.3 71.0 - - - +
315C LEU* 1.3 62.4 + - - +
316C PHE 3.1 0.4 - - - -
317C ARG* 3.2 45.3 + - - +
357C ILE* 5.3 1.2 - - - +
126D GLU* 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C GLN* 4.7 0.9 - - - +
310C SER* 5.2 3.8 - - - -
311C ASP 3.2 9.2 + - - +
312C TYR* 3.3 28.7 - - + +
313C SER 2.9 0.4 + - - -
314C GLY* 1.3 77.3 - - - +
316C PHE* 1.3 69.0 + - + +
317C ARG 3.3 4.4 + - - +
332C GLN* 5.6 1.4 + - - -
334C SER* 3.1 23.3 + - - -
335C THR 4.8 0.7 - - - +
355C GLY* 3.5 37.0 - - - +
356C GLN* 3.8 5.6 - - - +
357C ILE* 3.6 37.6 - - + +
381C VAL* 3.8 19.3 - - + -
383C ALA* 4.0 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C LYS* 5.0 4.2 + - - -
286C ARG* 3.4 70.6 + - + +
288C GLN* 3.3 42.3 + - + +
312C TYR* 3.7 37.0 - + - -
313C SER* 2.9 10.4 + - - +
315C LEU* 1.3 82.8 - - + +
317C ARG* 1.3 63.5 + - - +
318C ASP* 3.7 1.6 + - - -
334C SER* 3.5 27.8 - - - -
335C THR 4.1 4.5 - - - -
336C GLY* 3.9 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C GLN* 5.0 1.0 - - - +
290C LEU* 4.7 4.3 - - - +
308C MET* 3.7 32.9 - - - +
309C GLN 2.8 37.2 + - - -
310C SER* 3.4 13.5 - - - +
311C ASP* 5.0 1.4 + - - -
313C SER 3.8 1.6 + - - +
314C GLY* 3.2 30.2 + - - +
315C LEU 4.2 4.0 - - - +
316C PHE* 1.3 78.1 - - - +
318C ASP* 1.3 67.7 + - - +
319C ARG* 3.2 33.4 + - + +
332C GLN* 5.4 3.3 + - - -
122D VAL* 4.5 5.6 - - - -
123D LEU* 4.4 3.6 - - - +
126D GLU* 2.6 52.4 + - - +
----------------------------------------------------------
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