Contacts of the helix formed by residues 366 - 372 (chain C) in PDB entry 1EQB
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 366 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C VAL* 2.7 33.5 + - - +
294C ASN* 3.8 9.9 - - + -
295C ALA* 3.4 32.0 - - + +
298C MET* 4.0 20.6 - - - -
317C HIS 3.2 8.0 + - - +
319C PHE* 5.4 2.7 - - + -
365C GLY* 1.3 74.6 - - - -
367C PRO* 1.3 65.9 - - - +
368C ALA 3.2 3.0 + - - -
369C ILE* 3.4 9.7 - - + +
370C THR* 2.5 36.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 367 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ILE 5.4 0.9 - - - +
34C ALA* 4.2 8.3 - - - +
36C GLU 4.0 14.1 - - - +
37C ASN* 4.1 14.6 - - - +
229C LYS 5.5 0.2 - - - +
230C THR* 3.9 13.5 - - + -
287C TYR* 2.8 24.0 + - - +
291C VAL* 3.9 11.9 - - + -
317C HIS* 3.7 34.5 - - + -
365C GLY* 3.3 10.3 - - - -
366C THR* 1.3 93.9 - - - +
368C ALA* 1.3 61.5 + - - +
370C THR* 3.8 0.3 - - - -
371C ARG* 3.1 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 368 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLU* 3.4 32.1 - - + +
33C ILE 5.5 3.6 + - - +
36C GLU* 4.3 12.2 + - + +
37C ASN* 4.3 11.4 - - - +
38C TYR* 3.5 28.0 - - + +
365C GLY 5.1 0.6 + - - +
366C THR 3.3 0.8 - - - -
367C PRO* 1.3 76.6 - - - +
369C ILE* 1.3 66.4 + - + +
371C ARG* 3.2 4.5 + - - +
372C ARG* 3.0 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 369 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ILE* 3.6 31.0 - - + -
31C GLU 3.8 15.4 + - - +
32C LEU* 4.1 17.3 - - + -
294C ASN* 5.1 1.6 - - + -
298C MET* 4.3 13.5 - - - -
366C THR* 3.4 21.3 - - + +
368C ALA* 1.3 78.4 - - - +
370C THR* 1.3 65.8 + - - +
372C ARG* 3.2 19.7 + - - +
373C GLY 3.2 0.5 + - - -
374C PHE* 3.0 59.1 + - + +
379C ALA* 4.6 10.1 - - + -
382C LEU* 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 370 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C TYR* 3.7 9.9 - - + +
290C GLN* 3.4 34.1 - - + -
291C VAL* 3.5 29.2 - - + +
294C ASN* 2.9 23.1 + - - +
366C THR* 2.5 26.5 + - - -
367C PRO 3.8 0.9 - - - -
369C ILE* 1.3 73.5 - - - +
371C ARG* 1.3 57.7 + - - +
372C ARG 2.9 4.5 - - - -
373C GLY* 2.9 20.8 + - - -
374C PHE 4.0 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 371 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ASN* 3.3 15.3 - - - +
38C TYR* 2.6 48.3 + - + -
39C THR* 3.9 0.4 - - - +
40C SER* 3.7 14.6 - - - +
232C ALA* 3.8 23.0 + - - +
278C GLU* 5.1 10.3 + - - +
284C PHE* 5.1 11.7 - - - -
287C TYR* 3.3 29.0 - - + +
367C PRO 3.1 18.5 + - - +
368C ALA 3.2 4.2 + - - +
370C THR* 1.3 76.2 - - - +
372C ARG* 1.3 58.1 + - - +
373C GLY 3.3 0.6 + - - -
415C VAL 5.7 1.0 - - - +
1D MET* 3.8 19.6 - - - +
2D LEU* 3.5 37.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 372 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLN 3.8 1.6 + - - -
27C GLU* 2.4 37.6 + - - +
29C HIS 2.8 28.1 + - - -
30C ILE* 4.4 6.2 - - - +
31C GLU 4.9 0.2 - - - +
38C TYR* 3.8 19.2 + - + -
368C ALA 3.0 11.3 + - - +
369C ILE* 3.2 18.6 - - - +
370C THR 2.9 0.4 - - - -
371C ARG* 1.3 80.5 - - - +
373C GLY* 1.3 56.1 + - - +
374C PHE* 3.7 13.9 - - + -
410C CYS* 3.6 22.3 + - - +
413C TYR* 2.6 43.4 + - + +
414C PRO 4.4 5.2 - - - +
415C VAL* 3.5 24.9 - - + +
1D MET* 3.4 15.2 - - - +
----------------------------------------------------------
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