Contacts of the helix formed by residues 370 - 386 (chain C) in PDB entry 4QGC
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 370 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C MET* 3.9 15.3 + - + +
336C LYS 3.6 16.2 + - - -
337C LYS 3.4 21.3 - - - +
338C PRO* 3.5 38.7 - - + +
364C GLU 4.0 3.7 - - - +
368C GLY 3.3 0.4 - - - -
369C ASP* 1.3 98.4 - - + +
371C PRO* 1.3 64.7 - - - +
372C LEU 3.4 2.2 - - - -
373C GLU* 3.3 36.3 - - + +
374C ALA* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 371 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ALA* 3.7 24.2 - - + +
55C SER* 4.5 6.7 - - - -
60C THR* 4.6 8.3 - - + -
64C MET* 4.8 4.9 - - - -
364C GLU 3.4 12.9 - - - +
365C THR* 3.9 26.9 - - - +
368C GLY 3.9 7.6 - - - +
369C ASP 3.5 8.1 - - - +
370C TYR* 1.3 89.8 - - - +
372C LEU* 1.3 66.0 + - + +
373C GLU* 4.7 0.9 - - - +
374C ALA* 3.3 3.6 + - - +
375C VAL* 3.3 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 372 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C THR* 3.7 27.4 - - + +
63C GLU* 3.3 24.7 - - + +
64C MET* 3.6 22.7 - - + +
67C SER* 3.2 28.3 - - - +
370C TYR 3.4 0.4 - - - -
371C PRO* 1.3 82.8 - - + +
373C GLU* 1.3 73.6 + - - +
375C VAL* 3.4 4.6 + - - +
376C ARG* 3.2 52.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 373 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C MET* 3.5 16.8 - - + +
338C PRO* 4.1 12.3 - - + +
370C TYR* 3.3 43.9 - - + +
371C PRO* 4.1 0.9 - - - +
372C LEU* 1.3 81.8 + - - +
374C ALA* 1.3 60.3 + - - +
376C ARG* 3.9 17.7 + - - +
377C MET* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 374 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C LEU* 3.8 6.4 - - + +
334C MET* 3.6 18.8 - - + +
361C LEU* 3.6 11.5 - - + +
364C GLU* 3.8 31.0 - - + +
365C THR* 4.2 1.1 - - + -
370C TYR 3.1 18.2 + - - +
371C PRO 3.5 6.7 - - - +
372C LEU 3.2 0.2 - - - -
373C GLU* 1.3 78.0 - - - +
375C VAL* 1.3 56.7 + - - +
378C GLN* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 375 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ILE* 4.1 5.5 - - + +
49C CYS* 3.7 18.2 - - - -
64C MET* 3.6 52.0 - - + +
67C SER* 3.9 16.2 - - - +
68C GLY 4.3 2.0 - - - -
69C MET 4.0 13.2 - - - +
361C LEU* 4.1 6.1 - - - -
365C THR* 3.9 3.8 - - + -
371C PRO 3.3 15.4 + - - +
372C LEU* 3.8 5.8 - - - +
373C GLU 3.3 0.2 - - - -
374C ALA* 1.3 75.3 - - - +
376C ARG* 1.3 58.2 + - - +
378C GLN* 3.3 4.0 + - - +
379C HIS* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 376 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C GLU* 4.0 15.6 + - - +
67C SER* 3.0 29.7 + - - +
372C LEU* 3.2 42.6 + - - +
373C GLU* 3.9 17.1 + - - +
375C VAL* 1.3 75.1 - - - +
377C MET* 1.3 59.8 + - - +
379C HIS* 3.3 9.0 + - - +
380C LEU* 2.9 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA* 6.1 0.4 - - - -
304B GLU* 4.5 14.6 - - + -
331C LEU* 4.4 2.5 - - + -
334C MET* 3.9 14.4 - - + -
339C ARG* 3.6 34.5 - - - +
340C PRO* 3.5 38.1 - - + -
373C GLU 2.9 19.4 + - - +
374C ALA 3.9 0.9 - - - +
376C ARG* 1.3 73.0 - - - +
378C GLN* 1.3 61.1 + - - +
380C LEU* 3.2 18.0 + - + -
381C ILE* 2.9 54.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C THR* 5.3 0.2 + - - -
47C ILE* 3.8 25.6 - - + +
331C LEU* 3.9 16.3 - - + +
348C VAL* 3.4 27.4 - - - +
359C ILE* 3.4 43.7 - - + +
361C LEU* 4.1 16.7 - - + +
374C ALA 3.0 18.4 + - - +
375C VAL 3.5 5.2 - - - +
377C MET* 1.3 75.9 - - - +
379C HIS* 1.3 62.3 + - - +
381C ILE* 4.7 2.0 - - - -
382C ALA* 3.1 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ARG* 2.9 48.4 + - + +
47C ILE* 3.7 10.5 - - + +
67C SER 3.9 18.8 + - - +
68C GLY* 5.6 0.7 - - - -
375C VAL 2.9 14.5 + - - +
376C ARG* 3.4 11.0 - - - +
377C MET 3.2 0.2 - - - -
378C GLN* 1.3 78.4 - - - +
380C LEU* 1.3 70.7 + - + +
382C ALA* 3.8 1.2 - - - +
383C ARG* 3.0 52.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLU* 3.2 32.5 - - - +
39C PRO* 5.7 7.0 - - + -
339C ARG* 6.0 0.7 - - - +
376C ARG* 2.9 22.3 + - + +
377C MET* 3.2 21.1 + - + +
379C HIS* 1.3 84.7 - - + +
381C ILE* 1.3 59.3 + - - +
383C ARG* 3.4 11.3 + - - +
384C GLU* 3.0 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 381 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLU* 4.0 15.7 - - + +
307B PHE* 4.6 4.8 - - + -
331C LEU* 4.0 17.7 - - + -
340C PRO* 4.9 2.2 - - + -
345C GLY* 3.6 39.7 - - - +
348C VAL* 3.7 23.1 - - + -
349C ALA* 3.9 10.3 - - + +
377C MET* 2.9 47.0 + - + +
378C GLN* 4.0 3.1 - - - +
380C LEU* 1.3 75.2 - - - +
382C ALA* 1.3 58.0 + - - +
384C GLU* 3.2 6.6 + - - +
385C ALA* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ARG* 4.0 14.1 - - + -
45C THR* 3.2 26.2 + - - +
47C ILE* 5.6 0.2 - - + -
352C VAL* 4.5 16.2 - - + +
378C GLN* 3.1 29.9 + - + +
379C HIS 3.8 2.7 - - - +
381C ILE* 1.3 76.9 - - - +
383C ARG* 1.3 62.3 + - - +
385C ALA* 3.5 3.0 + - - +
386C GLU* 3.4 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C PRO* 3.2 43.0 + - + +
40C ILE* 3.8 10.3 + - - +
41C THR* 2.5 32.9 + - - +
42C ALA* 4.2 11.0 - - - +
43C ARG* 4.6 11.4 - - + +
379C HIS* 3.0 43.2 + - - +
380C LEU* 3.8 10.1 - - - +
382C ALA* 1.3 76.5 - - - +
384C GLU* 1.3 61.1 + - - +
386C GLU* 3.3 19.8 - - - +
387C ALA* 4.2 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLU* 3.6 31.3 - - - +
305B LYS* 2.5 38.7 + - - -
307B PHE* 4.1 5.6 - - + -
308B LEU* 3.2 31.8 - - + +
37C SER 4.9 3.7 - - - +
39C PRO* 3.6 29.5 - - + +
380C LEU* 3.0 21.9 + - + +
381C ILE 3.2 4.5 + - - +
383C ARG* 1.3 73.8 - - - +
385C ALA* 1.3 62.9 + - - +
386C GLU 3.1 2.9 + - - -
387C ALA* 3.4 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B PHE* 3.7 12.5 - - + -
349C ALA* 4.0 32.8 - - + +
352C VAL* 4.0 15.0 - - + -
353C LEU* 3.2 19.9 - - + +
381C ILE 2.9 15.9 + - - +
382C ALA* 3.8 7.0 - - - +
384C GLU* 1.3 74.4 - - - +
386C GLU* 1.3 64.5 + - - +
388C ALA* 3.0 13.2 + - - +
389C ILE* 3.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C THR* 3.8 24.2 - - + +
42C ALA 4.0 4.0 - - - +
44C ASN* 2.7 47.5 + - - +
45C THR* 4.8 2.3 + - - +
352C VAL* 4.6 2.4 - - - +
382C ALA 3.4 14.7 + - - +
383C ARG* 3.3 16.6 - - - +
384C GLU 3.1 0.6 - - - -
385C ALA* 1.3 79.2 - - - +
387C ALA* 1.3 62.9 + - - +
388C ALA 3.2 0.9 + - - -
389C ILE* 3.3 35.3 + - + +
391C HIS* 3.7 21.9 + - + +
467C ARG* 3.9 14.5 + - - -
----------------------------------------------------------
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