Contacts of the helix formed by residues 366 - 386 (chain A) in PDB entry 1GC5
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 GLU 366 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLY* 1.3 68.0 - - - -
367A GLU* 1.3 63.6 + - - +
368A VAL 3.1 3.4 - - - -
369A ARG* 2.8 39.2 + - - +
370A ASP* 3.0 19.1 + - - +
420A PHE* 4.3 5.2 - - - -
421A GLU* 2.6 44.7 - - - +
424A LEU* 3.4 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ARG 4.3 0.3 - - - +
365A GLY* 3.5 19.0 - - - -
366A GLU* 1.3 81.0 - - - +
368A VAL* 1.3 62.3 + - - +
370A ASP* 4.6 3.6 + - - +
371A ALA* 3.0 27.2 + - - +
461A GLU* 3.9 4.4 - - + +
464A MET* 3.2 48.8 - - + +
465A ARG* 3.7 36.8 + - + -
467A ARG* 5.6 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ALA* 3.7 29.6 - - + +
361A THR* 4.0 15.7 - - + +
363A TYR* 4.0 24.7 - - + -
365A GLY* 3.7 17.3 - - - +
366A GLU 3.1 0.8 - - - -
367A GLU* 1.3 79.2 - - + +
369A ARG* 1.3 59.7 + - - +
371A ALA* 3.8 2.1 - - - +
372A LEU* 3.1 31.4 + - + +
431A GLN* 4.0 12.8 - - - +
433A ALA* 4.3 7.6 - - + -
461A GLU* 3.4 26.2 - - + +
465A ARG* 5.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TRP* 4.3 6.7 - - - -
15A LEU* 3.8 40.0 - - - +
365A GLY 4.5 0.6 + - - -
366A GLU* 2.8 34.5 + - - +
368A VAL* 1.3 77.0 - - - +
370A ASP* 1.3 79.5 + - - +
372A LEU* 3.1 7.7 + - - +
373A LEU* 2.9 31.4 + - + +
421A GLU* 3.7 16.0 + - - +
422A ASN* 3.0 34.2 + - - +
423A GLY 4.3 4.5 - - - +
424A LEU* 4.1 16.6 - - + +
433A ALA* 4.4 7.4 - - + +
434A PHE 4.2 6.3 - - - +
435A VAL* 3.8 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 5.4 0.6 - - - +
18A ASN* 5.9 0.6 - - - +
19A ALA* 3.5 32.7 - - + +
22A ASN* 3.0 26.3 + - - +
366A GLU* 3.0 16.6 + - - +
367A GLU* 4.9 0.5 - - - -
369A ARG* 1.3 105.1 + - - +
371A ALA* 1.3 52.2 + - - +
373A LEU* 3.1 4.7 + - - +
374A PHE* 2.7 33.4 + - - +
464A MET* 3.9 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A GLU 3.0 20.0 + - - +
368A VAL 3.8 4.7 - - - +
370A ASP* 1.3 74.8 - - - +
372A LEU* 1.3 59.7 + - + +
374A PHE* 3.2 2.6 + - - +
375A ALA* 2.9 30.5 + - - +
457A ALA* 3.4 32.0 - - + +
460A SER* 3.6 10.3 - - - +
461A GLU* 3.4 15.3 - - + +
464A MET* 3.4 8.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ARG* 4.6 4.7 - - - +
350A HIS* 3.5 38.4 - - + +
357A TYR* 3.6 26.1 - - + +
359A ALA* 3.8 29.8 - - + +
368A VAL* 3.1 19.7 + - + +
369A ARG 3.1 7.0 + - - +
371A ALA* 1.3 78.1 - - - +
373A LEU* 1.3 57.2 + - - +
375A ALA* 3.4 4.1 + - - -
376A SER* 3.0 28.4 + - - -
433A ALA* 4.0 22.7 - - + +
435A VAL* 4.0 18.2 - - + -
457A ALA* 4.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TRP* 4.0 13.9 - - + -
15A LEU* 3.8 27.4 - - + +
16A TYR* 3.3 54.9 - - + +
19A ALA* 3.5 24.0 - - + -
369A ARG* 2.9 25.9 + - - +
370A ASP* 3.1 11.6 + - - +
372A LEU* 1.3 75.0 - - - +
374A PHE* 1.3 64.7 + - - +
376A SER* 3.4 1.5 + - - -
377A LEU* 3.2 20.2 + - - +
435A VAL* 3.6 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 4.5 4.6 - - - +
20A PHE* 4.0 35.7 - + - +
23A ALA* 3.3 28.3 - - + -
24A LEU* 4.7 7.2 - - + -
27A ILE* 4.4 13.2 - - + -
133A TYR* 3.7 44.4 - + - -
370A ASP 2.7 19.8 + - - +
371A ALA 3.2 4.7 + - - +
373A LEU* 1.3 72.7 - - - +
375A ALA* 1.3 59.8 + - - +
377A LEU* 3.1 9.7 + - - +
378A ALA* 2.9 26.2 + - + +
391A ILE* 4.5 9.0 - - + -
394A ILE* 4.3 11.4 - - + -
456A SER* 3.9 19.1 - - - -
460A SER* 4.0 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A TYR* 3.9 9.5 + - + -
371A ALA 2.9 17.1 + - - +
372A LEU* 3.6 5.2 - - - +
374A PHE* 1.3 78.3 - - - +
376A SER* 1.3 55.8 + - - +
378A ALA* 3.4 2.3 + - - +
379A ALA* 2.9 29.3 + - - +
453A ILE* 3.3 31.7 - - + +
456A SER* 4.0 13.5 - - - -
457A ALA* 3.6 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 2.9 28.7 + - - -
357A TYR* 3.5 23.0 + - - -
372A LEU 3.0 16.8 + - - -
373A LEU* 3.7 5.6 - - - -
374A PHE 3.2 0.2 - - - -
375A ALA* 1.3 73.6 - - - +
377A LEU* 1.3 65.9 + - - +
379A ALA* 3.5 2.3 + - - +
380A ALA* 3.1 23.0 + - - +
435A VAL* 4.6 1.1 - - - -
437A THR* 3.6 7.2 - - - -
438A LYS* 3.4 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 3.7 12.8 - - + +
20A PHE* 3.8 40.4 - - + -
373A LEU 3.2 13.8 + - - +
374A PHE* 3.1 10.2 + - - +
376A SER* 1.3 75.4 - - - +
378A ALA* 1.3 60.6 + - - +
380A ALA* 3.2 1.0 + - - -
381A ALA* 2.9 27.9 + - - +
394A ILE* 3.9 13.9 - - + +
397A ALA* 3.3 29.6 - - + +
398A LEU* 3.9 18.4 - - + +
438A LYS* 3.7 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TYR* 3.6 24.2 - - - +
374A PHE* 2.9 16.6 + - + +
375A ALA* 3.6 6.1 - - - +
376A SER 3.3 0.2 - - - -
377A LEU* 1.3 77.7 - - - +
379A ALA* 1.3 56.1 + - - +
381A ALA* 3.5 4.1 + - - +
382A LYS* 3.0 29.5 + - - +
388A LEU* 4.1 3.8 - - + +
394A ILE* 4.0 17.8 - - + +
452A THR* 4.0 11.1 - - + +
456A SER* 3.9 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A TYR* 3.8 8.3 - - - +
375A ALA 2.9 17.2 + - - +
376A SER 3.8 2.7 - - - +
378A ALA* 1.3 75.9 - - - +
380A ALA* 1.3 58.1 + - - +
382A LYS* 3.5 5.8 + - - +
383A ALA* 3.0 29.8 + - - +
449A ILE* 3.9 18.7 - - + +
452A THR* 4.3 4.7 - - - +
453A ILE* 3.6 26.2 - - + -
470A ADP 4.8 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A SER 3.1 16.9 + - - +
377A LEU* 3.6 4.5 - - - +
379A ALA* 1.3 75.1 - - - +
381A ALA* 1.3 56.2 + - - +
383A ALA* 3.2 1.2 + - - -
384A MET* 2.8 40.8 + - - +
397A ALA* 3.9 12.8 - - + -
400A VAL* 4.6 4.0 - - + -
438A LYS* 3.8 28.0 + - + +
440A VAL* 3.6 18.8 - - + +
470A ADP 5.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU 2.9 16.5 + - - +
378A ALA 3.7 4.9 - - - +
380A ALA* 1.3 76.9 - - - +
382A LYS* 1.3 57.3 + - - +
384A MET* 3.0 9.4 + - - +
385A LYS* 2.9 38.5 + - + +
388A LEU* 4.1 14.4 - - + -
393A GLN 4.2 5.8 - - - +
394A ILE* 3.8 28.3 - - + -
397A ALA* 3.8 7.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 4.9 9.6 - - - -
128A LEU* 6.2 1.1 - - + -
378A ALA 3.0 18.4 + - - +
379A ALA* 3.7 6.5 - - - +
381A ALA* 1.3 76.4 - - - +
383A ALA* 1.3 55.1 + - - +
385A LYS* 5.2 0.2 - - - -
386A GLY* 2.6 46.9 + - - +
387A ASN* 5.3 1.1 - - - +
388A LEU* 4.1 27.3 - - + +
445A SER* 2.7 33.0 + - - +
446A THR 4.4 0.4 - - - +
447A VAL* 4.1 1.8 - - - +
448A GLY* 3.4 25.3 - - - +
449A ILE* 4.4 10.5 - - + +
452A THR* 3.7 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ALA 3.0 18.0 + - - +
380A ALA 3.2 3.8 + - - +
382A LYS* 1.3 76.5 - - - +
384A MET* 1.3 58.8 + - - +
440A VAL* 4.1 12.6 - - + -
443A PRO* 3.3 24.1 - - + +
444A LYS* 2.6 32.7 + - - +
446A THR 4.9 4.3 - - - +
449A ILE* 3.6 20.2 - - + -
470A ADP 4.2 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ALA 2.8 15.9 + - - +
381A ALA* 3.0 9.4 + - - +
383A ALA* 1.3 76.6 - - - +
385A LYS* 1.3 95.1 + - - +
396A ASP* 3.9 15.3 - - + +
397A ALA* 4.1 12.3 - - - +
399A SER* 5.5 1.1 - - - +
400A VAL* 3.7 26.9 - - + -
440A VAL* 3.9 18.8 - - + +
444A LYS* 2.6 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ALA* 2.9 19.9 + - - +
384A MET* 1.3 98.3 - - - +
386A GLY* 1.3 57.1 + - - +
387A ASN* 2.9 26.1 + - - +
388A LEU* 5.0 1.3 - - + -
393A GLN* 3.1 45.3 - - + +
396A ASP* 2.8 28.9 + - - -
444A LYS* 3.8 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ARG* 5.4 1.5 + - - -
382A LYS* 2.6 34.7 + - - +
384A MET 3.3 2.2 - - - -
385A LYS* 1.3 71.0 - - - +
387A ASN* 1.3 63.4 + - - +
444A LYS* 3.4 3.5 - - - +
445A SER* 2.9 45.4 + - - -
----------------------------------------------------------
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