Contacts of the helix formed by residues 401 - 417 (chain A) in PDB entry 1GM5
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 401 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLN* 3.6 11.4 - - - -
399A GLY 3.6 0.4 - - - -
400A SER* 1.3 81.4 - - - +
402A LYS* 1.3 70.0 + - - +
403A THR 3.1 2.9 - - - -
404A VAL* 3.8 6.2 + - - +
405A VAL* 2.9 20.6 + - - +
545A ASP* 4.5 3.6 - - - -
548A PRO* 4.1 0.4 - - - +
1756A ADP 3.1 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LEU* 3.5 35.7 - - + +
395A GLN 4.4 1.1 - - - +
396A GLY* 1.6 69.0 + - - +
397A ASP* 2.0 13.9 - - - +
398A VAL* 3.9 4.0 - - - +
400A SER* 3.3 11.8 + - - +
401A GLY* 1.3 82.1 - - - +
403A THR* 1.3 65.4 + - - +
405A VAL* 3.1 18.8 - - - +
406A ALA* 3.4 4.3 + - - -
522A MET* 4.8 8.3 - - + -
523A SER 3.3 20.7 + - - +
524A ALA* 4.1 5.8 - - - +
545A ASP* 5.1 3.4 - - - -
1756A ADP 3.1 22.4 + - - +
1757A MG 4.7 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A GLY 3.1 0.8 - - - -
402A LYS* 1.3 73.3 - - - +
404A VAL* 1.3 75.2 + - - +
406A ALA* 3.0 21.2 + - + +
407A GLN* 2.9 26.8 - - + +
433A HIS* 5.3 11.0 + - + +
436A ARG* 3.5 29.3 + - + +
437A THR* 6.3 1.1 - - + -
522A MET* 5.1 4.7 - - + -
1756A ADP 3.0 22.4 + - - -
1757A MG 3.2 18.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A PHE* 5.7 4.3 - - + -
365A LEU* 5.0 10.5 - - + -
367A PHE* 4.3 16.8 - - + -
369A LEU* 4.7 15.0 - - + -
373A GLN* 5.1 1.8 - - - +
401A GLY* 3.8 9.4 - - - +
403A THR* 1.3 71.8 - - - +
405A VAL* 1.3 55.4 + - + +
407A GLN* 2.4 56.2 + - + +
408A LEU* 3.1 14.4 - - + +
436A ARG* 5.1 1.3 - - - +
1756A ADP 3.4 45.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU* 5.9 0.7 - - + -
373A GLN* 4.0 27.1 - - + +
376A ALA* 3.4 35.4 - - + -
377A HIS* 4.6 6.2 + - + +
380A ILE* 4.6 11.4 - - + +
394A LEU* 4.5 10.8 - - + -
401A GLY 2.9 24.0 - - - +
402A LYS* 3.1 7.0 - - - +
404A VAL* 1.3 74.6 - - + +
406A ALA* 1.3 65.5 + - - +
408A LEU* 2.8 25.9 + - + +
409A ALA* 2.9 11.4 + - - +
545A ASP* 5.4 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LEU* 4.5 4.4 - - + +
402A LYS 3.4 3.1 + - - +
403A THR* 3.0 17.1 + - + +
405A VAL* 1.3 75.6 - - - +
407A GLN* 1.3 63.0 + - + +
409A ALA* 3.0 14.2 - - - +
410A ILE* 2.9 25.3 + - + +
422A PHE* 5.5 4.3 - - + -
495A ILE* 3.8 19.5 - - + +
520A LEU* 4.9 6.5 - - + -
522A MET* 4.2 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A PHE* 3.7 29.1 - - + -
403A THR* 2.9 27.3 - - + +
404A VAL* 2.4 52.7 + - - +
406A ALA* 1.3 66.8 - - + +
408A LEU* 1.3 59.0 + - - +
410A ILE* 2.8 28.5 + - + +
411A LEU* 2.9 17.3 + - - +
436A ARG* 4.8 2.8 + - - +
437A THR* 4.1 20.4 + - - +
440A SER* 3.3 35.9 + - - -
441A PHE* 4.0 7.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ALA* 4.4 5.6 - - + -
361A PHE* 4.5 13.5 - - + -
362A ILE* 3.6 28.9 - - + -
365A LEU* 6.3 0.4 - - + -
369A LEU* 5.7 4.7 - - + -
377A HIS* 3.4 42.0 - - + +
404A VAL* 3.1 19.5 - - + +
405A VAL* 2.8 37.4 + - + +
407A GLN* 1.3 72.1 - - + +
409A ALA* 1.3 67.7 + - - +
410A ILE 2.6 3.0 + - - -
411A LEU* 2.9 16.7 + - - +
412A ASP* 2.8 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A HIS* 5.2 0.6 + - - -
380A ILE* 4.4 11.0 - - + +
384A MET* 3.9 24.5 - - + +
405A VAL 2.9 9.2 + - - +
406A ALA* 3.0 19.7 - - - +
408A LEU* 1.3 75.5 - - - +
410A ILE* 1.3 56.0 + - - +
412A ASP* 4.0 1.1 - - - +
413A ASN* 3.0 32.1 + - - +
493A LEU* 4.0 13.4 - - + +
495A ILE* 4.5 6.5 - - + -
520A LEU* 4.6 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ALA* 2.9 15.3 + - + +
407A GLN* 2.8 13.8 + - + +
408A LEU 2.6 6.3 + - - -
409A ALA* 1.3 76.7 - - - +
411A LEU* 1.3 54.8 + - - -
414A TYR* 3.1 26.0 + - - +
420A THR* 3.9 26.5 - - + +
422A PHE* 4.6 20.4 - - + -
437A THR* 5.1 7.6 - - + -
441A PHE* 2.6 46.4 - - + -
446A ILE* 5.3 1.8 - - + -
474A VAL* 4.4 17.9 - - + -
493A LEU* 4.9 0.4 - - + -
495A ILE* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 3.8 30.5 - - + -
358A ALA* 4.2 3.8 - - + +
361A PHE* 3.2 41.5 - - + -
407A GLN 2.9 14.1 + - - +
408A LEU* 2.9 7.5 + - - +
410A ILE* 1.3 72.4 - - - +
412A ASP* 1.3 61.1 + - - +
413A ASN 3.1 1.3 - - - -
414A TYR* 2.9 4.6 + - - -
415A GLU* 2.4 39.9 + - - +
441A PHE* 3.8 16.6 - - + -
444A PHE* 3.1 36.3 - - + -
446A ILE* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ILE* 3.4 15.2 - - + +
358A ALA* 4.8 3.0 + - - +
377A HIS* 3.5 1.6 - - - -
380A ILE* 6.2 0.4 - - - -
381A ARG* 1.5 68.1 + - + +
384A MET* 4.5 13.2 - - + -
408A LEU* 2.8 29.0 + - - +
409A ALA* 4.0 3.8 - - - +
411A LEU* 1.3 80.6 - - - +
413A ASN* 1.3 64.5 + - - +
415A GLU* 3.6 10.8 - - - +
416A ALA* 2.8 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ILE* 5.9 0.2 - - - -
384A MET* 4.6 10.3 - - - -
409A ALA 3.0 20.6 + - - +
410A ILE 4.1 1.8 - - - +
412A ASP* 1.3 78.1 - - - +
414A TYR* 1.3 66.9 + - - +
416A ALA* 2.9 21.1 + - - +
417A GLY 3.3 1.2 + - - -
418A PHE* 2.9 30.9 + - - +
420A THR* 3.7 16.8 - - + +
492A GLY* 2.7 40.7 - - - +
493A LEU* 3.2 16.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 4.4 9.9 - - + -
410A ILE* 3.1 17.7 + - + +
411A LEU 2.9 3.3 + - - +
413A ASN* 1.3 78.2 - - - +
415A GLU* 1.3 63.8 + - - +
416A ALA 2.8 11.8 + - - -
417A GLY* 3.2 14.0 + - - -
418A PHE 3.5 14.6 - - - +
420A THR* 5.2 3.6 - - + -
445A ASN* 2.9 24.9 + - - +
446A ILE* 3.3 34.1 - - + -
471A GLN* 4.5 14.2 + - + -
473A ASP* 3.0 48.0 + - + +
474A VAL* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LYS 5.0 0.2 - - - +
353A ILE* 4.3 8.5 - - + -
354A GLU* 2.0 86.2 + - - +
357A LEU* 2.5 59.6 - - + +
358A ALA 4.4 0.2 + - - -
411A LEU 2.4 26.6 + - - +
412A ASP* 3.6 9.2 - - - +
414A TYR* 1.3 73.9 - - - +
416A ALA* 1.3 63.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LYS* 3.8 32.4 + - + -
352A LYS 3.8 22.4 - - - +
353A ILE* 4.6 4.3 - - + -
412A ASP 2.8 14.7 + - - +
413A ASN* 3.0 13.9 - - - +
414A TYR 2.8 1.2 + - - -
415A GLU* 1.3 82.1 - - - +
417A GLY* 1.3 59.2 + - - +
418A PHE* 4.6 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LYS* 3.9 16.9 - - - +
414A TYR 3.2 6.3 + - - -
416A ALA* 1.3 81.1 - - - +
418A PHE* 1.3 71.5 + - - +
488A PHE* 5.6 2.1 - - - -
490A ASN* 4.2 6.1 - - - +
----------------------------------------------------------
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