Contacts of the helix formed by residues 431 - 444 (chain G) in PDB entry 4E2I
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 431 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393G TRP* 5.2 3.4 - - - -
397G LEU* 4.0 11.5 - - - +
430G SER* 1.3 80.2 - - - +
432G LYS* 1.3 61.8 + - - +
433G THR 3.6 1.8 - - - -
434G THR* 3.2 19.8 + - - -
435G LEU* 2.9 26.2 + - - +
547G PHE* 3.3 17.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 432 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424G PHE* 3.9 16.1 - - + +
426G GLY 3.2 28.5 - - - +
427G PRO 2.9 22.0 + - - -
428G ILE* 4.2 0.6 - - - +
429G ASP* 3.5 15.8 - - - +
430G SER* 2.9 22.6 + - - +
431G GLY* 1.3 72.5 - - - +
433G THR* 1.3 66.8 + - - +
434G THR 2.9 5.5 + - - -
435G LEU* 3.0 1.7 + - - +
436G ALA* 2.7 38.3 + - - +
474G ASP* 4.8 3.6 - - - -
527G THR* 4.9 7.0 - - + -
528G MET 3.9 4.5 - - - +
529G ASN* 3.3 21.3 - - - +
547G PHE* 3.4 27.3 - - + -
418L LYS* 4.6 6.3 - - - +
540L ARG* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 433 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432G LYS* 1.3 86.5 + - - +
434G THR* 1.3 57.3 + - - +
436G ALA* 4.6 0.2 - - - -
437G ALA* 3.1 24.5 + - + +
473G GLU* 3.1 34.4 + - - +
474G ASP* 4.4 7.6 + - - -
527G THR* 5.8 0.9 - - - -
418L LYS* 5.2 8.3 + - + -
499L ASP* 6.0 0.2 - - - -
502L ASP* 4.1 22.7 + - + +
504L SER* 3.6 28.2 - - - +
505L VAL* 5.5 0.7 - - + -
540L ARG* 4.6 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 434 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393G TRP* 3.9 13.9 - - + -
394G LEU* 4.8 1.8 - - + -
397G LEU* 5.3 1.3 - - + -
431G GLY* 3.4 21.7 - - - -
432G LYS 2.9 0.8 - - - -
433G THR* 1.3 80.7 - - - +
435G LEU* 1.3 60.4 + - - +
438G ALA* 3.5 7.4 + - - +
569G ILE* 3.2 51.3 - - + +
570G GLN* 3.5 26.3 - - + +
504L SER* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 435 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394G LEU* 5.5 4.7 - - + -
397G LEU* 4.4 6.7 - - + -
398G LEU* 4.1 4.0 - - + -
401G MET* 3.8 35.0 - - + -
404G VAL* 6.4 1.6 - - + -
405G VAL* 5.5 1.1 - - + -
424G PHE* 3.5 28.7 - - + -
431G GLY 2.9 15.4 + - - +
434G THR* 1.3 75.6 - - - +
436G ALA* 1.3 62.8 + - - +
437G ALA 2.9 5.3 + - - -
438G ALA* 3.1 3.2 + - + +
439G LEU* 2.9 51.6 + - + +
545G ILE* 5.6 1.3 - - + -
547G PHE* 3.6 15.0 - - + -
569G ILE 5.4 0.4 - - - -
575G LEU* 4.2 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 436 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424G PHE* 3.8 13.6 - - + -
432G LYS 2.7 20.5 + - - +
433G THR* 4.6 0.2 - - - -
435G LEU* 1.3 72.5 - - - +
437G ALA* 1.3 58.1 + - - +
439G LEU* 4.2 7.0 - - - +
440G LEU* 3.7 14.0 + - - +
471G VAL* 3.7 23.0 - - + +
473G GLU* 3.8 13.5 - - - +
525G ILE* 4.6 6.9 - - + +
527G THR* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 437 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433G THR 3.1 22.3 + - - +
434G THR 4.1 3.6 - - - +
435G LEU 2.9 0.4 - - - -
436G ALA* 1.3 79.3 - - - +
438G ALA* 1.3 64.8 + - - +
440G LEU* 3.1 20.4 + - - +
441G GLU* 3.4 6.6 + - - +
473G GLU* 5.2 0.2 + - - -
570G GLN* 4.3 10.5 - - + +
504L SER* 3.1 33.9 - - - +
505L VAL* 4.2 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 438 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394G LEU* 5.8 0.4 - - + -
434G THR 3.5 11.7 + - - +
435G LEU* 3.1 5.3 + - + +
437G ALA* 1.3 79.3 - - - +
439G LEU* 1.3 58.7 + - - +
441G GLU* 3.1 3.4 + - - +
442G LEU* 2.9 24.4 + - - +
569G ILE 4.4 3.8 - - - +
570G GLN* 3.7 21.7 + - - -
571G SER 3.5 19.1 - - - +
572G GLY* 3.4 9.2 - - - +
575G LEU* 3.5 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 439 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405G VAL* 4.5 15.0 - - + -
408G PHE* 4.4 27.4 - - + -
424G PHE* 3.6 20.0 - - + -
435G LEU* 2.9 36.2 + - + +
436G ALA 4.4 3.4 - - - +
438G ALA* 1.3 77.3 - - - +
440G LEU* 1.3 63.0 + - - +
442G LEU* 3.6 13.3 - - + +
443G CYS* 3.0 29.2 + - - +
469G LEU* 4.7 2.3 - - - +
525G ILE* 3.5 28.3 - - + -
575G LEU* 3.5 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 440 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436G ALA 3.7 11.2 + - - +
437G ALA 3.1 14.1 + - - +
439G LEU* 1.3 80.2 - - - +
441G GLU* 1.3 55.7 + - - +
444G GLY* 2.8 29.8 + - - -
445G GLY 3.4 32.2 + - - +
446G LYS* 3.4 8.7 - - + +
447G ALA* 3.8 29.2 - - + +
469G LEU* 3.5 24.7 - - + -
471G VAL* 3.5 13.7 - - + -
504L SER 5.6 0.4 - - - +
505L VAL* 4.4 15.5 - - + -
506L LYS* 4.9 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 441 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364G ARG* 2.8 49.2 + - - +
368G LEU* 3.7 7.1 - - + +
371G ARG* 3.4 23.1 + - - +
437G ALA 3.4 5.3 + - - +
438G ALA* 3.1 8.5 + - - +
440G LEU* 1.3 78.7 - - + +
442G LEU* 1.3 62.0 + - - +
443G CYS 3.3 0.4 - - - -
570G GLN 5.0 0.7 - - - +
571G SER* 3.6 12.1 + - - -
572G GLY* 2.8 29.6 + - - +
573G ILE* 4.1 2.8 + - - +
506L LYS* 5.6 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 442 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364G ARG* 3.5 6.8 - - - +
365G PHE* 3.9 13.6 - - + -
368G LEU* 3.5 26.7 - - + +
405G VAL* 3.7 24.2 - - + -
409G LEU* 4.3 11.2 - - + -
438G ALA 2.9 15.3 + - - +
439G LEU* 3.2 12.3 + - + +
441G GLU* 1.3 78.9 - - - +
443G CYS* 1.3 61.0 + - - +
572G GLY* 3.6 21.3 - - - +
575G LEU* 3.6 27.1 - - + -
576G LEU* 3.8 11.4 - - + +
579G LEU* 3.8 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 443 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360G MET 5.4 0.2 - - - +
361G LEU* 3.7 24.9 - - + +
364G ARG* 3.2 19.9 - - - +
408G PHE* 3.9 14.4 - - - -
409G LEU* 3.5 32.1 - - - -
412G MET* 5.2 0.2 - - - -
439G LEU 3.0 14.3 + - - +
442G LEU* 1.3 83.3 - - - +
444G GLY* 1.3 60.6 + - - +
468G PHE* 3.8 10.8 - - + +
469G LEU* 3.5 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 444 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364G ARG* 4.2 17.9 - - - -
440G LEU 2.8 21.8 + - - -
441G GLU 4.1 0.6 + - - -
442G LEU 3.8 0.2 - - - -
443G CYS* 1.3 75.7 - - - +
445G GLY* 1.3 58.9 + - - -
468G PHE* 3.3 23.3 - - - +
469G LEU* 3.4 13.8 - - - +
----------------------------------------------------------
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