Contacts of the helix formed by residues 432 - 449 (chain A) in PDB entry 1M7X
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 ASN 432 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A HIS* 5.6 4.4 + - - -
374A ILE* 6.1 2.6 - - - +
375A TYR 5.8 0.2 + - - -
377A TYR* 4.2 12.1 - - - -
410A MET 3.0 17.9 + - - +
411A ILE 3.0 10.8 + - - -
412A TYR 4.1 9.8 + - - +
413A ARG 4.7 4.7 - - - +
430A ARG 3.4 3.4 + - - -
431A GLU* 1.3 66.3 - - - +
433A LEU* 1.3 52.9 + - - +
434A GLU* 2.6 39.8 + - - +
435A ALA* 2.8 34.3 + - - +
436A ILE* 3.2 11.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLY* 3.2 24.2 - - - +
431A GLU* 2.7 47.6 + - + +
432A ASN* 1.3 69.1 - - - +
434A GLU* 1.3 58.9 + - - +
436A ILE* 4.0 13.9 - - + +
437A GLU* 3.3 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A HIS* 2.7 39.6 + - - -
376A ASN* 3.4 2.8 + - - -
377A TYR* 3.0 15.5 + - - +
378A GLY* 2.8 41.6 + - - +
432A ASN* 2.6 17.8 + - - +
433A LEU* 1.3 72.7 - - - +
435A ALA* 1.3 59.6 + - - +
437A GLU* 3.1 7.7 + - - +
438A PHE* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 3.8 28.7 - - + -
410A MET* 3.2 24.7 - - + +
432A ASN* 2.8 30.9 + - - +
434A GLU* 1.3 71.2 - - - +
436A ILE* 1.3 67.5 + - - +
437A GLU 3.0 1.6 - - - -
438A PHE* 2.9 13.4 + - + +
439A LEU* 3.0 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ILE* 3.5 39.0 - - + +
431A GLU* 3.8 36.3 - - + +
432A ASN 3.2 10.9 + - - +
433A LEU* 4.1 13.2 - - + +
435A ALA* 1.3 76.9 - - - +
437A GLU* 1.3 59.5 + - - +
439A LEU* 3.9 5.3 + - - +
440A ARG* 3.2 53.5 + - - +
463A PHE* 4.3 15.0 - - + -
475A LEU* 4.3 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A LEU 3.3 18.0 + - - +
434A GLU* 3.1 7.9 + - - +
435A ALA 3.0 0.6 - - - -
436A ILE* 1.3 80.3 - - - +
438A PHE* 1.3 63.3 + - - +
440A ARG* 3.3 35.6 + - - +
441A ASN* 2.9 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A TRP* 4.1 10.5 - + - -
338A PRO* 4.1 14.4 - - + -
377A TYR* 3.4 35.9 - + + +
383A SER* 3.8 22.4 - - - -
386A LEU* 3.2 45.5 - - + -
387A VAL* 3.6 13.0 - - + -
410A MET* 5.5 1.8 - - - -
434A GLU 3.0 11.3 + - - +
435A ALA* 2.9 7.8 + - + +
437A GLU* 1.3 75.1 - - - +
439A LEU* 1.3 75.3 + - + +
441A ASN* 3.1 6.4 + - + +
442A THR* 2.7 56.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A TRP* 5.6 1.3 - - + -
338A PRO* 5.1 1.6 - - + -
404A VAL* 4.7 10.1 - - + -
407A VAL* 3.6 19.3 - - + -
410A MET* 3.4 36.8 - - + -
411A ILE* 4.5 10.8 - - + -
435A ALA* 3.0 18.4 + - + +
436A ILE* 4.2 4.5 - - - +
438A PHE* 1.3 95.6 - - + +
440A ARG* 1.3 63.4 + - - +
442A THR* 3.2 6.5 + - + +
443A ASN* 2.9 37.0 + - - +
475A LEU* 4.6 10.5 - - + -
477A PHE* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ILE* 3.2 33.5 + - - +
437A GLU* 3.3 35.0 + - - +
438A PHE 3.3 0.2 - - - -
439A LEU* 1.3 77.9 - - - +
441A ASN* 1.3 62.6 + - - +
444A ARG* 2.8 12.7 + - - +
463A PHE* 4.9 6.1 - - - -
470A GLN* 2.7 44.9 + - + -
472A MET 5.1 1.2 + - - -
473A GLY 3.1 23.6 + - - -
474A GLY* 3.2 14.7 - - - -
475A LEU 3.1 27.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A SER* 5.9 2.2 - - - +
387A VAL* 5.7 2.0 - - + -
437A GLU* 2.9 37.6 + - - +
438A PHE* 3.1 6.6 + - - +
440A ARG* 1.3 80.1 - - - +
442A THR* 1.3 57.9 + - - +
444A ARG* 3.0 29.9 + - - +
445A ILE* 2.7 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A TRP* 4.0 28.3 - - + -
387A VAL* 3.6 17.5 - - + +
390A ALA* 4.6 3.6 - - + -
438A PHE* 2.7 52.2 + - - -
439A LEU* 3.6 8.7 - - + -
441A ASN* 1.3 72.5 - - - +
443A ASN* 1.3 55.4 + - - +
445A ILE* 3.8 2.1 - - - +
446A LEU* 2.6 60.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A LEU* 2.9 22.0 + - - +
440A ARG 3.8 1.3 - - - +
442A THR* 1.3 81.4 - - - +
444A ARG* 1.3 61.6 + - - +
446A LEU* 3.4 7.7 - - - +
447A GLY* 3.4 18.0 + - - -
455A THR* 2.7 34.1 + - - +
470A GLN* 3.9 4.3 - - - +
475A LEU 2.9 28.5 + - - +
476A GLY 3.6 21.9 + - - +
477A PHE* 4.0 20.3 - - - -
478A TRP* 4.3 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ARG 2.8 18.4 + - - +
441A ASN* 3.0 46.0 + - - +
443A ASN* 1.3 72.5 - - - +
445A ILE* 1.3 83.9 + - - +
447A GLY* 3.4 1.9 + - - -
448A GLU* 3.1 55.2 + - + +
470A GLN* 3.3 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.8 29.2 - - + -
387A VAL* 3.7 32.3 - - + -
391A LEU* 4.7 5.2 - - + -
441A ASN* 2.7 35.9 + - + +
442A THR 3.8 1.8 - - - +
444A ARG* 1.3 90.1 - - - +
446A LEU* 1.3 52.8 + - - +
447A GLY 2.6 16.8 + - - -
448A GLU* 2.8 8.5 + - - +
449A GLN* 2.8 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A TRP* 5.4 0.9 - - + -
387A VAL* 6.0 1.6 - - + -
390A ALA* 3.7 13.9 - - + -
391A LEU* 4.2 18.6 - - + -
394A ILE* 3.1 28.0 - - + -
402A LEU* 3.5 28.9 - - + -
442A THR* 2.6 33.0 + - + +
443A ASN* 3.4 9.0 - - - +
445A ILE* 1.3 70.7 - - + +
447A GLY* 1.3 54.5 + - - +
450A VAL* 3.3 21.8 - - + +
453A ALA* 4.5 8.7 - - + +
455A THR* 3.9 19.9 - - + +
478A TRP* 3.6 15.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ASN 3.4 11.1 + - - -
444A ARG 3.7 3.4 - - - -
445A ILE 2.6 4.2 + - - -
446A LEU* 1.3 76.1 - - - +
448A GLU* 1.3 65.9 + - - +
449A GLN 3.6 0.4 - - - +
451A SER* 3.8 26.9 - - - -
453A ALA 5.9 0.2 - - - -
478A TRP* 4.2 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ARG* 3.1 47.9 + - + +
445A ILE* 2.8 7.2 + - - +
447A GLY* 1.3 81.5 - - - +
449A GLN* 1.3 77.0 + - - +
450A VAL 3.5 0.4 - - - -
451A SER* 4.5 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.5 21.7 - - + +
120A ARG* 2.9 32.5 + - - +
391A LEU* 4.1 17.7 - - + -
395A GLU* 4.3 4.0 - - - +
445A ILE* 2.8 34.9 + - + +
448A GLU* 1.3 96.0 + - - +
450A VAL* 1.3 64.9 + - + +
451A SER 3.9 0.4 - - - -
----------------------------------------------------------
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