Contacts of the helix formed by residues 410 - 422 (chain W) in PDB entry 2Q4G
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 410 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383W ASP* 2.4 31.5 + - - -
408W CYS 3.4 1.8 + - - -
409W LEU* 1.3 74.5 - - - +
411W ASP* 1.3 62.5 + - - -
412W ALA 3.2 2.2 - - - -
414W ILE* 2.9 34.9 + - - +
437W TYR 5.3 2.5 - - - -
67X ASN* 4.6 13.0 - - - -
69X GLN* 5.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 411 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383W ASP* 4.4 0.2 + - - -
410W GLY* 1.3 73.0 - - - -
412W ALA* 1.3 62.6 + - - +
414W ILE* 4.8 2.7 - - - -
415W LEU* 3.1 25.1 + - - +
437W TYR 5.2 3.4 + - - +
438W TRP* 3.0 31.7 - - - +
439W SER* 2.8 31.9 + - - +
441W GLU* 5.3 0.2 - - - +
442W MET* 3.2 17.0 + - - +
445W ARG* 4.8 3.6 + - - -
67X ASN* 5.5 1.4 - - - +
69X GLN* 5.7 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 412 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383W ASP* 4.1 14.1 + - + +
410W GLY 3.2 0.6 - - - -
411W ASP* 1.3 79.6 - - - +
413W GLY* 1.3 55.6 + - - +
415W LEU* 3.8 8.3 - - - +
416W GLN* 2.7 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 413 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383W ASP* 2.8 25.3 + - - -
386W CYS* 3.6 22.7 - - - +
410W GLY 3.1 0.4 + - - -
412W ALA* 1.3 74.7 - - - +
414W ILE* 1.3 65.8 + - - +
416W GLN* 3.0 26.1 + - - +
417W LEU* 3.1 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 414 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386W CYS* 4.8 0.2 - - - -
409W LEU* 4.7 15.9 - - + +
410W GLY 2.9 22.5 + - - +
411W ASP* 4.3 2.5 - - - +
413W GLY* 1.3 72.8 - - - +
415W LEU* 1.3 67.7 + - - +
417W LEU* 2.6 25.9 + - + +
418W VAL* 2.8 27.1 + - + -
431W LEU* 6.4 0.7 - - + -
433W LEU* 4.9 13.7 - - + -
436W ILE* 3.9 14.8 - - + -
437W TYR 5.5 0.2 - - - -
438W TRP* 3.4 42.6 - - + -
442W MET* 4.0 16.8 - - + -
446W LEU* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 415 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411W ASP 3.1 18.6 + - - +
412W ALA* 3.8 9.2 - - - +
414W ILE* 1.3 78.0 - - - +
416W GLN* 1.3 58.6 + - + +
418W VAL* 3.2 5.9 + - + +
419W GLU* 2.8 58.2 + - + +
442W MET* 4.1 9.1 - - + -
445W ARG* 3.8 32.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 416 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383W ASP* 4.0 12.8 + - - +
386W CYS 4.1 3.1 - - - +
387W SER* 3.1 37.0 + - - -
390W ALA* 3.1 27.2 - - + +
412W ALA* 2.7 36.9 + - - +
413W GLY* 3.2 14.3 - - - +
414W ILE 2.8 1.0 + - - -
415W LEU* 1.3 74.7 - - + +
417W LEU* 1.3 68.0 + - - +
419W GLU* 3.3 15.4 + - - +
420W SER* 3.4 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 417 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386W CYS* 4.0 9.9 - - - +
389W LEU* 3.6 34.1 - - + -
390W ALA* 4.0 11.7 - - - +
393W LEU* 4.3 11.4 - - + -
402W LEU* 5.4 0.4 - - + -
404W LEU* 3.5 28.9 - - + -
409W LEU* 4.5 11.9 - - + -
413W GLY 3.1 9.9 + - - +
414W ILE* 2.6 26.9 + - + +
416W GLN* 1.3 72.3 - - - +
418W VAL* 1.3 62.1 + - + +
420W SER* 3.0 13.9 + - - -
421W VAL* 3.0 19.7 + - + +
431W LEU* 5.0 20.6 - - + -
433W LEU* 5.1 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 418 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414W ILE* 2.8 17.0 + - + +
415W LEU* 3.4 10.8 - - + +
417W LEU* 1.3 72.5 - - + +
419W GLU* 1.3 62.3 + - - +
420W SER 2.7 15.6 + - - -
421W VAL* 3.1 7.3 + - + -
422W ARG* 3.0 41.5 + - + +
431W LEU* 6.3 2.5 - - + -
442W MET* 3.9 13.7 - - + -
445W ARG* 4.9 15.0 - - + +
446W LEU* 3.8 29.6 - - + -
449W LEU* 4.2 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 419 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394W LEU* 5.2 0.2 - - - +
415W LEU* 2.8 47.0 + - + +
416W GLN* 3.3 9.4 + - - +
418W VAL* 1.3 75.9 - - - +
420W SER* 1.3 59.7 + - - +
422W ARG* 3.2 44.1 + - - +
423W GLN* 2.8 24.9 + - - -
445W ARG* 5.4 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 420 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390W ALA* 2.3 46.7 + - - +
393W LEU* 4.3 8.1 - - - -
394W LEU* 3.5 26.4 - - - +
416W GLN 3.4 1.5 + - - -
417W LEU 3.0 8.8 + - - -
418W VAL 2.7 2.4 + - - -
419W GLU* 1.3 80.4 - - - +
421W VAL* 1.3 64.4 + - - -
422W ARG 3.3 0.2 - - - -
423W GLN* 3.3 10.1 + - - +
426W CYS* 3.3 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 421 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393W LEU* 4.1 10.1 - - + -
417W LEU* 3.0 20.0 + - + +
418W VAL* 3.6 8.5 - - + +
420W SER* 1.3 71.9 - - - +
422W ARG* 1.3 59.6 + - - +
423W GLN 3.0 5.1 + - - -
426W CYS* 3.9 16.4 - - - -
428W LEU* 3.8 29.8 - - + -
431W LEU* 5.1 12.6 - - + -
449W LEU* 3.6 26.0 - - + -
453W LYS* 2.8 34.7 + - - +
456W LEU* 3.5 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 422 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418W VAL* 3.0 32.6 + - + +
419W GLU* 3.2 48.6 + - - +
421W VAL* 1.3 77.1 - - - +
423W GLN* 1.3 77.4 + - - +
424W PRO* 3.8 3.1 - - - +
449W LEU* 3.5 25.7 - - + +
452W ASP* 5.6 6.2 - - + +
453W LYS* 4.4 8.8 - - - +
----------------------------------------------------------
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