Contacts of the helix formed by residues 404 - 415 (chain A) in PDB entry 4WTM
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 PRO 404 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.1 8.3 - - + -
394A ARG 3.8 9.2 - - - +
395A ALA 3.4 25.8 - - - +
397A TRP 3.4 23.3 - - - +
398A GLU* 3.4 26.7 - - + +
402A HIS* 4.1 6.7 - - - +
403A SER* 1.3 85.4 - - - +
405A ILE* 1.3 64.1 + - - +
406A ASN 3.2 3.4 - - - -
407A SER* 2.9 17.1 + - - -
408A TRP* 3.1 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.4 11.7 - - + -
403A SER* 3.3 17.6 + - - +
404A PRO* 1.3 76.3 - - - +
406A ASN* 1.3 64.8 + - - +
408A TRP* 3.2 33.6 + - + +
409A LEU* 3.0 20.4 + - - +
429A PHE* 4.1 11.1 - - + -
432A ILE* 4.6 2.9 - - + -
433A LEU* 4.2 22.0 - - + -
436A GLN* 4.3 20.4 - - - +
443A LEU* 3.8 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A HIS* 6.4 0.9 - - + -
403A SER* 3.8 21.9 + - - +
404A PRO 3.2 0.6 - - - -
405A ILE* 1.3 80.4 + - - +
407A SER* 1.3 55.8 + - - +
409A LEU* 3.2 6.4 + - - +
410A GLY* 2.9 26.2 + - - -
443A LEU* 4.4 12.4 - - - +
444A ASN* 3.0 50.5 + - + +
445A PHE* 5.0 2.6 - - - -
446A GLU 5.5 2.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PRO 4.5 0.7 + - - -
394A ARG* 3.7 36.3 - - - +
395A ALA* 4.0 2.4 + - - +
402A HIS* 5.5 5.8 - - - -
403A SER 5.3 0.4 + - - -
404A PRO* 2.9 13.9 + - - -
406A ASN* 1.3 74.2 - - - +
408A TRP* 1.3 67.4 + - - +
410A GLY* 3.3 2.6 + - - +
411A ASN* 3.1 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.6 17.5 - - + -
27A SER* 4.9 0.2 - - - -
30A LEU* 4.8 0.4 - - + +
395A ALA* 2.8 48.2 + - + +
404A PRO* 3.1 30.5 + - + +
405A ILE* 3.2 31.6 + - + +
407A SER* 1.3 78.1 - - - +
409A LEU* 1.3 58.2 + - - +
411A ASN* 3.4 2.6 + - - +
412A ILE* 2.9 36.1 + - + +
425A LEU* 4.4 19.7 - - + +
428A HIS* 3.5 37.4 - + - -
429A PHE* 3.8 34.8 - + + -
432A ILE* 3.7 26.5 - - + -
433A LEU* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A ILE 3.0 13.2 + - - +
406A ASN* 3.5 6.7 - - - +
407A SER 3.2 0.2 - - - -
408A TRP* 1.3 77.0 - - - +
410A GLY* 1.3 63.0 + - - +
412A ILE* 3.2 10.1 + - + +
413A ILE* 3.1 39.0 + - + +
429A PHE* 4.1 17.4 - - + -
443A LEU* 3.9 27.6 - - + -
444A ASN 4.0 5.6 - - - +
445A PHE* 3.8 24.2 - - + -
454A VAL* 4.2 17.5 - - + +
456A PRO* 5.6 2.2 - - + -
459A LEU* 4.1 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ASN 2.9 14.8 + - - -
407A SER* 3.3 4.4 + - - -
409A LEU* 1.3 75.6 - - - +
411A ASN* 1.3 61.8 + - - +
413A ILE* 3.3 1.6 + - - +
414A GLN* 3.1 33.2 + - - +
445A PHE* 3.6 27.3 - - - -
446A GLU 5.2 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ARG* 5.1 1.4 - - - +
391A PRO* 3.6 35.8 - - - +
394A ARG* 5.8 0.2 - - - +
407A SER* 3.1 28.4 + - - +
408A TRP 3.9 0.2 - - - +
410A GLY* 1.3 73.2 - - - +
412A ILE* 1.3 65.8 + - - +
414A GLN* 4.8 4.6 + - - -
415A TYR* 2.9 54.8 + - - +
420A TRP* 4.1 4.5 - - + -
421A VAL* 3.6 3.3 - - - +
425A LEU* 3.7 23.1 - - + +
1P C 5.6 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A TRP* 2.9 23.7 + - + +
409A LEU* 3.2 7.4 + - + +
411A ASN* 1.3 76.3 - - - +
413A ILE* 1.3 57.6 + - - +
416A ALA* 3.1 31.5 + - - +
421A VAL* 3.7 16.8 - - + -
425A LEU* 3.9 17.3 - - + +
426A MET* 3.7 31.2 - - + +
429A PHE* 3.5 47.3 - - + -
459A LEU* 4.4 24.9 - - + -
463A ILE* 4.6 1.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A LEU* 3.1 34.6 + - + +
410A GLY 3.7 3.4 - - - +
411A ASN 3.1 0.4 - - - -
412A ILE* 1.3 76.7 - - - +
414A GLN* 1.3 63.7 + - - +
415A TYR 3.4 0.2 + - - -
416A ALA* 4.8 1.1 - - - -
445A PHE* 3.8 45.5 - - + -
454A VAL* 4.5 9.9 - - + -
459A LEU* 3.8 23.3 - - + -
462A ILE* 4.6 7.0 - - + -
463A ILE* 5.4 4.0 - - + +
466A LEU* 3.7 24.1 - - + +
467A HIS* 2.8 28.6 + - - -
550A TRP* 4.1 11.2 - - + -
551A PHE* 5.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PRO* 3.8 22.4 - - + +
384A LEU* 5.1 2.0 - - - +
410A GLY* 3.1 21.7 + - - +
411A ASN* 5.0 3.6 + - - -
413A ILE* 1.3 78.0 - - - +
415A TYR* 1.3 96.4 + - + +
416A ALA 3.6 0.2 - - - -
417A PRO* 4.5 0.3 - - - +
445A PHE* 4.8 8.3 - - + -
446A GLU 5.2 0.5 - - - +
447A MET* 3.2 31.3 - - + +
467A HIS* 3.4 17.7 - - - -
551A PHE* 4.3 23.2 - - + -
1P C 4.8 15.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PRO* 6.1 0.2 - - + -
366A CYS 5.1 1.7 + - - -
368A SER* 3.9 14.4 - - - -
384A LEU* 3.6 31.9 - - + +
385A THR* 3.9 20.0 - - - -
386A ARG* 3.5 38.9 + - + -
411A ASN* 2.9 35.0 + - - +
414A GLN* 1.3 110.0 + - + +
416A ALA* 1.3 58.5 + - - +
417A PRO* 3.1 7.4 - - - -
418A THR* 2.7 39.0 + - + -
420A TRP* 3.7 11.4 - + + -
421A VAL* 3.2 17.7 - - + +
1P C 4.9 7.5 - - - -
----------------------------------------------------------
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