Contacts of the helix formed by residues 354 - 367 (chain A) in PDB entry 1A8H
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 354 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU 2.7 21.1 + - - -
350A ALA 3.8 4.7 - - - -
353A LEU* 1.3 72.9 - - - +
355A ASN* 1.3 56.3 + - - +
357A VAL* 3.2 6.3 + - - +
358A GLN* 2.9 30.8 + - - +
495A VAL* 5.9 3.1 - - - -
496A LEU* 4.3 16.3 + - - +
497A PHE* 4.2 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ALA 3.2 13.4 + - - +
351A ASP* 3.1 32.1 + - - +
354A GLY* 1.3 71.7 - - - +
356A LEU* 1.3 54.0 + - - +
358A GLN* 3.6 19.0 - - - +
359A ARG* 2.6 67.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ASP 3.6 3.0 + - - -
352A ASP 3.5 17.3 - - - +
353A LEU 3.4 3.5 + - - +
354A GLY 3.3 0.8 - - - -
355A ASN* 1.3 77.0 - - - +
357A VAL* 1.3 56.8 + - - +
359A ARG* 3.5 29.9 - - - +
360A THR* 2.8 48.3 + - - +
411A VAL* 4.4 2.7 - - + +
414A LEU* 3.9 25.6 - - + +
415A ASN* 3.6 21.3 - - - +
418A ILE* 4.2 16.2 - - + -
441A VAL* 4.5 7.0 - - + -
445A LEU* 3.9 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU 3.1 16.3 + - - +
354A GLY* 3.5 8.7 - - - +
356A LEU* 1.3 74.7 - - - +
358A GLN* 1.3 65.2 + - + +
360A THR* 3.4 5.7 + - - -
361A ARG* 3.0 34.5 + - - +
445A LEU* 4.1 18.6 - - + -
463A LEU* 3.5 35.2 - - + -
466A ALA* 4.5 11.9 - - + -
467A LEU* 4.4 16.6 - - + +
496A LEU* 4.6 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A GLY 2.9 15.0 + - - +
355A ASN* 3.7 21.1 - - - +
357A VAL* 1.3 77.8 - - + +
359A ARG* 1.3 62.3 + - - +
361A ARG* 3.5 8.5 + - - +
362A ALA* 3.2 23.2 + - - +
493A ALA 5.8 3.1 - - - +
495A VAL* 3.4 42.1 - - + +
496A LEU 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ASP* 4.8 1.0 + - - -
355A ASN* 2.6 69.7 + - - +
356A LEU* 3.5 25.9 - - + +
358A GLN* 1.3 72.7 - - - +
360A THR* 1.3 65.9 + - - +
362A ALA* 3.4 6.1 + - - +
363A MET* 3.1 51.0 + - + +
415A ASN* 2.8 26.5 + - - -
418A ILE* 3.7 8.1 - - - +
419A ASN* 3.6 26.7 + - - +
424A TRP* 6.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LEU* 2.8 28.5 + - - +
357A VAL* 3.8 5.8 - - - -
359A ARG* 1.3 74.2 - - - +
361A ARG* 1.3 60.8 + - - +
363A MET* 3.3 10.1 + - - +
364A LEU* 3.0 52.4 + - + +
418A ILE* 4.6 4.3 - - - +
438A LEU* 4.9 7.0 - - + +
441A VAL* 3.2 35.0 - - + +
442A VAL* 4.9 8.7 - - + +
445A LEU* 4.3 1.7 - - - +
467A LEU* 4.5 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A VAL* 3.0 24.9 + - - +
358A GLN* 3.7 8.9 - - - +
360A THR* 1.3 74.9 - - - +
362A ALA* 1.3 65.9 + - - +
364A LEU* 3.2 13.1 + - - +
365A PHE* 3.3 39.6 + - + -
466A ALA* 2.8 45.2 + - - +
467A LEU* 3.6 17.7 - - + -
489A ILE* 4.0 12.6 - - + +
490A PRO* 2.8 36.3 + - - +
491A GLU 3.6 5.7 + - - -
492A GLU* 3.7 0.2 - - - +
493A ALA* 3.4 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A GLN 3.2 14.7 + - - +
359A ARG* 3.7 6.3 - - - +
360A THR 3.4 0.2 - - - -
361A ARG* 1.3 79.5 - - - +
363A MET* 1.3 62.6 + - + +
365A PHE* 3.5 10.2 + - - +
366A ARG* 3.3 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ARG* 3.1 45.3 + - + +
360A THR 3.7 5.6 - - - +
361A ARG 3.2 0.2 - - - -
362A ALA* 1.3 78.9 - - + +
364A LEU* 1.3 60.0 + - - +
366A ARG* 3.8 1.8 - - - +
367A PHE* 2.9 54.3 + - + +
418A ILE* 3.2 35.4 - - + -
423A PRO* 4.5 1.8 - - - -
424A TRP* 3.8 32.8 - - + -
438A LEU* 3.8 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A THR* 3.0 37.9 + - + +
361A ARG* 3.2 6.7 + - - +
363A MET* 1.3 73.9 - - - +
365A PHE* 1.3 61.2 + - - +
368A ALA* 2.8 28.0 + - + -
369A GLU 3.0 0.9 + - - -
370A GLY 2.9 14.3 + - - -
371A ARG 4.3 11.4 - - - +
372A ILE* 4.6 10.1 - - + -
373A PRO* 4.1 15.7 - - + -
438A LEU* 3.9 34.8 - - + +
442A VAL* 5.3 5.6 - - + -
467A LEU* 4.8 8.1 - - + -
489A ILE* 4.0 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ARG* 3.3 42.9 + - + -
362A ALA* 3.7 9.9 - - - +
363A MET 3.3 0.2 - - - -
364A LEU* 1.3 81.6 - - - +
366A ARG* 1.3 61.7 + - + +
369A GLU* 4.0 6.6 + - - -
370A GLY* 3.4 30.3 + - - +
489A ILE* 3.7 18.6 - - + -
490A PRO 3.4 21.1 - - - -
491A GLU* 3.6 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ALA 3.3 15.1 + - - +
363A MET* 4.1 3.1 - - - +
364A LEU 3.2 0.6 - - - -
365A PHE* 1.3 83.4 - - + +
367A PHE* 1.3 99.8 + - + +
369A GLU 4.8 1.5 + - - -
424A TRP* 5.5 1.4 - - - +
427A PHE* 4.7 5.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A MET* 2.9 51.5 + - + +
366A ARG* 1.3 105.5 - - + +
368A ALA* 1.3 59.9 + - - +
369A GLU 3.7 1.1 - - - -
423A PRO* 4.7 5.8 - - + -
424A TRP* 3.5 38.1 - - + -
427A PHE* 3.5 64.8 - + + -
434A ALA* 5.1 2.5 - - + -
435A ARG* 3.7 18.7 + - + +
438A LEU* 4.2 14.4 - - + -
----------------------------------------------------------
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