Contacts of the helix formed by residues 398 - 407 (chain A) in PDB entry 6MOL
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 THR 398 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A HIS* 3.6 2.5 - - - -
389A VAL 4.6 4.5 - - - -
390A ASN* 4.0 20.0 - - + +
391A ALA 3.2 13.2 - - - +
392A TYR* 4.6 5.8 - - + -
396A GLY 4.7 2.5 - - - +
397A ALA* 1.3 75.7 - - - +
399A PRO* 1.3 69.9 - - - +
400A LEU* 3.6 9.6 + - - +
401A HIS* 2.7 50.4 + - + +
402A LEU* 3.1 12.8 + - - +
421A ASP 5.1 2.6 + - - +
424A ALA* 4.6 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A THR* 5.1 0.9 - - - +
367A LEU* 3.9 35.0 - - + +
368A HIS* 3.3 27.6 - - + +
371A ALA* 3.7 9.3 - - + +
388A ASP 4.3 4.3 - - - +
389A VAL 3.6 17.0 - - - +
391A ALA* 3.4 8.7 - - + +
398A THR* 1.3 86.9 - - - +
400A LEU* 1.3 54.5 + - - +
402A LEU* 3.6 2.6 + - + +
403A ALA* 3.1 28.9 + - - +
415A LEU* 3.5 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A VAL 5.1 2.1 + - - +
398A THR* 3.1 9.7 + - - +
399A PRO* 1.3 76.7 - - - +
401A HIS* 1.3 66.9 + - - +
403A ALA* 4.1 1.2 - - - +
404A ALA* 3.2 23.6 + - - +
412A VAL* 3.7 35.8 - - + +
415A LEU* 3.8 27.0 - - + +
416A LEU* 4.2 1.8 - - + -
420A ALA* 3.8 24.0 - - + -
421A ASP 4.1 11.4 - - - +
422A VAL* 4.1 21.1 - - + -
432A ALA* 3.8 25.3 - - + +
448A LEU* 4.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A GLY 4.6 2.9 - - - -
397A ALA* 3.9 12.1 - - + -
398A THR* 2.7 42.4 + - + +
400A LEU* 1.3 79.5 - - - +
402A LEU* 1.3 61.8 + - - +
404A ALA* 3.6 4.6 + - - +
405A ARG* 3.2 22.2 + - - +
421A ASP 5.4 1.6 - - - -
422A VAL 5.6 0.2 - - - -
424A ALA* 3.3 32.6 + - + -
425A GLN 4.5 1.3 - - - -
426A ASP* 3.3 27.6 + - + -
430A LYS 3.2 20.5 + - - -
431A THR* 3.7 13.6 - - - -
432A ALA* 4.2 11.6 + - + +
435A ILE* 4.2 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A THR* 5.7 3.4 - - + -
368A HIS* 3.7 40.6 - - + +
371A ALA* 4.8 2.0 - - + -
372A THR* 3.3 32.8 - - + +
393A ASP* 4.5 7.4 - - - +
397A ALA* 4.1 17.5 - - + -
398A THR 3.1 9.4 + - - +
399A PRO* 4.1 3.8 - - + +
401A HIS* 1.3 74.8 - - - +
403A ALA* 1.3 66.1 + - - +
405A ARG* 3.3 16.0 + - - +
406A MET* 3.1 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ALA* 4.0 23.5 + - + +
399A PRO 3.1 19.2 + - - +
400A LEU 4.1 1.6 - - - +
401A HIS 3.4 0.2 - - - -
402A LEU* 1.3 77.5 - - - +
404A ALA* 1.3 57.5 + - - +
406A MET 3.9 0.2 - - - -
407A GLY 2.8 21.7 + - - -
408A HIS* 3.0 24.0 + - + +
411A ILE* 4.7 4.0 - - + -
412A VAL* 3.7 23.1 - - + -
415A LEU* 4.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LEU* 3.2 19.7 + - + +
401A HIS 4.0 3.4 - - - +
403A ALA* 1.3 75.9 - - - +
405A ARG* 1.3 63.7 + - - +
407A GLY* 3.5 6.4 + - - -
412A VAL* 4.5 3.5 - - + +
432A ALA* 3.9 25.6 - - + +
435A ILE* 4.1 14.5 - - + +
436A SER* 4.2 10.5 + - - +
439A ASN* 5.2 1.2 - - - +
441A ASN* 5.0 4.5 + - - -
444A LEU* 3.7 23.4 - - + +
448A LEU* 5.0 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A THR* 5.6 3.6 - - - +
401A HIS 3.2 17.5 + - - +
402A LEU* 3.3 17.4 + - - +
404A ALA* 1.3 78.1 - - - +
406A MET* 1.3 77.5 + - - +
435A ILE* 3.6 26.0 - - + +
439A ASN* 3.9 17.9 + - - +
441A ASN* 5.9 0.2 + - - -
24B GLU* 3.3 60.1 + - - +
108B ARG* 3.3 33.7 + - - +
109B TYR* 4.2 7.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A THR* 3.4 40.6 - - + +
373A MET* 5.4 4.7 - - - +
402A LEU 3.1 16.0 + - - +
405A ARG* 1.3 90.8 - - + +
407A GLY* 1.3 63.1 + - - +
408A HIS* 3.6 23.1 + - + +
24B GLU* 4.2 21.1 - - - +
25B GLU* 4.3 24.0 - - + +
109B TYR* 5.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ALA 2.8 11.2 + - - -
404A ALA 3.5 1.7 + - - -
405A ARG 3.4 2.6 - - - -
406A MET* 1.3 80.5 - - - +
408A HIS* 1.3 66.4 + - - -
409A VAL* 4.1 3.3 + - - +
441A ASN* 5.5 5.6 - - - -
444A LEU* 3.8 22.2 - - - -
----------------------------------------------------------
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