Contacts of the helix formed by residues 415 - 426 (chain X) in PDB entry 6AH0
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 415 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413X GLU 3.5 3.4 + - - -
414X PRO* 1.3 74.1 - - - +
416X PRO* 1.3 67.7 - - - +
417X ILE 3.3 2.2 - - - -
418X GLN* 3.0 7.6 + - - +
419X ARG* 2.9 19.4 + - - -
439X SER 4.7 10.1 - - - -
440X GLY* 6.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 416 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377X TYR* 4.8 16.2 - - - +
415X THR* 1.3 70.1 - - - +
417X ILE* 1.3 61.1 + - - +
419X ARG* 3.2 11.1 + - - +
420X GLN* 3.4 8.8 + - - -
439X SER 5.1 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 417 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415X THR 3.3 0.6 - - - -
416X PRO* 1.3 74.9 - - - +
418X GLN* 1.3 57.7 + - - +
420X GLN* 3.4 0.4 + - - +
421X ALA* 2.8 30.7 + - - -
439X SER 4.8 8.7 + - - -
440X GLY 5.6 1.3 - - - -
441X LYS* 6.5 2.0 - - - +
444X ALA* 5.4 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 418 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414X PRO* 5.5 3.4 - - - -
415X THR* 3.0 12.7 + - - +
417X ILE* 1.3 78.1 - - - +
419X ARG* 1.3 61.8 + - - +
422X ILE* 3.2 22.2 + - - -
439X SER 5.4 1.0 + - - -
440X GLY 5.0 7.0 + - - -
444X ALA* 4.5 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 419 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389X PRO* 3.2 6.0 - - - +
390X ILE* 2.9 41.4 + - - +
414X PRO* 5.0 5.3 - - - +
415X THR 2.9 13.2 + - - +
416X PRO* 3.2 6.6 + - - -
418X GLN* 1.3 77.4 - - - +
420X GLN* 1.3 58.2 + - - +
422X ILE 4.7 1.0 + - - -
423X PRO* 4.8 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 420 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387X PRO 5.4 3.3 - - - +
389X PRO* 4.4 8.1 - - - -
416X PRO 3.4 9.6 + - - -
417X ILE* 4.1 0.4 - - - +
418X GLN 3.2 0.2 - - - -
419X ARG* 1.3 77.3 - - - +
421X ALA* 1.3 67.3 + - - +
422X ILE 3.4 0.4 - - - -
423X PRO* 4.0 2.3 - - - +
424X ILE* 3.7 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 421 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417X ILE 2.8 16.4 + - - -
420X GLN* 1.3 75.4 - - - +
422X ILE* 1.3 66.5 + - - +
424X ILE* 3.1 4.0 + - - +
425X GLY* 2.9 21.3 + - - -
444X ALA* 5.0 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 422 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418X GLN* 3.2 17.9 + - - +
421X ALA* 1.3 77.1 - - - +
423X PRO* 1.3 56.6 - - - +
425X GLY* 3.3 2.4 + - - -
426X LEU* 2.9 24.8 + - - -
444X ALA* 4.5 13.7 + - - +
448X PRO* 5.4 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 423 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387X PRO* 5.9 7.6 - - + -
388X ASN 5.3 8.1 - - - +
419X ARG 4.8 5.0 - - - +
420X GLN 4.0 4.9 - - - +
421X ALA 3.4 0.2 - - - -
422X ILE* 1.3 74.2 - - - +
424X ILE* 1.3 62.4 + - - +
426X LEU* 3.3 10.1 + - - +
427X GLN* 3.5 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 424 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387X PRO 5.9 4.4 - - - -
420X GLN 3.7 9.4 + - - -
421X ALA* 3.1 7.1 + - - +
423X PRO* 1.3 73.8 - - - +
425X GLY* 1.3 57.2 + - - +
427X GLN* 2.9 18.9 + - - +
429X ARG* 3.3 21.5 + - - -
583X GLU 5.7 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 425 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421X ALA 2.9 13.0 + - - -
422X ILE* 3.6 4.9 - - - -
424X ILE* 1.3 75.8 - - - +
426X LEU* 1.3 57.2 + - - +
427X GLN 3.1 0.2 - - - -
428X ASN* 3.0 18.6 + - - -
429X ARG 4.3 10.0 + - - -
448X PRO* 5.1 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 426 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422X ILE 2.9 13.9 + - - -
423X PRO* 3.3 7.1 + - - -
424X ILE 3.2 0.8 - - - -
425X GLY* 1.3 76.0 - - - +
427X GLN* 1.3 56.2 + - - +
428X ASN 3.3 2.0 + - - -
448X PRO* 5.3 6.5 - - - +
589X LEU* 4.8 5.7 - - - +
592X PHE* 5.2 5.9 - - - -
----------------------------------------------------------
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