Contacts of the helix formed by residues 397 - 410 (chain A) in PDB entry 1YAA
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 VAL 397 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A MET* 3.3 31.0 - - - +
336A ALA* 4.3 15.5 - - + -
337A LEU* 4.4 5.7 - - + +
340A HIS* 4.4 18.1 - - + +
392A LEU* 3.7 28.7 - - + -
393A ASN 3.0 14.5 + - - +
394A GLN* 3.6 27.1 - - - +
396A ASN* 1.3 74.7 + - - +
398A GLU* 1.3 60.8 + - + +
400A VAL* 3.3 2.1 + - - +
401A ALA* 2.9 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A HIS* 4.1 27.9 - - + +
394A GLN 5.5 2.4 + - - +
395A GLY 6.2 0.9 - - - +
396A ASN* 3.2 0.9 - - - -
397A VAL* 1.3 81.0 - - + +
399A TYR* 1.3 61.5 + - - +
401A ALA* 3.4 6.3 + - - +
402A LYS* 3.1 43.8 + - - +
85D LYS* 4.5 16.1 + - - +
90D THR* 3.5 31.7 + - - +
91D GLN* 4.0 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A THR* 3.4 39.0 + - + +
33A VAL* 4.1 18.4 - - + -
377A HIS* 2.7 43.5 + - + +
379A VAL* 4.0 11.7 - - + -
395A GLY 5.4 0.9 - - - +
396A ASN* 3.0 17.2 + - + +
398A GLU* 1.3 78.2 - - - +
400A VAL* 1.3 63.1 + - - +
402A LYS* 3.4 4.9 + - + +
403A ALA* 3.0 25.4 + - + +
91D GLN* 4.3 28.8 - - + +
96D GLN* 4.8 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 3.8 31.2 - - + -
35A LEU* 4.1 12.1 - - + -
337A LEU* 4.5 4.7 - - + -
379A VAL* 4.1 21.5 - - + -
381A LEU* 5.7 0.2 - - + -
392A LEU* 3.6 26.5 - - + -
396A ASN 3.0 15.5 + - - +
397A VAL 4.0 1.3 - - - +
399A TYR* 1.3 76.0 - - + +
401A ALA* 1.3 64.6 + - - +
403A ALA* 3.8 5.6 - - - +
404A ILE* 3.1 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 4.1 4.7 - - + +
340A HIS* 3.5 23.8 - - + +
341A LEU* 3.4 33.8 - - + +
344A LEU* 3.7 9.4 - - + -
397A VAL 2.9 16.5 + - - +
398A GLU 3.5 7.0 - - - +
399A TYR 3.2 0.2 - - - -
400A VAL* 1.3 78.2 - - - +
402A LYS* 1.3 56.8 + - + +
404A ILE* 3.5 0.3 + - - +
405A ASP* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A HIS* 5.9 1.8 - - - -
344A LEU* 3.8 35.9 - - + -
398A GLU* 3.1 36.8 + - + +
399A TYR* 3.4 9.2 + - + +
400A VAL 3.3 0.2 - - - -
401A ALA* 1.3 78.9 - - + +
403A ALA* 1.3 64.4 + - - +
405A ASP* 3.3 3.9 + - + +
406A GLU* 3.0 24.6 + - - +
90D THR* 3.4 29.4 + - - +
91D GLN* 3.5 10.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
373A LEU* 3.8 10.5 - - + -
377A HIS* 3.6 40.5 + - + +
379A VAL* 4.1 11.0 - - + -
399A TYR* 3.0 19.9 + - + +
400A VAL* 4.0 4.5 - - - +
402A LYS* 1.3 76.7 - - - +
404A ILE* 1.3 60.5 + - + +
406A GLU* 3.5 3.1 + - - +
407A VAL* 3.2 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 6.2 0.2 - - + -
337A LEU* 4.5 20.2 - - + -
341A LEU* 4.5 15.3 - - + -
346A THR* 5.0 0.4 - - + -
350A TRP* 4.3 11.7 - - + -
363A THR* 5.6 7.0 - - + -
365A LEU* 4.2 27.1 - - + -
373A LEU* 4.2 13.0 - - + -
381A LEU* 6.0 3.8 - - + -
400A VAL* 3.1 36.5 + - + +
401A ALA* 3.8 3.8 - - - +
403A ALA* 1.3 75.2 - - - +
405A ASP* 1.3 65.8 + - - +
406A GLU 3.1 0.4 + - - -
407A VAL* 3.2 6.8 + - - +
408A VAL* 3.0 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 4.0 20.7 - - + +
346A THR* 2.7 48.9 + - - +
401A ALA 3.0 17.2 + - - +
402A LYS* 3.6 6.5 - - + +
404A ILE* 1.3 76.1 - - - +
406A GLU* 1.3 62.0 + - - +
408A VAL* 3.6 1.6 + - - +
409A ARG* 3.1 59.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ARG* 2.9 39.0 + - - -
376A THR* 5.6 0.2 - - - -
377A HIS* 2.9 32.7 + - + -
402A LYS 3.0 16.2 + - - +
403A ALA 3.6 4.7 - - - +
404A ILE 3.1 0.2 - - - -
405A ASP* 1.3 78.1 + - - +
407A VAL* 1.3 58.8 + - - +
409A ARG* 3.4 6.0 + - - +
410A PHE* 3.0 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LEU* 4.9 2.5 - - + -
369A MET* 3.8 27.5 - - + +
372A ARG* 3.9 19.5 - - + +
373A LEU* 3.6 30.3 - - + -
377A HIS* 3.9 7.0 - - + +
403A ALA 3.2 14.3 + - - +
404A ILE* 3.2 18.6 - - + +
406A GLU* 1.3 88.9 - - - +
408A VAL* 1.3 69.7 + - + +
410A PHE* 4.2 3.8 - - - -
411A TYR* 3.3 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A THR* 4.0 5.2 - - + -
347A PRO* 4.1 35.8 - - + +
350A TRP* 3.7 29.6 - - + -
365A LEU* 4.2 10.1 - - + -
369A MET* 4.0 11.9 - - + -
404A ILE* 3.0 24.3 + - + +
405A ASP 4.0 4.0 - - - +
407A VAL* 1.3 75.9 - - + +
409A ARG* 1.3 59.2 + - - +
412A ALA* 3.0 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU 3.3 13.7 + - - -
345A GLY 2.9 27.3 + - - -
347A PRO* 3.9 23.4 - - + +
405A ASP* 3.1 46.0 + - - +
406A GLU* 3.9 5.2 - - - +
407A VAL 3.3 0.2 - - - -
408A VAL* 1.3 76.9 - - - +
410A PHE* 1.3 66.4 + - - +
412A ALA* 3.6 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ARG* 3.3 46.2 - - - +
406A GLU* 3.0 25.4 + - - +
407A VAL* 3.4 5.1 + - - +
409A ARG* 1.3 79.9 - - - +
411A TYR* 1.3 96.8 + + - +
----------------------------------------------------------
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