Contacts of the helix formed by residues 495 - 503 (chain A) in PDB entry 4S15
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 TYR 495 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ARG* 3.3 28.4 + - - -
317A GLU* 4.0 16.1 + - + -
491A PHE* 2.8 31.5 + + + +
492A LYS 3.6 2.7 - - - -
494A ILE* 1.3 103.1 - - + +
496A PRO* 1.3 63.8 - - - +
497A ASP 3.3 2.5 - - - -
498A ILE* 3.3 35.3 + - + -
499A VAL* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A LYS* 3.2 25.1 - - + +
493A ALA 4.0 6.3 - - - +
494A ILE 3.3 11.7 - - - +
495A TYR* 1.3 87.6 - - - +
497A ASP* 1.3 67.9 + - - +
499A VAL* 3.5 3.9 + - + +
500A ARG* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A TYR 3.3 0.6 - - - -
496A PRO* 1.3 84.0 - - - +
498A ILE* 1.3 62.8 + - + +
500A ARG* 2.7 38.8 + - - +
501A LEU* 2.9 43.5 + - + +
502A HIS* 5.2 0.2 - - - -
314B LYS* 5.6 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A GLN* 6.1 0.7 - - - +
317A GLU* 4.3 21.8 - - + +
321A GLN* 6.3 0.2 - - + -
491A PHE* 4.0 20.0 - - + -
495A TYR* 3.3 40.8 + - + +
497A ASP* 1.3 78.4 - - + +
499A VAL* 1.3 57.4 + - - +
502A HIS* 2.9 49.3 + - + +
503A PHE* 3.7 11.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A LEU* 4.9 3.6 - - + -
491A PHE* 3.5 32.1 - - + -
492A LYS* 3.7 35.4 - - + -
495A TYR 3.2 9.7 + - - +
496A PRO 3.8 6.5 - - - +
498A ILE* 1.3 80.2 - - - +
500A ARG* 1.3 63.6 + - - +
503A PHE* 3.3 31.2 + - + +
508A LYS* 3.1 34.8 - - + +
512A THR* 4.9 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A PRO* 2.9 23.4 + - - +
497A ASP* 2.7 34.7 + - - +
498A ILE 3.4 0.2 - - - -
499A VAL* 1.3 78.2 - - - +
501A LEU* 1.3 76.9 + - - +
503A PHE 4.8 0.9 - - - +
508A LYS* 2.9 35.6 + - - +
311B TYR* 4.3 1.8 + - - -
325B ILE* 5.7 1.4 - - - +
326B LYS* 4.1 8.8 + - - +
382B ASP* 2.8 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A ASP* 2.9 25.9 + - + +
500A ARG* 1.3 95.5 - - - +
502A HIS* 1.3 70.7 + - + +
503A PHE 3.8 1.1 - - - -
311B TYR* 4.6 6.1 - - + +
314B LYS* 4.0 31.2 - - - +
322B LEU* 3.5 41.2 - - + +
325B ILE* 3.9 12.7 - - - +
326B LYS* 3.9 15.1 + - - +
382B ASP* 3.5 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A GLN* 2.8 38.8 + - + +
497A ASP 4.6 0.2 - - - -
498A ILE* 2.9 37.3 + - + +
501A LEU* 1.3 90.8 - - + +
503A PHE* 1.3 64.0 + - + +
314B LYS* 5.2 3.2 + - - -
318B VAL* 3.4 48.5 - - + +
321B GLN* 2.7 22.9 + - + +
322B LEU* 3.7 16.7 - - + +
325B ILE* 3.1 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLU 4.7 1.1 - - - -
320A TRP* 3.8 36.3 - + + -
321A GLN* 4.0 25.4 - - + -
324A ALA* 4.3 3.4 - - + -
488A LEU* 4.0 12.8 - - + -
491A PHE* 3.4 33.2 - + - -
498A ILE* 3.9 18.6 - - + -
499A VAL* 3.3 24.7 + - + +
500A ARG 4.8 0.5 - - - +
502A HIS* 1.3 86.3 + - - +
504A PRO* 1.3 73.0 - - + +
505A PRO* 3.5 4.0 - - - +
507A TYR* 3.6 24.7 - + + -
508A LYS* 3.8 20.9 + - + -
325B ILE* 4.0 9.0 - - - +
----------------------------------------------------------
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