Contacts of the helix formed by residues 497 - 503 (chain J) in PDB entry 4E2I
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 LEU 497 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450J VAL* 5.0 6.5 - - + -
457J LEU* 4.3 13.0 - - + -
461J LEU* 3.9 35.9 - - + -
472J PHE* 5.3 6.7 - - + -
493J ASN 3.2 21.5 - - - +
494J LEU* 3.2 11.9 + - + +
495J ASP 2.9 0.8 - - - -
496J ASN* 1.3 87.7 - - - +
498J ARG* 1.3 65.6 + - - +
499J ASP* 3.5 3.1 - - - -
500J TYR* 3.3 42.3 + - + -
501J LEU* 3.1 25.8 + - + +
521J PHE* 6.2 0.7 - - + -
452K LEU* 4.0 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 498 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494J LEU 5.0 0.7 - - - -
495J ASP* 2.8 49.8 + - - +
496J ASN 3.8 0.8 - - - -
497J LEU* 1.3 72.2 - - - +
499J ASP* 1.3 67.3 + - - +
501J LEU* 2.9 17.5 + - - +
502J ASP* 2.7 25.0 + - - +
536J THR* 2.9 36.4 + - - +
537J LEU* 5.3 0.6 - - - +
540J ARG* 3.2 36.2 - - - +
451K ASN* 4.9 2.1 - - - +
473K GLU 5.1 0.9 - - - +
474K ASP* 3.5 45.8 + - + +
476K LYS* 5.1 2.6 - - + +
486K PRO* 4.3 1.6 - - - +
529K ASN* 3.7 10.1 + - - +
531K TYR* 3.3 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 499 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498J ARG* 1.3 78.4 + - - +
500J TYR* 1.3 73.2 + - - -
502J ASP* 3.5 9.4 - - - -
503J GLY* 2.8 31.0 + - - -
505J VAL* 3.6 20.6 - - + +
507J VAL* 3.1 29.0 - - - +
433K THR* 5.9 0.7 - - - -
447K ALA 5.5 1.9 - - - +
448K LEU 5.1 3.3 - - - +
449K ASN* 3.5 26.8 - - - +
473K GLU* 3.5 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 500 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420J ARG* 3.2 17.8 + - - -
421J TYR* 3.9 0.9 + - - -
458J ASN* 5.7 1.4 + - - -
461J LEU* 4.0 21.4 - - + +
497J LEU* 3.3 42.4 - - + +
498J ARG 3.1 0.6 - - - -
499J ASP* 1.3 116.3 - - - +
501J LEU* 1.3 59.5 + - + +
507J VAL* 3.8 26.0 - - + -
508J ASN 3.5 21.4 + - - -
509J LEU* 4.7 3.4 - - + -
521J PHE* 3.3 52.2 - + + +
449K ASN* 4.6 12.8 - - + -
452K LEU* 5.2 5.9 - - + +
460K GLU* 4.1 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 501 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418J LYS* 4.4 5.8 + - - -
420J ARG* 3.3 13.7 + - - +
421J TYR* 3.8 45.9 - - + -
472J PHE* 4.9 9.2 - - + -
494J LEU* 3.3 34.3 - - + +
495J ASP* 5.4 0.4 - - - -
497J LEU* 3.1 15.7 + - + +
498J ARG* 2.9 9.0 + - - +
500J TYR* 1.3 78.8 - - + +
502J ASP* 1.3 64.4 + - - +
521J PHE* 6.2 0.4 - - + -
526J VAL* 5.1 2.9 - - + -
537J LEU* 3.8 21.8 - - + -
540J ARG* 3.9 31.2 - - + +
541J PHE* 5.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 502 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417J PRO* 3.4 8.2 - - - +
418J LYS* 3.1 47.7 + - + +
420J ARG* 3.2 14.7 + - - -
498J ARG 2.7 23.0 + - - +
499J ASP* 3.5 7.0 + - - +
501J LEU* 1.3 77.3 - - - +
503J GLY* 1.3 59.7 + - - +
504J SER* 3.4 12.6 - - - +
540J ARG* 2.8 35.6 + - - -
433K THR* 4.3 16.0 - - + +
473K GLU* 4.7 0.2 - - - +
474K ASP* 4.2 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 503 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417J PRO* 5.0 0.9 - - - -
420J ARG* 3.2 20.1 - - - +
499J ASP 2.8 17.6 + - - -
500J TYR 4.8 0.4 - - - -
502J ASP* 1.3 74.8 - - - +
504J SER* 1.3 58.3 + - - +
505J VAL 3.2 8.7 - - - -
520J ILE* 3.1 29.1 - - - +
521J PHE* 4.7 2.7 - - - -
567K ARG* 4.0 15.3 + - - -
----------------------------------------------------------
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