Contacts of the helix formed by residues 497 - 503 (chain L) 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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452G LEU* 3.8 15.3 - - + -
450L VAL* 5.0 6.5 - - + -
457L LEU* 4.3 13.5 - - + -
461L LEU* 3.9 32.8 - - + -
472L PHE* 5.3 6.5 - - + -
493L ASN 3.2 21.1 - - - +
494L LEU* 3.2 12.3 + - + +
495L ASP 2.9 1.0 - - - -
496L ASN* 1.3 88.4 - - - +
498L ARG* 1.3 63.4 + - - +
499L ASP* 3.5 3.4 - - - -
500L TYR* 3.6 45.1 - - + -
501L LEU* 3.1 26.0 + - + +
521L PHE* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 498 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451G ASN* 4.7 1.9 - - - +
473G GLU 4.8 1.6 - - - +
474G ASP* 3.4 49.5 + - + +
476G LYS* 4.6 3.0 - - - +
486G PRO* 4.5 0.6 - - - +
529G ASN* 3.7 8.5 + - - -
531G TYR* 3.2 25.0 + - - -
494L LEU 5.0 0.7 - - - -
495L ASP* 2.8 50.3 + - - +
496L ASN 3.8 1.0 - - - -
497L LEU* 1.3 72.4 - - - +
499L ASP* 1.3 66.2 + - - +
501L LEU* 2.9 9.5 + - - +
502L ASP* 2.7 31.9 + - - +
536L THR* 2.9 35.0 + - - +
537L LEU* 5.3 0.8 - - - +
540L ARG* 3.2 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 499 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433G THR* 6.0 0.2 - - - -
447G ALA 5.2 2.1 - - - +
448G LEU 4.9 4.0 - - - +
449G ASN* 3.3 28.7 - - - +
473G GLU* 3.4 29.0 - - + +
498L ARG* 1.3 79.5 + - - +
500L TYR* 1.3 73.6 + - - +
502L ASP* 3.6 10.1 - - - -
503L GLY* 2.8 31.4 + - - -
505L VAL* 3.6 20.4 - - + +
507L VAL* 3.1 29.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 500 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449G ASN* 4.5 13.2 - - + -
452G LEU* 5.1 4.9 - - + +
460G GLU* 3.8 16.6 + - - -
420L ARG* 3.1 17.7 + - - -
421L TYR* 3.9 0.9 + - - -
458L ASN* 5.7 1.2 + - - -
461L LEU* 4.0 21.1 - - + +
497L LEU* 3.4 44.6 - - + +
498L ARG 3.1 0.4 - - - -
499L ASP* 1.3 116.1 - - - +
501L LEU* 1.3 58.5 + - + +
507L VAL* 3.8 24.9 - - + -
508L ASN 3.5 21.1 + - - -
509L LEU* 4.7 2.9 - - + -
521L PHE* 3.3 52.5 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 501 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418L LYS* 4.4 6.2 + - - -
419L LYS 5.3 0.2 + - - -
420L ARG* 3.3 13.7 + - - +
421L TYR* 3.8 45.5 - - + -
472L PHE* 4.9 8.7 - - + -
494L LEU* 3.3 33.4 - - + +
495L ASP* 5.3 0.2 - - - -
497L LEU* 3.1 15.1 + - + +
498L ARG* 2.9 9.7 + - - +
500L TYR* 1.3 79.2 - - + +
502L ASP* 1.3 64.4 + - - +
521L PHE* 6.3 0.4 - - + -
526L VAL* 5.1 3.6 - - + -
537L LEU* 3.8 22.2 - - + -
540L ARG* 3.9 32.1 - - + +
541L PHE* 5.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 502 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433G THR* 4.1 22.4 - - + +
473G GLU* 4.4 0.5 - - - +
474G ASP* 4.1 4.0 - - - +
567G ARG* 5.6 0.2 + - - -
417L PRO* 3.4 7.5 - - - +
418L LYS* 3.1 45.0 + - + +
420L ARG* 3.2 14.9 + - - -
498L ARG 2.7 22.7 + - - +
499L ASP* 3.6 7.1 + - - +
501L LEU* 1.3 76.9 - - - +
503L GLY* 1.3 59.9 + - - +
504L SER* 3.4 8.7 - - - +
540L ARG* 2.8 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 503 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567G ARG* 4.2 13.7 + - - -
417L PRO* 5.0 2.2 - - - -
420L ARG* 3.2 20.4 - - - +
499L ASP 2.8 18.8 + - - -
500L TYR 4.7 0.4 - - - -
502L ASP* 1.3 73.9 - - - +
504L SER* 1.3 59.6 + - - +
505L VAL 3.2 8.7 - - - -
520L ILE* 3.1 28.3 - - - +
521L PHE 4.7 2.0 - - - -
----------------------------------------------------------
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