Contacts of the helix formed by residues 497 - 503 (chain K) 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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450K VAL* 5.0 6.7 - - + -
457K LEU* 4.3 12.6 - - + -
461K LEU* 3.9 34.5 - - + -
472K PHE* 5.3 6.1 - - + -
493K ASN 3.2 20.6 - - - +
494K LEU* 3.2 11.9 + - + +
495K ASP 2.9 1.0 - - - -
496K ASN* 1.3 87.9 - - + +
498K ARG* 1.3 63.6 + - - +
499K ASP* 3.5 3.4 - - - -
500K TYR* 3.3 42.7 + - + -
501K LEU* 3.1 26.4 + - + +
521K PHE* 6.2 0.4 - - + -
452L LEU* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 498 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494K LEU 5.0 0.7 - - - -
495K ASP* 2.8 49.4 + - - +
496K ASN 3.8 0.8 - - - -
497K LEU* 1.3 72.6 - - - +
499K ASP* 1.3 66.0 + - - +
501K LEU* 2.9 18.8 + - - +
502K ASP* 2.7 24.1 + - - +
536K THR* 2.9 35.1 + - - +
537K LEU* 5.3 0.4 - - - +
540K ARG* 3.2 35.8 - - - +
451L ASN* 4.8 1.6 - - - +
473L GLU 4.8 1.1 - - - +
474L ASP* 3.1 50.2 + - + +
476L LYS* 5.1 2.0 - - + +
486L PRO* 4.5 0.2 - - - +
529L ASN* 3.4 9.5 + - - -
531L TYR* 3.1 25.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 499 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498K ARG* 1.3 78.3 + - - +
500K TYR* 1.3 72.9 + - - -
502K ASP* 3.5 9.8 + - - -
503K GLY* 2.8 31.9 + - - -
505K VAL* 3.6 15.0 - - + +
507K VAL* 3.1 28.4 - - - +
433L THR* 5.7 0.2 - - - -
447L ALA* 5.3 3.0 - - - +
448L LEU 4.9 3.1 - - - +
449L ASN* 3.5 26.8 - - - +
473L GLU* 3.4 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 500 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420K ARG* 3.2 17.0 + - - -
421K TYR* 3.9 1.0 + - - -
458K ASN* 5.7 1.2 + - - -
461K LEU* 4.0 20.8 - - + +
497K LEU* 3.4 42.6 - - + +
498K ARG 3.1 0.4 - - - -
499K ASP* 1.3 117.4 - - - +
501K LEU* 1.3 60.4 + - + +
507K VAL* 3.8 26.0 - - + -
508K ASN 3.5 22.0 + - - -
509K LEU* 4.7 2.9 - - + -
521K PHE* 3.3 52.5 - + + +
449L ASN* 4.4 12.7 - - + +
452L LEU* 5.4 4.6 - - + +
460L GLU* 4.0 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 501 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418K LYS* 4.4 6.0 + - - -
420K ARG* 3.3 13.7 + - - +
421K TYR* 3.8 46.5 - - + +
472K PHE* 4.9 8.5 - - + -
494K LEU* 3.3 34.1 - - + +
495K ASP* 5.3 0.2 - - - -
497K LEU* 3.1 15.7 + - + +
498K ARG* 2.9 9.7 + - - +
500K TYR* 1.3 79.4 - - + +
502K ASP* 1.3 64.3 + - - +
521K PHE* 6.2 0.4 - - + -
526K VAL* 5.1 3.1 - - + -
537K LEU* 3.8 22.4 - - + -
540K ARG* 3.9 30.6 - - + +
541K PHE* 5.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 502 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417K PRO* 3.3 7.8 - - - +
418K LYS* 3.1 46.9 + - + +
420K ARG* 3.2 14.3 + - - -
498K ARG 2.7 22.7 + - - +
499K ASP* 3.2 6.8 + - - +
501K LEU* 1.3 77.6 - - - +
503K GLY* 1.3 59.9 + - - +
504K SER* 3.4 4.0 - - - +
540K ARG* 2.8 36.7 + - - -
433L THR* 4.0 27.2 - - + +
473L GLU* 4.4 0.2 - - - +
474L ASP* 4.1 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 503 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417K PRO* 5.0 1.1 - - - -
420K ARG* 3.2 21.0 - - - +
499K ASP 2.8 18.4 + - - -
500K TYR 4.8 0.4 - - - -
502K ASP* 1.3 73.8 - - - +
504K SER* 1.3 59.9 + - - +
505K VAL 3.2 8.7 - - - -
520K ILE* 3.1 29.2 - - - +
521K PHE* 4.7 2.2 - - - -
567L ARG* 3.9 15.4 + - - -
----------------------------------------------------------
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