Contacts of the helix formed by residues 500 - 506 (chain S) in PDB entry 5NTI
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 500 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492C ILE* 4.8 0.5 - - - +
495C GLN* 3.6 46.4 - - + +
496C ALA* 3.8 15.0 - - + -
500D PRO* 3.4 44.9 - - + +
501D LEU* 3.9 7.4 - - + +
504D GLU* 2.9 24.1 + - - +
499S THR* 1.3 71.5 - - - +
501S LEU* 1.3 57.1 + - - +
503S LEU* 3.3 13.5 + - + +
504S LEU* 2.9 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 501 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D VAL* 4.9 11.7 - - + -
350D ILE* 4.0 35.4 - - + +
353D LEU* 3.8 18.8 - - + -
354D LYS* 4.1 12.3 - - + +
501D LEU* 4.5 8.1 - - + +
504D GLU* 3.1 15.0 + - - +
505D LEU* 3.7 29.8 - - + -
499S THR* 4.1 2.9 - - - +
500S LEU* 1.3 74.5 - - - +
502S GLN* 1.3 64.4 + - - +
504S LEU* 3.4 7.5 + - + +
505S LEU* 3.1 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 502 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346D GLN* 5.4 4.0 - - - +
350D ILE* 3.9 20.8 - - + +
499S THR* 2.9 55.4 + - - +
501S LEU* 1.3 77.3 - - - +
503S LEU* 1.3 56.0 + - + +
505S LEU 3.8 0.3 - - - -
506S GLY 2.9 7.4 + - - -
507S HIS* 2.7 54.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 503 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492C ILE* 3.8 34.2 - - + +
495C GLN* 3.9 33.9 - - - +
499S THR 3.0 18.0 + - - +
500S LEU* 3.5 18.6 - - + +
501S LEU 3.3 0.2 - - - -
502S GLN* 1.3 75.4 - - + +
504S LEU* 1.3 64.9 + - - +
506S GLY* 3.0 14.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 504 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492C ILE* 4.2 23.1 - - + +
493C VAL* 5.7 4.5 - - + +
496C ALA* 4.5 11.9 - - + -
329D GLN* 5.4 14.6 - - + +
332D VAL* 4.2 25.6 - - + -
333D GLU* 5.4 6.5 - - - +
336D LYS* 3.6 28.1 + - - +
501D LEU* 3.8 37.0 - - + -
500S LEU 2.9 21.9 + - - +
501S LEU* 3.8 7.2 - - + +
503S LEU* 1.3 75.7 - - - +
505S LEU* 1.3 60.1 + - - +
506S GLY 3.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 505 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D VAL* 4.1 5.8 - - + +
336D LYS* 3.9 27.6 - - + +
341D PHE* 4.1 11.9 - - + -
342D MET* 4.3 18.1 - - - +
349D GLN* 4.0 16.2 - - + +
350D ILE* 3.8 7.4 - - + -
353D LEU* 3.7 24.5 - - + -
501S LEU* 3.1 37.5 + - + +
502S GLN 4.2 0.2 - - - +
504S LEU* 1.3 75.6 - - - +
506S GLY* 1.3 61.8 + - - +
507S HIS* 3.6 38.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 506 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502S GLN 2.9 3.6 + - - -
503S LEU* 3.0 15.1 + - - -
504S LEU 3.3 0.4 - - - -
505S LEU* 1.3 81.3 - - - +
507S HIS* 1.3 65.2 + - - +
----------------------------------------------------------
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