Contacts of the helix formed by residues 82 - 88 (chain N) in PDB entry 5X22
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 LYS 82 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1115M LEU* 4.8 12.7 - - + +
52N PRO* 4.0 1.6 - - - +
55N ASP* 3.5 15.5 - - - +
56N TYR* 3.4 28.9 - - + +
69N GLU* 4.7 4.5 - - - +
81N THR* 1.3 77.7 - - + +
83N SER* 1.3 64.2 + - - +
84N ILE* 3.1 28.9 + - + +
85N VAL* 3.2 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52N PRO* 3.3 17.3 - - - -
53N ILE* 3.1 28.0 - - - -
54N LYS 4.0 0.2 - - - -
55N ASP* 3.1 25.8 + - - +
81N THR 3.6 2.4 + - - -
82N LYS* 1.3 66.8 - - - +
84N ILE* 1.3 57.6 + - - +
85N VAL 2.9 11.5 + - - -
86N ARG* 2.9 26.6 + - - +
523N ASP* 4.7 2.6 - - - +
337P HIS* 2.8 24.9 + - - -
338P LEU* 5.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060M ILE* 4.5 11.2 - - + -
1115M LEU* 3.5 26.0 - - + -
55N ASP* 4.5 1.3 + - - +
82N LYS* 3.7 30.3 - - + +
83N SER* 1.3 80.6 + - - +
85N VAL* 1.3 58.6 + - - +
86N ARG 3.0 0.9 - - - -
87N ARG* 2.9 47.5 + - - +
88N TYR* 3.3 24.8 - - + +
523N ASP* 5.5 0.7 - - - -
337P HIS* 6.3 0.7 - - - -
338P LEU* 3.8 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1115M LEU* 3.8 34.1 - - + +
50N PHE 3.6 14.6 - - - +
51N GLY* 4.0 0.9 - - - -
52N PRO* 4.0 16.4 - - + -
81N THR* 4.7 6.3 - - + +
82N LYS* 3.2 23.3 - - + +
83N SER 2.9 2.6 + - - +
84N ILE* 1.3 76.9 - - - +
86N ARG* 1.3 57.2 + - - +
87N ARG 3.1 1.6 - - - -
88N TYR* 3.0 10.1 + - - -
89N ARG* 2.9 64.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39N PRO* 4.5 4.0 - - - +
45N PHE* 2.3 48.9 + - - +
46N ASP 4.0 5.5 + - - -
47N GLU* 4.6 1.2 - - - +
50N PHE* 3.5 17.5 - - - +
51N GLY 3.3 14.3 + - - +
52N PRO 3.4 22.7 - - - +
53N ILE* 4.1 20.0 - - - +
83N SER* 2.9 18.1 + - - +
85N VAL* 1.3 76.6 - - + +
87N ARG* 1.3 55.6 + - - +
88N TYR 3.2 1.3 - - - -
521N PRO* 3.2 13.1 - - - +
522N PRO* 3.3 39.3 - - + +
523N ASP* 3.1 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 87 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015M LEU 3.3 16.8 + - - -
1016M ILE* 2.6 31.5 + - - +
1018M GLN* 3.6 22.7 - - - +
1083M GLU* 2.7 36.7 + - - +
1087M VAL* 4.4 2.8 - - - +
1090M LYS* 4.2 3.6 - - - +
84N ILE* 2.9 40.7 + - - +
86N ARG* 1.3 77.0 - - - +
88N TYR* 1.3 70.3 + - + +
521N PRO* 3.7 7.6 - - - +
523N ASP* 3.3 33.0 + - + +
524N LEU* 3.8 34.7 - - + +
338P LEU* 5.1 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060M ILE* 5.6 0.2 - - - +
1083M GLU* 2.8 36.9 + - - -
1086M ARG* 3.5 29.5 + - + -
1090M LYS* 3.1 28.4 + - + +
1112M PHE* 3.5 26.0 - + + -
1115M LEU* 4.1 24.0 - - + -
1116M ALA* 4.1 18.8 - - + +
84N ILE* 3.3 38.5 - - + +
85N VAL* 3.0 13.2 + - + +
86N ARG 3.2 1.2 + - - -
87N ARG* 1.3 91.2 - - + +
89N ARG* 1.3 67.5 + - + +
90N MET 3.3 0.7 + - - -
521N PRO* 3.2 10.2 - - - +
----------------------------------------------------------
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