Contacts of the helix formed by residues 62 - 74 (chain C) in PDB entry 1KR2
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 PRO 62 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ASP* 3.5 11.0 - - - +
61C ILE* 1.3 93.1 - - + +
63C ALA* 1.3 65.0 + - - +
64C TYR* 4.4 7.9 - - + +
65C HIS* 3.1 36.5 + - + +
66C ARG* 3.3 9.4 + - - +
261C ARG* 3.9 25.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C VAL 4.0 8.1 - - - +
53C ASP* 3.0 25.1 + - - +
62C PRO* 1.3 69.3 - - - +
64C TYR* 1.3 60.2 + - - +
66C ARG* 3.1 27.8 + - - +
67C VAL* 2.8 35.5 + - - +
87C SER* 4.2 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PRO* 3.2 6.4 - - + +
63C ALA* 1.3 79.3 - - - +
65C HIS* 1.3 65.4 + + + +
67C VAL* 3.4 11.9 + - + +
68C ILE* 3.0 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ILE* 4.0 14.1 - - + -
62C PRO* 3.1 33.0 + - + +
64C TYR* 1.3 84.1 - + + +
66C ARG* 1.3 58.9 - - - +
68C ILE* 3.1 6.2 + - - +
69C MET* 2.9 35.0 + - - +
247C TYR* 2.7 36.3 + + + -
251C HIS* 4.9 8.7 + - - +
253C LEU* 3.8 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C SER 3.1 26.5 + - - +
17C PHE* 3.6 18.1 - - - +
18C ASN* 3.6 20.9 - - - +
20C ILE* 5.7 0.5 - - - +
50C PRO* 4.1 11.0 - - + +
51C VAL* 2.8 41.8 + - - +
52C GLY 4.0 0.4 - - - -
53C ASP* 3.1 25.5 + - - -
60C LEU* 3.5 24.9 - - - +
61C ILE* 2.9 32.1 + - + -
62C PRO 3.3 1.0 + - - +
63C ALA* 3.1 18.2 + - - +
65C HIS* 1.3 74.2 - - - +
67C VAL* 1.3 63.7 + - - +
69C MET* 3.4 12.0 + - + +
70C ALA* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C PRO* 4.3 21.3 - - + -
63C ALA 2.8 22.0 + - - +
64C TYR* 3.6 12.8 - - + +
66C ARG* 1.3 76.7 - - - +
68C ILE* 1.3 59.6 + - + +
70C ALA* 3.1 4.2 + - - +
71C GLU* 2.9 44.9 + - - +
82C VAL* 4.4 4.4 - - + +
84C THR* 3.9 19.7 - - + -
87C SER* 3.6 32.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C TYR* 3.0 58.8 + - + +
65C HIS 3.1 5.8 + - - +
67C VAL* 1.3 78.2 - - + +
69C MET* 1.3 62.6 + - - +
71C GLU* 3.1 9.2 + - + +
72C LEU* 2.9 36.0 + - + +
247C TYR* 3.7 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PHE 4.7 0.2 - - - +
19C PRO* 3.7 17.5 - - + -
20C ILE* 4.0 15.9 - - + +
61C ILE* 4.2 2.0 - - + -
65C HIS 2.9 22.9 + - - +
66C ARG* 3.8 16.4 - - + +
68C ILE* 1.3 75.0 - - - +
70C ALA* 1.3 57.6 + - - +
72C LEU* 3.3 4.2 + - - -
73C ALA* 2.9 29.3 + - - +
244C VAL* 3.5 17.4 - - + +
247C TYR* 3.8 19.7 - - + -
248C ILE* 3.6 31.6 - - - -
253C LEU* 3.9 16.2 - - + -
254C TYR* 3.7 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PHE* 5.5 2.0 - - + -
20C ILE* 4.2 19.2 - - + +
48C ILE* 4.1 20.6 - - + -
50C PRO* 4.3 5.6 - - + -
66C ARG 3.0 14.2 + - - +
67C VAL 3.5 7.9 - - - +
69C MET* 1.3 77.1 - - - +
71C GLU* 1.3 59.6 + - - +
73C ALA* 3.3 2.6 + - - +
74C THR* 2.9 29.5 + - - +
82C VAL* 3.6 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C VAL* 2.9 35.4 + - - +
68C ILE* 3.1 11.9 + - + +
70C ALA* 1.3 75.4 - - - +
72C LEU* 1.3 64.4 + - + +
74C THR* 3.3 3.8 + - - +
75C LYS* 3.0 23.2 + - - +
82C VAL* 3.4 32.8 + - + +
84C THR* 4.9 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ILE* 2.9 27.8 + - + +
69C MET* 3.6 6.5 - - - +
71C GLU* 1.3 76.6 - - + +
73C ALA* 1.3 63.2 + - - +
74C THR 3.3 0.3 + - - -
75C LYS* 3.4 23.3 - - + +
76C ASN* 5.1 0.3 + - - +
241C PRO* 5.3 0.7 - - - +
243C LEU* 3.8 62.3 - - + +
244C VAL* 4.5 3.6 - - + +
247C TYR* 3.9 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ILE* 4.0 18.4 - - + -
25C LEU* 4.0 21.6 - - + +
69C MET 2.9 17.2 + - - +
70C ALA 3.6 6.3 - - - +
71C GLU 3.3 0.4 - - - -
72C LEU* 1.3 78.4 - - - +
74C THR* 1.3 57.5 + - - +
75C LYS 3.5 0.6 + - - -
76C ASN 5.0 1.6 + - - -
77C SER 5.6 0.2 + - - -
241C PRO* 3.8 30.3 - - + +
244C VAL* 4.0 6.0 - - + +
238D TYR* 4.4 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 3.8 18.6 - - + -
48C ILE* 3.9 9.2 - - + -
70C ALA 2.9 18.5 + - - +
71C GLU* 3.4 6.2 + - - -
73C ALA* 1.3 76.9 - - - +
75C LYS* 1.3 66.1 + - - +
76C ASN 3.2 3.1 - - - -
77C SER* 3.0 26.1 + - - +
80C VAL* 3.5 42.9 + - + +
81C GLU* 4.7 1.2 - - - -
82C VAL* 3.6 14.4 - - + +
238D TYR* 5.2 0.4 - - - +
----------------------------------------------------------
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