Contacts of the helix formed by residues 62 - 75 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ASP* 3.5 11.4 - - - +
61B ILE* 1.4 91.7 - - + +
63B ALA* 1.3 65.5 + - - +
64B TYR* 3.2 35.0 - - + +
65B HIS* 3.0 27.8 + - + +
66B ARG* 3.3 8.0 + - - +
261B ARG* 4.1 26.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL 4.2 4.5 - - - +
52B GLY* 4.5 3.6 - - - -
53B ASP* 2.7 30.2 + - - +
62B PRO* 1.3 69.1 - - - +
64B TYR* 1.3 65.7 + - - +
66B ARG* 3.0 27.6 + - - +
67B VAL* 2.8 29.4 + - + +
87B SER* 4.6 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PRO* 3.2 26.0 - - + +
63B ALA* 1.3 76.9 - - - +
65B HIS* 1.3 112.2 + + - +
67B VAL* 3.9 5.3 - - - +
68B ILE* 3.0 41.6 + - + +
247B TYR* 4.4 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 3.9 15.4 - - + +
62B PRO* 3.0 24.4 + - + +
64B TYR* 1.3 119.9 + + - +
66B ARG* 1.3 62.7 + - - +
68B ILE* 4.0 1.0 - - - +
69B MET* 3.1 30.3 + - - +
247B TYR* 2.6 43.2 + + - -
251B HIS* 3.9 16.3 + - + -
253B LEU* 3.5 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B SER 2.9 29.0 + - - +
17B PHE* 3.5 18.9 - - + +
18B ASN* 3.6 14.6 - - - +
20B ILE* 5.6 0.5 - - - +
50B PRO* 4.1 10.5 - - + +
51B VAL* 2.7 38.8 + - - +
53B ASP* 3.1 26.3 + - - +
60B LEU* 3.2 26.2 - - - +
61B ILE* 2.8 36.7 + - + -
62B PRO 3.3 1.4 + - - +
63B ALA* 3.0 15.5 + - - +
65B HIS* 1.3 77.6 - - - +
67B VAL* 1.3 61.6 + - - +
69B MET* 3.6 10.2 + - + +
70B ALA* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PRO* 4.2 22.0 - - + -
63B ALA* 2.8 21.7 + - + +
64B TYR* 3.9 6.1 - - - +
66B ARG* 1.3 73.3 - - - +
68B ILE* 1.3 62.2 - - + +
70B ALA* 3.1 2.6 + - - +
71B GLU* 2.7 56.9 + - + +
82B VAL* 4.3 3.6 - - + -
84B THR* 3.6 19.3 - - + -
87B SER* 3.9 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 3.0 32.8 + - + +
65B HIS 4.1 2.0 - - - +
67B VAL* 1.3 78.7 - - + +
69B MET* 1.3 52.4 + - - +
71B GLU* 3.0 17.7 + - + +
72B LEU* 2.7 49.6 + - + +
247B TYR* 3.7 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PHE 4.5 0.7 - - - +
19B PRO* 3.5 30.3 - - + -
20B ILE* 4.0 6.7 - - + -
61B ILE* 4.4 0.4 - - + -
65B HIS 3.1 23.4 + - - +
66B ARG* 3.8 15.5 - - + +
68B ILE* 1.3 75.1 - - - +
70B ALA* 1.3 58.8 + - - +
72B LEU* 3.2 7.3 + - - +
73B ALA* 2.8 30.3 + - - +
244B VAL* 3.5 21.3 - - + +
247B TYR* 3.4 23.6 - - + -
248B ILE* 3.7 20.6 - - - -
253B LEU* 3.6 24.9 - - + -
254B TYR* 3.8 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PHE* 5.2 2.7 - - + -
20B ILE* 4.0 27.0 - - + +
48B ILE* 4.3 4.7 - - + -
50B PRO* 4.3 15.3 - - + -
66B ARG 3.1 17.7 + - - +
67B VAL 3.6 4.7 - - - +
69B MET* 1.3 77.3 - - - +
71B GLU* 1.3 61.5 + - - +
73B ALA* 3.3 3.3 + - - +
74B THR* 2.9 28.1 + - - +
82B VAL* 3.5 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 2.7 40.0 + - + +
68B ILE* 3.0 18.3 + - + +
70B ALA* 1.3 70.6 - - - +
72B LEU* 1.3 65.2 + - - +
74B THR* 3.1 8.6 + - - -
75B LYS* 3.0 22.9 + - - +
82B VAL* 3.8 20.9 - - + +
84B THR* 4.2 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 2.7 29.9 + - + +
69B MET* 3.6 8.5 - - - +
71B GLU* 1.3 72.7 - - + +
73B ALA* 1.3 62.5 + - - +
74B THR 3.3 0.5 + - - -
75B LYS* 3.4 25.4 + - + +
76B ASN* 4.7 1.7 + - - +
241B PRO* 5.4 0.5 - - - +
243B LEU* 3.6 60.1 - - + +
244B VAL* 4.6 3.4 - - + -
247B TYR* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A TYR* 4.7 6.8 + - - -
20B ILE* 3.8 31.4 - - + -
25B LEU* 3.9 16.9 - - + +
69B MET 2.8 18.4 + - - +
70B ALA 3.5 5.8 - - - +
71B GLU 3.1 0.2 - - - -
72B LEU* 1.3 77.5 - - - +
74B THR* 1.3 60.6 + - - +
75B LYS 3.4 0.4 + - - -
76B ASN* 4.8 4.0 + - - +
77B SER 5.2 0.5 + - - -
241B PRO* 4.1 17.8 - - + +
244B VAL* 3.9 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.9 16.6 - - + -
48B ILE* 4.0 10.3 - - + -
70B ALA 2.9 16.8 + - - +
71B GLU* 3.1 6.5 + - - -
73B ALA* 1.3 77.7 - - + +
75B LYS* 1.3 65.4 + - - +
76B ASN 3.2 2.9 - - - -
77B SER* 2.8 24.6 + - - +
80B VAL* 3.3 45.3 + - + +
81B GLU* 4.3 2.1 - - - +
82B VAL* 3.7 14.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLU 3.0 10.7 + - - +
72B LEU* 3.4 23.0 + - + +
73B ALA 3.4 0.2 - - - -
74B THR* 1.3 77.9 - - - +
76B ASN* 1.3 69.5 + - - +
77B SER 3.4 6.1 + - - +
243B LEU* 3.9 21.7 - - + +
----------------------------------------------------------
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