Contacts of the helix formed by residues 64 - 76 (chain B) in PDB entry 3KCN
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 GLU 64 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B MSE 3.4 19.7 - - - +
59B ARG* 3.9 32.4 + - - -
60B MSE 3.9 16.9 - - - +
62B GLY 5.8 0.9 - - - -
63B MSE 1.3 76.6 - - - +
65B GLY* 1.3 67.1 + - - +
66B THR* 3.2 15.1 - - + +
67B GLU* 3.1 17.4 + - + +
68B VAL* 3.1 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 3.6 11.4 - - - -
57B ASP 3.2 12.0 + - - -
58B MSE 3.0 13.3 + - - -
60B MSE 4.1 1.8 - - - +
64B GLU* 1.3 70.3 - - - +
66B THR* 1.3 64.1 + - - +
68B VAL* 3.2 2.5 + - - +
69B ILE* 2.9 26.9 + - - +
83B MSE 3.1 26.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B MSE 3.1 32.1 - - + +
64B GLU* 4.7 11.7 - - + +
65B GLY* 1.3 75.3 - - - +
67B GLU* 1.3 65.5 + - + +
69B ILE* 3.2 6.0 + - - +
70B GLN* 3.1 31.4 + - - +
83B MSE 4.5 3.8 - - - -
96B ALA* 3.8 32.9 + - + +
97B VAL* 3.9 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLY 5.4 0.9 - - - +
63B MSE 3.2 31.3 - - + +
64B GLU* 3.1 12.8 + - + +
66B THR* 1.3 81.2 + - + +
68B VAL* 1.3 57.4 + - - +
70B GLN* 3.4 17.0 + - + +
71B LYS* 2.8 65.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY* 3.6 23.8 - - - +
41B ALA* 4.4 15.3 - - + -
42B LEU* 4.1 6.8 - - + +
45B ILE* 6.1 0.7 - - + -
54B ILE* 6.2 0.9 - - + -
56B VAL* 4.1 23.8 - - + -
60B MSE 3.8 12.6 - - + -
63B MSE 3.5 29.2 - - + -
64B GLU 3.1 15.3 + - - +
65B GLY 3.2 6.7 + - - +
67B GLU* 1.3 76.4 - - - +
69B ILE* 1.3 57.4 + - - +
71B LYS* 3.4 3.2 + - - +
72B ALA* 2.8 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 4.0 12.1 - - + -
65B GLY 2.9 17.8 + - - +
66B THR* 3.7 7.0 - - - +
68B VAL* 1.3 76.8 - - - +
70B GLN* 1.3 59.4 + - - +
72B ALA* 3.2 5.8 + - - +
73B ARG* 2.8 40.1 + - + +
81B TYR* 3.9 30.0 - - + -
82B LEU 4.4 5.6 - - - +
83B MSE 3.8 29.4 - - + -
97B VAL* 6.0 0.9 - - + -
101B GLN* 3.7 32.8 - - + +
102B VAL* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B THR* 3.1 27.7 + - - +
67B GLU* 3.4 19.4 + - + +
69B ILE* 1.3 76.8 - - + +
71B LYS* 1.3 63.5 + - + +
73B ARG* 3.8 13.0 + - - +
74B LEU* 3.7 19.6 + - - +
96B ALA 4.2 7.9 + - - +
98B ASN* 4.6 4.9 + - - -
101B GLN* 3.5 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 4.0 30.5 - - + -
63B MSE 3.9 9.2 - - + +
67B GLU* 2.8 53.6 + - + +
68B VAL 3.9 2.9 - - - +
70B GLN* 1.3 76.4 - - + +
72B ALA* 1.3 63.5 + - - +
74B LEU* 3.3 19.8 + - + +
75B ILE* 3.6 14.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.9 9.5 - - + +
45B ILE* 3.8 22.2 - - + -
54B ILE* 5.6 0.9 - - + -
68B VAL* 2.8 20.5 + - + +
69B ILE 3.7 0.7 - - - +
71B LYS* 1.3 75.4 - - - +
73B ARG* 1.3 56.1 + - - +
75B ILE* 3.1 7.1 + - - +
76B SER* 2.7 32.6 + - - -
81B TYR* 3.1 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 2.8 32.6 + - + +
70B GLN* 3.9 10.8 - - - +
71B LYS 3.4 0.4 - - - -
72B ALA* 1.3 73.8 - - - +
74B LEU* 1.3 63.3 + - + +
76B SER 4.1 3.1 - - - -
77B PRO* 3.4 39.4 + - - +
79B SER 5.5 1.6 + - - -
81B TYR* 3.5 28.6 + - + -
99B GLU 4.8 2.2 + - - -
100B GLY* 3.2 28.8 + - - -
101B GLN* 3.7 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLN 3.7 16.2 - - - +
71B LYS* 3.3 12.4 + - + +
72B ALA 3.2 0.8 - - - -
73B ARG* 1.3 80.2 - - + +
75B ILE* 1.3 61.8 + - + +
77B PRO* 4.7 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 4.0 24.7 - - + +
45B ILE* 3.6 24.0 - - + +
46B LYS* 4.0 47.6 - - + -
71B LYS 3.6 13.7 + - - +
72B ALA* 3.1 4.8 + - - +
74B LEU* 1.3 79.7 - - + +
76B SER* 1.3 56.6 + - - +
77B PRO* 3.6 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 3.7 22.7 - - - +
50B PRO* 4.7 13.9 - - - +
51B PHE* 4.6 2.9 + - - -
54B ILE* 4.9 1.3 - - - +
72B ALA 2.7 10.5 + - - +
73B ARG 3.9 0.4 - - - +
75B ILE* 1.3 75.1 - - - +
77B PRO* 1.4 64.0 - - - +
78B ASN 3.4 2.2 - - - -
79B SER* 2.8 30.9 + - - -
81B TYR* 3.0 26.5 + - - -
----------------------------------------------------------
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