Contacts of the helix formed by residues 77 - 90 (chain B) in PDB entry 6K0X
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 ASN 77 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 6.4 0.2 - - - +
73B GLY 3.7 9.4 + - - +
74B TYR* 3.2 13.5 + - - +
75B GLU 3.6 0.2 - - - -
76B GLU* 1.3 76.7 - - - +
78B GLU* 1.3 64.0 + - - +
79B GLU* 3.2 15.6 + - - +
80B PHE* 3.0 32.6 + - + +
81B LEU* 3.1 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 4.4 9.9 - - + -
39B PRO* 6.1 1.1 - - + -
76B GLU 3.6 5.6 + - - +
77B ASN* 1.3 73.1 + - - +
79B GLU* 1.3 57.4 + - - +
81B LEU* 3.3 10.0 + - + +
82B ARG* 2.7 68.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 3.2 11.1 + - - +
78B GLU* 1.3 79.8 - - - +
80B PHE* 1.3 58.2 + - - +
82B ARG* 3.4 7.7 + - - +
83B THR* 2.9 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 4.0 13.7 - - + -
51B TRP* 3.8 20.2 - + - -
67B PRO* 3.8 28.0 - - + -
69B GLY 4.2 8.3 - - - -
70B PRO* 4.3 9.4 - - + -
71B VAL* 5.4 3.8 - - + -
74B TYR* 3.6 39.5 - + + -
77B ASN* 3.0 31.5 + - - +
79B GLU* 1.3 78.3 - - - +
81B LEU* 1.3 61.9 + - + +
83B THR* 3.2 6.4 + - - -
84B MET* 2.9 54.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.6 13.6 - - + -
39B PRO* 4.0 26.5 - - + +
42B VAL* 3.7 25.7 - - + +
43B ALA* 3.9 20.4 - - + +
46B ILE* 4.5 1.8 - - + -
74B TYR* 3.6 18.4 - - + +
75B GLU 3.8 22.7 - - - +
76B GLU* 5.4 0.2 - - - -
77B ASN 3.1 22.3 + - - +
78B GLU* 3.3 7.4 + - - +
80B PHE* 1.3 85.7 - - + +
82B ARG* 1.3 53.2 + - - +
85B HIS* 2.7 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.4 49.9 - - + +
78B GLU* 2.7 49.4 + - - +
79B GLU* 3.8 5.8 - - - +
81B LEU* 1.3 72.6 - - - +
83B THR* 1.3 67.1 + - - +
85B HIS* 3.5 5.0 - - + +
86B HIS* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLN 4.3 6.5 - - - +
67B PRO* 3.6 33.7 - - + -
79B GLU* 2.9 23.8 + - - +
80B PHE* 3.5 10.5 - - - -
82B ARG* 1.3 76.6 - - - +
84B MET* 1.3 57.8 + - - +
86B HIS* 3.1 8.1 + - - +
87B LEU* 3.0 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 4.1 16.6 - - + -
46B ILE* 4.0 4.9 - - + -
49B VAL* 5.2 1.6 - - + -
51B TRP* 3.7 24.5 - - + -
54B PHE* 3.5 35.9 - - + -
67B PRO* 3.5 28.3 - - + -
80B PHE* 2.9 46.4 + - + +
81B LEU* 4.7 0.2 - - - -
83B THR* 1.3 68.5 - - - +
85B HIS* 1.3 61.1 + - - +
87B LEU* 4.4 2.2 - - - +
88B LEU* 2.8 58.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 2.8 44.2 + - + -
36B GLU 3.5 16.4 - - - -
37B PHE* 3.6 31.9 - + + +
38B ASN 4.4 1.8 + - - -
42B VAL* 3.8 15.5 - - + +
81B LEU 2.7 23.0 + - - +
82B ARG* 3.5 7.0 - - - +
83B THR 3.2 0.2 - - - -
84B MET* 1.3 73.1 - - - +
86B HIS* 1.3 65.6 + - + +
89B LEU* 3.0 48.8 + - + +
90B GLU* 3.1 21.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE* 4.0 29.4 - - + +
63B LEU* 5.6 2.8 - - + +
82B ARG 3.0 10.6 + - - +
83B THR* 3.1 9.6 + - - +
85B HIS* 1.3 79.2 - - + +
87B LEU* 1.3 78.2 + - + +
90B GLU* 2.8 63.2 + - + +
91B VAL* 3.5 16.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 3.5 23.9 + - - +
54B PHE* 3.8 28.3 - - + -
58B ALA* 5.4 0.2 - - + -
63B LEU* 3.8 37.7 - - + -
64B ILE 4.8 7.0 - - - +
65B GLN 4.6 1.1 - - - +
66B VAL* 4.1 13.5 - - + -
67B PRO* 4.0 14.8 - - + -
83B THR* 3.0 39.2 + - + +
84B MET* 4.3 2.2 - - - +
86B HIS* 1.3 93.4 - - + +
88B LEU* 1.3 62.6 + - - +
89B LEU 3.7 0.2 + - - -
91B VAL* 4.1 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LYS* 3.5 2.8 - - - +
3B LEU* 3.4 9.9 + - - +
4B LEU* 3.1 51.3 + - + +
7B ASN* 5.5 2.5 - - + -
42B VAL* 5.1 6.3 - - + -
45B MET* 5.1 7.6 - - + -
46B ILE* 4.7 5.8 - - + -
49B VAL* 4.2 26.9 - - + -
54B PHE* 3.8 25.1 - - + -
84B MET* 2.8 45.6 + - + +
85B HIS* 5.1 0.2 - - - -
87B LEU* 1.3 77.7 - - - +
89B LEU* 1.3 73.4 + - + +
91B VAL 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 5.8 2.0 - - + -
2B LYS* 2.9 48.8 + - + +
4B LEU* 4.1 24.9 - - + -
35B VAL* 3.7 21.5 - - + +
41B PHE* 3.5 31.9 - - + -
42B VAL* 4.7 5.4 - - + -
85B HIS* 3.0 38.1 + - + +
88B LEU* 1.3 95.2 - - + +
90B GLU* 1.3 60.9 + - + +
91B VAL 3.6 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ARG 3.6 0.2 - - - +
32B ILE* 3.2 11.5 - - + +
33B CYS* 2.8 44.4 + - - +
34B PRO* 3.5 9.1 - - - +
35B VAL* 2.9 36.4 + - + +
85B HIS* 3.1 22.8 + - + +
86B HIS* 2.8 51.5 + - + +
89B LEU* 1.3 78.2 - - - +
91B VAL* 1.3 61.5 + - - +
92B GLU* 3.9 0.9 - - - -
----------------------------------------------------------
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