Contacts of the helix formed by residues 68 - 87 (chain A) in PDB entry 2KAT
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 ASP 68 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.0 16.8 + - + +
64A GLN* 4.6 1.5 + - - -
66A GLN* 4.2 15.8 - - - +
67A GLY* 1.3 77.2 - - - +
69A ARG* 1.3 59.8 + - - +
70A ALA* 3.3 10.6 + - - +
71A GLY* 2.8 31.7 + - - +
72A ALA* 3.0 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 5.9 0.4 - - - +
67A GLY 3.9 3.2 + - - -
68A ASP* 1.3 73.3 + - - +
70A ALA* 1.3 63.0 + - - +
72A ALA* 3.4 1.1 + - - -
73A ARG* 3.1 26.9 + - - +
102A LEU* 3.4 33.8 - - + +
105A GLU* 2.7 53.6 + - - +
106A ASP* 4.5 14.1 - - + +
109A GLU* 3.1 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 3.3 8.1 + - - +
69A ARG* 1.3 77.6 - - - +
71A GLY* 1.3 65.2 + - - +
73A ARG* 3.2 16.7 + - - +
74A GLN* 3.0 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.7 21.4 - - - +
68A ASP* 2.8 22.6 + - - -
70A ALA* 1.3 73.0 - - - +
72A ALA* 1.3 57.2 + - - +
74A GLN* 3.4 10.4 + - - +
75A ALA* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLY 4.2 2.9 - - - +
63A LEU* 3.4 9.9 - - + +
64A GLN* 3.8 29.8 - - + +
68A ASP 3.0 17.4 + - - +
69A ARG* 3.7 6.1 - - - +
71A GLY* 1.3 72.3 - - - +
73A ARG* 1.3 66.7 + - - +
75A ALA* 3.3 3.8 + - - +
76A TRP* 3.1 37.3 + - + -
102A LEU* 3.7 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 3.1 20.7 + - - +
70A ALA* 3.4 18.4 - - - +
72A ALA* 1.3 79.0 - - - +
74A GLN* 1.3 68.6 + - + +
76A TRP 3.4 0.2 + - - -
77A GLU* 3.1 36.6 + - + +
99A LEU* 3.9 13.3 - - + +
102A LEU* 3.5 15.4 - - + +
103A ALA* 5.4 4.8 - - - +
106A ASP* 2.8 43.6 + - - +
110A HIS* 5.3 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 3.0 24.7 + - + +
71A GLY* 3.9 7.4 - - - +
73A ARG* 1.3 82.2 - - + +
75A ALA* 1.3 53.1 + - - +
77A GLU* 3.4 8.0 + - - +
78A SER* 2.7 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TRP 5.6 1.7 - - - +
59A LEU* 4.6 4.0 - - + +
60A GLY* 4.1 21.8 - - - +
63A LEU* 4.4 13.5 - - + -
71A GLY 2.8 18.4 + - - +
72A ALA* 3.5 7.4 - - - +
74A GLN* 1.3 77.1 - - - +
76A TRP* 1.3 59.0 + - - +
78A SER* 3.1 8.0 + - - -
79A GLY* 2.9 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TRP 5.2 0.9 - - - -
57A LYS 4.6 0.4 + - - -
60A GLY* 3.3 32.1 - - - -
61A LYS* 4.2 1.0 - - + +
64A GLN* 3.5 44.0 - - + -
72A ALA* 3.1 20.4 + - + +
75A ALA* 1.3 75.5 - - - +
77A GLU* 1.3 59.8 + - - +
79A GLY* 4.4 1.1 - - - +
80A LEU* 2.9 35.3 + - + +
95A LEU* 3.4 44.7 - - + +
98A PHE* 3.6 28.9 - + + +
99A LEU* 3.7 42.0 - - + -
102A LEU* 3.5 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 3.1 29.3 + - + +
74A GLN* 3.5 8.7 - - - +
76A TRP* 1.3 77.7 - - - +
78A SER* 1.3 61.9 + - - +
80A LEU* 3.8 17.9 + - - +
81A ALA* 3.9 7.4 + - - +
99A LEU* 3.3 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLN* 2.7 23.1 + - - +
75A ALA* 3.1 7.4 + - - -
77A GLU* 1.3 79.6 - - - +
79A GLY* 1.3 61.1 + - - +
80A LEU 3.4 0.5 + - - -
81A ALA* 3.7 5.8 + - - +
82A ALA* 3.4 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TRP* 4.0 21.7 - - - -
75A ALA 2.9 14.7 + - - -
76A TRP 3.9 1.3 - - - -
78A SER* 1.3 75.5 - - - +
80A LEU* 1.3 60.5 + - - +
82A ALA* 3.2 10.1 + - - +
83A ALA* 2.8 30.5 + - - +
95A LEU* 4.6 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TRP 2.9 18.4 + - - +
77A GLU* 3.8 12.6 - - - +
78A SER 3.3 0.2 - - - -
79A GLY* 1.3 76.5 - - - +
81A ALA* 1.3 59.0 + - - +
83A ALA* 3.1 7.2 + - - +
84A GLN* 2.8 34.4 + - + +
92A VAL* 3.4 45.9 - - + +
95A LEU* 4.5 8.0 - - + +
96A GLN* 4.3 22.9 - - + +
99A LEU* 4.8 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU 3.9 6.8 + - - +
78A SER* 3.7 7.7 + - - +
79A GLY 3.4 0.2 - - - -
80A LEU* 1.3 75.8 - - - +
82A ALA* 1.3 60.3 + - - +
84A GLN* 3.5 11.8 - - + +
85A SER* 2.8 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TRP* 3.4 36.6 - - + +
78A SER 3.4 12.8 + - - +
79A GLY* 3.2 13.1 + - - +
81A ALA* 1.3 79.4 - - - +
83A ALA* 1.3 57.7 + - - +
85A SER* 3.3 6.8 + - - -
86A ARG* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TRP* 3.3 16.5 - - + -
79A GLY 2.8 12.7 + - - +
80A LEU* 3.5 4.7 - - - +
82A ALA* 1.3 73.2 - - - +
84A GLN* 1.3 61.6 + - - +
86A ARG* 3.2 2.6 + - - +
87A GLY 2.8 23.0 + - - -
88A ASP* 2.9 20.4 + - + +
91A VAL* 4.0 18.8 - - + -
92A VAL* 3.4 24.2 - - + +
95A LEU* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 2.8 21.6 + - + +
81A ALA* 3.5 13.2 - - + +
83A ALA* 1.3 77.2 - - - +
85A SER* 1.3 56.6 + - - +
87A GLY* 2.9 19.9 + - - +
89A GLN* 2.9 30.1 + - - +
92A VAL* 3.3 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA 2.8 21.2 + - - -
82A ALA* 3.3 7.6 + - - -
84A GLN* 1.3 72.8 - - - +
86A ARG* 1.3 63.0 + - - +
87A GLY 3.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 4.6 28.2 + - + +
53A SER* 5.6 2.6 - - - -
56A TRP* 3.4 33.2 - - + -
82A ALA 3.0 11.5 + - - +
83A ALA* 3.7 5.4 - - - +
84A GLN 3.1 0.2 - - - -
85A SER* 1.3 79.7 - - - +
87A GLY* 1.3 62.8 + - - +
88A ASP* 3.4 8.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA 2.8 3.2 + - - -
84A GLN* 2.9 15.3 + - - -
85A SER 3.3 0.8 - - - -
86A ARG* 1.3 80.1 - - - +
88A ASP* 1.3 58.7 + - - +
89A GLN* 3.4 15.7 + - - +
----------------------------------------------------------
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