Contacts of the helix formed by residues 79 - 100 (chain A) in PDB entry 5JKC
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 79 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 1.3 77.1 - - - +
80A GLU* 1.3 66.9 + - - +
81A ALA* 3.7 12.0 - - - +
82A THR* 2.3 46.2 + - - -
83A LEU* 3.0 18.0 + - - +
129A PHE* 3.3 27.6 - - + -
133A ALA* 3.8 11.6 - - - +
144A GLN* 5.1 5.1 + - - +
145A THR 4.5 14.6 - - - +
146A LEU* 4.8 1.3 - - + -
147A ILE* 3.9 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASP* 1.3 74.3 - - - +
81A ALA* 1.3 51.8 + - - +
83A LEU* 3.3 13.1 + - - +
84A GLN* 2.8 68.8 + - + +
145A THR* 5.3 2.5 + - + -
147A ILE* 3.5 18.1 - - + +
154A LYS* 2.7 35.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
79A ASP* 3.7 13.6 - - - +
80A GLU* 1.3 78.9 - - - +
82A THR* 1.3 56.3 + - - +
84A GLN* 3.3 6.1 + - - +
85A LYS* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 3.4 21.8 - - + -
79A ASP* 2.3 33.9 + - - -
81A ALA* 1.3 70.6 - - - +
83A LEU* 1.3 65.0 + - - +
85A LYS* 3.2 8.6 + - - +
86A GLY* 3.0 21.0 + - - -
122A PHE* 4.0 5.4 - - + -
125A TYR* 3.9 35.1 - - + +
126A VAL* 4.4 8.5 - - + +
129A PHE* 3.4 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A CYS* 3.2 31.4 - - + +
23A VAL* 3.7 11.9 - - - -
25A CYS* 4.2 25.8 - - + +
26A ASP* 4.2 9.2 - - + +
78A VAL* 3.7 9.8 - - + +
79A ASP 3.0 12.3 + - - +
80A GLU* 3.5 19.5 - - - +
82A THR* 1.3 76.4 - - - +
84A GLN* 1.3 56.0 + - - +
86A GLY* 3.5 0.9 + - - -
87A SER* 2.7 47.8 + - - +
122A PHE* 4.6 4.7 - - + -
147A ILE* 3.8 24.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
26A ASP* 2.8 26.1 + - - +
80A GLU* 2.8 43.2 + - + +
81A ALA* 3.6 5.8 - - - +
83A LEU* 1.3 77.3 - - - +
85A LYS* 1.3 59.7 + - - +
87A SER* 4.0 3.1 - - - +
88A TRP* 2.9 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA 2.8 18.2 + - - +
82A THR* 3.2 9.6 + - - +
84A GLN* 1.3 76.5 - - - +
86A GLY* 1.3 60.4 - - - +
88A TRP* 4.0 5.0 - - - +
89A SER* 3.3 23.6 + - - -
125A TYR* 3.8 45.1 + - + +
128A ARG* 3.7 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TRP* 5.9 0.3 - - - -
23A VAL* 4.5 4.1 - - - +
82A THR 3.0 9.5 + - - -
85A LYS* 1.3 75.2 - - - +
87A SER* 1.3 64.7 + - - +
88A TRP 3.3 0.2 + - - -
89A SER* 3.4 3.9 + - - -
90A LEU* 3.0 23.6 + - - +
118A GLN* 4.7 2.5 + - - -
122A PHE* 3.5 32.5 - - - -
125A TYR* 4.0 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 4.0 15.3 + - - +
26A ASP* 3.2 42.8 + - - +
29A VAL* 3.9 6.7 - - - -
83A LEU* 2.7 32.5 + - - +
84A GLN* 4.0 5.6 - - - -
86A GLY* 1.3 73.2 - - - +
88A TRP* 1.3 57.5 + - - +
90A LEU* 3.3 1.3 + - - +
91A LEU* 2.8 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN* 2.9 29.3 + - + +
85A LYS* 4.0 4.9 - - - +
87A SER* 1.3 75.5 - - - +
89A SER* 1.3 66.2 + - - +
91A LEU* 3.8 9.9 - - + +
92A LYS* 3.0 62.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LYS 3.3 13.2 + - - -
86A GLY* 3.4 10.8 - - - -
88A TRP* 1.3 83.5 - - - +
90A LEU* 1.3 64.8 + - - +
92A LYS* 3.5 8.7 + - - +
93A ASP* 3.2 20.1 + - - +
118A GLN* 3.1 29.7 + - - +
121A THR* 4.7 6.6 - - - +
125A TYR* 4.7 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TRP* 3.9 20.4 - - + -
23A VAL* 3.3 28.9 - - + -
29A VAL* 4.1 17.0 - - + -
33A LEU* 5.8 6.3 - - + -
61A VAL* 6.3 1.3 - - + -
86A GLY 3.0 13.3 + - - +
87A SER 3.9 2.5 - - - +
89A SER* 1.3 78.2 - - - +
91A LEU* 1.3 56.7 + - + +
93A ASP* 3.1 4.2 + - - +
94A LEU* 2.8 49.7 + - + -
114A MET* 4.1 23.6 - - + -
115A LEU* 4.2 11.0 - - + -
118A GLN* 3.9 20.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASP* 4.3 3.4 - - - +
28A SER* 3.7 32.3 - - - +
29A VAL* 4.1 15.9 - - + -
32A ALA* 3.5 32.8 - - + -
87A SER* 2.8 31.1 + - - +
88A TRP* 3.8 10.5 - - + +
90A LEU* 1.3 73.4 - - + +
92A LYS* 1.3 62.7 + - - +
94A LEU* 3.7 7.1 - - + +
95A LYS* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TRP* 3.0 56.4 + - + +
89A SER* 3.7 8.1 - - - +
91A LEU* 1.3 79.3 - - - +
93A ASP* 1.3 63.3 - - - +
95A LYS* 3.1 4.3 + - - +
96A ARG* 2.9 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER* 3.2 7.6 + - - +
90A LEU 3.1 7.6 + - - +
92A LYS* 1.3 81.8 - - - +
94A LEU* 1.3 63.4 + - - +
96A ARG* 3.2 27.7 + - - +
97A ILE* 3.1 23.9 + - - +
114A MET* 4.1 21.4 - - + +
118A GLN* 3.0 22.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA* 4.0 32.5 - - + +
33A LEU* 4.2 21.1 - - + -
36A LEU* 4.3 24.2 - - + -
90A LEU* 2.8 31.6 + - + +
91A LEU* 3.7 7.2 - - - +
93A ASP* 1.3 72.9 - - - +
95A LYS* 1.3 64.8 + - - +
97A ILE* 3.2 11.5 + - + +
98A THR* 3.0 23.5 + - + +
111A LEU* 4.4 12.1 - - + -
114A MET* 4.0 21.0 - - + +
115A LEU* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU 3.0 17.2 + - - +
92A LYS* 3.7 4.7 - - - +
94A LEU* 1.3 77.6 - - - +
96A ARG* 1.3 53.8 + - - +
98A THR* 3.4 10.1 - - - +
99A ASP* 2.7 69.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LYS* 2.9 17.1 + - - +
93A ASP* 3.2 31.9 + - - +
95A LYS* 1.3 75.8 - - - +
97A ILE* 1.3 61.4 + - + +
99A ASP* 4.0 5.8 - - - +
100A SER* 3.1 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 3.8 0.8 + - - +
93A ASP 3.1 8.3 + - - +
94A LEU* 3.2 11.9 + - + +
96A ARG* 1.3 77.1 - - + +
98A THR* 1.3 67.1 + - + +
100A SER* 2.7 24.0 + - - -
101A ASP 3.5 2.9 + - - -
102A VAL* 3.7 22.5 - - + +
107A PHE* 4.1 21.5 - - + -
110A GLU* 4.0 21.3 - - + +
111A LEU* 3.9 20.6 - - + -
114A MET* 3.7 42.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.6 31.4 - - + -
40A TYR* 3.4 39.5 - - + -
94A LEU* 3.0 13.2 + - + +
95A LYS* 3.2 24.6 + - - +
97A ILE* 1.3 78.0 - - + +
99A ASP* 1.3 62.4 + - - +
101A ASP* 3.1 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LYS* 2.7 68.9 + - - +
96A ARG* 4.0 6.5 - - - +
98A THR* 1.3 73.9 + - - +
100A SER* 1.3 61.8 + - - +
101A ASP* 3.1 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ARG 3.1 17.4 + - - -
97A ILE* 2.7 19.4 + - - -
99A ASP* 1.3 74.9 - - - +
101A ASP* 1.3 66.4 + - - +
102A VAL* 3.1 19.9 + - - +
110A GLU* 4.4 4.4 + - - -
----------------------------------------------------------
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