Contacts of the helix formed by residues 88 - 110 (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 88 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER* 4.4 11.6 + - - -
83A ALA* 2.9 12.2 + - + +
84A GLN* 5.1 0.2 - - - +
86A ARG* 4.6 11.4 - - + +
87A GLY* 1.3 74.5 - - - +
89A GLN* 1.3 65.1 + - - +
90A GLN* 3.4 14.9 + - - +
91A VAL* 3.1 38.9 + - + +
92A VAL* 3.2 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN* 2.9 30.9 + - - +
87A GLY* 3.4 12.3 + - - +
88A ASP* 1.3 71.0 - - - +
90A GLN* 1.3 66.8 + - - +
92A VAL* 3.5 6.3 - - - +
93A LYS* 3.0 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASP* 3.2 13.0 + - - +
89A GLN* 1.3 78.5 - - - +
91A VAL* 1.3 59.6 + - + +
93A LYS* 3.4 10.2 + - - +
94A GLU* 2.9 55.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER* 4.2 30.3 - - - +
54A VAL* 5.2 4.9 - - + +
56A TRP* 4.7 3.4 - - + -
57A LYS* 4.5 10.5 - - + -
83A ALA* 4.0 14.8 - - + -
88A ASP* 3.1 27.4 + - - +
90A GLN* 1.3 76.8 - - + +
92A VAL* 1.3 67.5 + - - +
94A GLU* 4.2 12.8 - - - +
95A LEU* 3.0 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.4 32.5 - - + +
83A ALA* 3.4 19.5 - - + -
84A GLN* 3.3 36.3 - - - +
88A ASP 3.2 19.4 + - - +
89A GLN* 3.3 12.1 + - - +
91A VAL* 1.3 76.1 - - - +
93A LYS* 1.3 61.4 + - + +
96A GLN* 2.9 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLN* 3.0 36.7 + - + +
90A GLN* 3.9 7.6 - - - +
92A VAL* 1.3 78.2 - - + +
94A GLU* 1.3 66.8 + - + +
96A GLN* 3.4 16.5 - - - +
97A VAL* 3.0 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS* 3.2 37.7 + - + +
90A GLN* 2.9 53.1 + - + +
91A VAL* 3.3 10.4 + - - +
93A LYS* 1.3 77.9 - - + +
95A LEU* 1.3 62.6 + - - +
97A VAL* 3.5 8.7 + - - +
98A PHE* 3.4 26.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TRP* 4.4 6.3 - - + +
57A LYS* 3.4 52.9 - - + +
61A LYS* 6.1 0.4 - - + -
76A TRP* 3.4 40.0 - - + +
79A GLY* 4.6 22.0 - - - -
80A LEU* 4.5 10.5 - - + +
83A ALA* 5.7 0.2 - - + -
91A VAL* 3.0 30.3 + - + +
92A VAL 4.1 2.5 - - - +
94A GLU* 1.3 75.5 - - - +
96A GLN* 1.3 65.7 + - - +
98A PHE* 3.3 8.8 + - + +
99A LEU* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 4.3 17.5 - - + +
92A VAL* 2.9 28.9 + - - +
93A LYS* 3.2 17.5 + - - +
95A LEU* 1.3 77.1 - - - +
97A VAL* 1.3 63.0 + - - +
99A LEU* 3.1 13.2 + - + +
100A ARG* 2.9 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LYS* 3.0 18.9 + - + +
94A GLU* 3.7 9.2 - - - +
95A LEU 3.2 0.2 - - - -
96A GLN* 1.3 78.4 - - + +
98A PHE* 1.3 69.8 + - + +
100A ARG* 3.2 11.7 + - - +
101A ARG* 3.1 21.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS* 6.0 7.2 - - - -
61A LYS* 4.4 19.1 - - + -
64A GLN* 3.6 29.6 - - - -
76A TRP* 3.6 24.9 - + + +
94A GLU* 3.4 17.5 - - + +
95A LEU* 3.3 9.7 + - + +
97A VAL* 1.3 84.9 - - + +
99A LEU* 1.3 57.8 + - - +
101A ARG* 3.2 12.9 + - - +
102A LEU* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 3.9 23.8 - - + +
76A TRP* 3.7 41.0 - - + +
77A GLU* 3.3 27.8 - - + +
80A LEU* 4.8 15.9 - - + -
95A LEU 2.9 14.2 + - - +
96A GLN* 3.4 15.3 - - + +
98A PHE* 1.3 77.2 - - - +
100A ARG* 1.3 75.1 + - - +
102A LEU* 3.6 3.4 + - + +
103A ALA* 3.3 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLN* 2.9 37.0 + - + +
97A VAL* 3.4 9.6 - - + +
99A LEU* 1.3 87.5 + - - +
101A ARG* 1.3 65.8 + - - +
103A ALA* 3.0 27.6 + - - +
104A ARG* 3.2 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 5.8 4.4 - - - +
97A VAL* 3.1 10.7 + - + +
98A PHE* 3.2 14.1 + - - +
100A ARG* 1.3 81.1 - - - +
102A LEU* 1.3 62.3 + - - +
104A ARG* 3.1 34.8 + - + +
105A GLU* 3.7 8.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 5.2 8.7 - - + +
69A ARG* 3.4 51.1 - - + +
72A ALA* 3.7 5.6 - - + -
73A ARG* 3.5 27.1 - - + +
76A TRP* 3.5 24.2 - - + -
98A PHE 2.9 16.1 + - - +
99A LEU* 3.8 6.3 - - + +
101A ARG* 1.3 77.1 - - - +
103A ALA* 1.3 62.6 + - - +
105A GLU* 3.1 31.3 + - - +
106A ASP* 3.4 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 5.4 4.3 - - - +
99A LEU 3.3 11.3 + - - +
100A ARG* 3.0 25.2 + - - +
102A LEU* 1.3 79.0 - - - +
104A ARG* 1.3 51.0 + - + +
106A ASP* 3.1 11.7 + - + +
107A ALA* 2.8 33.7 + - - +
112A HIS* 5.0 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG* 3.3 24.1 + - - +
101A ARG* 3.3 29.5 - - + +
102A LEU 3.1 0.8 - - - -
103A ALA* 1.3 78.5 - - + +
105A GLU* 1.3 59.0 + - + +
107A ALA* 3.3 20.8 - - - +
108A LEU* 3.4 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 2.7 44.9 + - - +
101A ARG* 4.3 8.3 - - + +
102A LEU* 3.1 22.4 + - - +
104A ARG* 1.3 77.4 - - + +
106A ASP* 1.3 65.8 + - - +
108A LEU* 3.0 29.2 + - + +
109A GLU* 3.3 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 4.5 11.4 - - - +
73A ARG* 2.8 35.0 + - - +
102A LEU 3.4 3.9 + - - +
103A ALA* 3.1 15.0 + - + +
105A GLU* 1.3 77.9 - - - +
107A ALA* 1.3 56.9 + - - +
109A GLU* 5.3 2.5 - - - -
110A HIS* 2.7 74.6 + - - +
111A HIS 3.4 0.5 + - - -
112A HIS* 3.6 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA 2.8 13.0 + - - +
104A ARG* 3.3 18.8 - - - +
105A GLU 3.1 0.2 - - - -
106A ASP* 1.3 77.5 + - - +
108A LEU* 1.3 55.1 + - + +
111A HIS* 3.0 22.3 + - - -
112A HIS* 3.1 21.6 + - + +
113A HIS* 3.2 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG 3.4 16.8 - - - +
105A GLU* 3.0 18.2 + - + +
107A ALA* 1.3 83.1 - - - +
109A GLU* 1.3 67.8 + - + +
111A HIS* 3.7 8.1 + - - +
113A HIS* 4.9 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 3.1 32.3 + - - -
105A GLU* 3.3 12.1 + - - +
106A ASP* 5.3 1.7 - - - -
108A LEU* 1.3 81.1 - - + +
110A HIS* 1.3 60.8 + - + +
111A HIS* 3.3 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 5.8 1.3 - - - -
106A ASP* 2.7 45.0 + - - +
109A GLU* 1.3 78.2 - - + +
111A HIS* 1.3 71.6 + - - +
112A HIS* 3.4 8.9 - - + +
----------------------------------------------------------
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