Contacts of the helix formed by residues 94 - 119 (chain A) in PDB entry 5HNK
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 THR 94 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLN 3.7 2.6 + - - +
93A ARG* 1.3 76.1 - - - +
95A GLU* 1.3 60.5 + - - +
96A GLU* 3.4 23.3 - - - +
97A GLU* 2.8 40.0 + - - +
98A LYS* 3.0 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR* 1.3 74.4 - - - +
96A GLU* 1.3 66.2 + - - +
98A LYS* 3.3 16.2 - - - +
99A ALA* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR* 3.4 25.2 - - - +
95A GLU* 1.3 84.3 + - - +
97A GLU* 1.3 67.5 + - + +
98A LYS 3.2 0.2 - - - -
99A ALA* 3.4 7.7 + - - +
100A LEU* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LYS* 5.1 9.0 + - - -
92A GLN 4.5 1.2 - - - +
93A ARG* 3.3 20.9 - - + -
94A THR* 2.8 46.7 + - - +
96A GLU* 1.3 77.5 - - + +
98A LYS* 1.3 62.9 + - - +
100A LEU* 3.4 6.6 + - - +
101A ASP* 3.1 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR 5.7 1.3 - - - -
91A ALA 5.9 0.4 + - - -
93A ARG* 3.9 49.4 + - - +
94A THR 3.0 11.2 + - - +
95A GLU* 3.3 18.7 - - + +
97A GLU* 1.3 75.7 - - - +
99A ALA* 1.3 61.6 + - - +
101A ASP* 3.4 2.9 + - - +
102A GLU* 3.1 47.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLU 3.0 14.0 + - - +
96A GLU* 3.4 11.4 + - - +
98A LYS* 1.3 75.9 - - - +
100A LEU* 1.3 57.1 + - - +
102A GLU* 3.6 8.3 + - - +
103A GLN* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS* 4.7 11.1 + - - -
39A SER* 5.3 6.7 - - - +
96A GLU 3.1 16.3 + - - +
97A GLU* 3.8 7.2 - - - +
98A LYS 3.3 0.2 - - - -
99A ALA* 1.3 74.8 - - - +
101A ASP* 1.3 62.9 + - - +
103A GLN* 3.5 22.3 + - - +
104A PHE* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS* 2.7 33.9 + - - +
90A TYR* 5.3 1.6 - - - -
93A ARG* 2.8 45.3 + - - +
97A GLU* 3.1 16.9 + - - +
98A LYS 3.8 0.9 - - - +
100A LEU* 1.3 75.2 - - - +
102A GLU* 1.3 54.6 + - + +
104A PHE* 3.1 2.3 + - - +
105A PHE* 2.8 56.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG* 5.7 1.8 - - - +
98A LYS* 3.1 37.9 + - + +
99A ALA* 4.0 7.4 - - - +
101A ASP* 1.3 72.8 - - + +
103A GLN* 1.3 65.5 + - - +
105A PHE* 4.1 5.3 - - + +
106A GLU* 3.2 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER* 4.4 14.8 + - - +
99A ALA 3.1 14.9 + - - +
100A LEU* 3.5 29.6 - - - +
102A GLU* 1.3 77.9 - - - +
104A PHE* 1.3 62.0 + - - +
106A GLU* 3.6 8.2 + - - +
107A TYR* 3.4 57.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR 5.3 0.2 - - - -
31A GLY* 3.3 38.1 - - - -
32A PHE* 3.7 28.0 - + - -
35A LYS* 3.7 43.1 - - + +
43A PHE* 3.8 24.5 - + - -
100A LEU 3.0 17.9 + - - +
101A ASP 3.1 3.8 + - - +
103A GLN* 1.3 77.0 + - - +
105A PHE* 1.3 83.5 + + - +
107A TYR* 3.1 9.5 + - - +
108A LEU* 2.9 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 5.7 2.9 - - + -
32A PHE* 4.8 15.7 - + - -
35A LYS* 6.0 0.4 - - - -
90A TYR* 5.5 10.5 - + - -
93A ARG* 5.5 0.4 - - - -
101A ASP* 2.8 50.1 + - + +
102A GLU* 4.3 5.4 - - + +
104A PHE* 1.3 95.3 - + - +
106A GLU* 1.3 57.3 + - - +
108A LEU* 3.8 19.1 - - + +
109A LYS* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLU* 3.2 25.2 + - - +
103A GLN* 3.8 7.4 - - - +
104A PHE 3.2 0.2 - - - -
105A PHE* 1.3 74.3 - - - +
107A TYR* 1.3 62.3 + - + +
109A LYS* 3.4 6.5 + - - +
110A ASP* 3.0 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER 4.7 6.7 + - - -
40A LYS 4.8 6.6 + - - -
41A LYS 4.1 11.2 - - - -
42A PRO* 3.5 42.7 - - + +
43A PHE* 3.4 29.8 - + + -
103A GLN* 3.4 49.0 + - + +
104A PHE* 3.1 6.8 + - - +
106A GLU* 1.3 80.0 - - + +
108A LEU* 1.3 57.9 + - - +
110A ASP* 3.4 13.4 + - - +
111A ALA* 2.9 27.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
27A GLY 4.3 2.9 - - - +
28A THR* 4.5 21.5 - - + +
31A GLY* 3.9 26.2 - - - -
43A PHE* 3.8 10.5 - - + -
47A TYR* 4.4 7.4 - - + -
104A PHE* 2.9 29.7 + - + +
105A PHE* 3.8 28.0 - - + +
107A TYR* 1.3 73.4 - - - +
109A LYS* 1.3 61.3 + - - +
111A ALA* 3.2 3.7 + - + +
112A PHE* 2.9 54.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS* 5.0 12.1 - - - +
105A PHE 3.0 18.7 + - - +
106A GLU* 3.4 9.0 - - - +
108A LEU* 1.3 75.2 - - - +
110A ASP* 1.3 65.4 + - - +
112A PHE* 3.3 7.4 + - + +
113A GLU* 3.0 51.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PRO* 5.7 3.5 - - + +
44A ALA* 4.2 13.5 - - + +
106A GLU* 3.0 17.8 + - - +
107A TYR* 3.6 17.1 - - + +
109A LYS* 1.3 78.9 - - - +
111A ALA* 1.3 62.3 + - - +
113A GLU* 3.9 11.1 - - - +
114A LEU* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 4.1 9.2 - - + -
44A ALA* 4.0 17.2 - - - +
47A TYR* 3.8 37.4 - - + -
48A VAL* 4.2 3.5 - - - +
107A TYR 2.9 13.8 + - - +
108A LEU* 3.5 9.6 - - + +
110A ASP* 1.3 77.3 - - - +
112A PHE* 1.3 57.6 + - - +
114A LEU* 3.5 2.5 + - - +
115A CYS* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLY* 3.8 17.0 - - - -
28A THR* 4.0 3.8 - - - -
47A TYR* 3.4 20.6 - + - -
65A VAL* 4.3 5.2 - - + -
66A LEU 3.6 9.6 - - - -
67A GLY* 3.4 39.5 - - - -
108A LEU* 2.9 38.7 + - + +
109A LYS* 3.8 8.1 - - + +
111A ALA* 1.3 78.7 - - - +
113A GLU* 1.3 57.8 + - + +
115A CYS* 3.4 6.7 + - + +
116A LYS* 2.9 28.2 + - - +
121A THR* 3.6 31.2 - - + +
123A THR* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LYS* 3.0 46.1 + - + +
110A ASP* 3.9 11.1 - - - +
112A PHE* 1.3 72.5 - - + +
114A LEU* 1.3 65.6 + - - +
116A LYS* 3.4 14.6 + - - +
117A THR* 3.6 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA* 3.6 37.9 - - + +
45A SER* 3.8 13.9 - - - +
48A VAL* 3.8 14.1 - - + -
110A ASP 3.1 16.4 + - - +
111A ALA 3.7 3.1 - - - +
113A GLU* 1.3 75.0 - - - +
115A CYS* 1.3 61.0 + - - +
117A THR* 2.7 33.7 + - + +
118A THR* 3.6 7.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TYR* 4.5 4.5 - - + -
48A VAL* 3.8 13.6 - - + +
51A ILE* 4.3 9.2 - - - -
65A VAL* 3.5 42.0 - - - -
111A ALA 2.9 19.4 + - - +
112A PHE* 3.4 10.5 - - - +
113A GLU 3.3 0.2 - - - -
114A LEU* 1.3 77.4 - - - +
116A LYS* 1.3 52.2 + - - +
118A THR* 3.1 6.6 + - - +
119A PHE* 2.7 43.1 + - - +
121A THR* 3.5 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE 2.9 17.1 + - - +
113A GLU* 3.8 8.5 - - - +
114A LEU 3.3 1.0 - - - -
115A CYS* 1.3 74.4 - - - +
117A THR* 1.3 59.9 + - + +
119A PHE 3.2 17.8 + - - +
121A THR* 3.5 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLU 3.6 14.8 - - - +
114A LEU* 2.7 27.2 + - + +
116A LYS* 1.3 78.1 - - - +
118A THR* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 4.1 11.6 - - + +
52A GLN* 3.9 22.9 - - - +
114A LEU* 3.6 11.9 + - - +
115A CYS 3.1 5.7 + - - -
116A LYS 4.7 0.2 - - - -
117A THR* 1.3 83.6 + - - +
119A PHE* 1.3 89.6 + - + +
120A PRO* 4.6 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 4.3 7.6 - - + -
51A ILE* 3.6 29.8 - - + -
52A GLN* 3.6 33.0 - - + -
55A ALA* 5.2 3.4 - - + -
63A THR* 3.7 37.5 - - + +
65A VAL* 4.1 8.5 - - + -
115A CYS* 2.7 30.3 + - - +
116A LYS 3.2 17.5 - - - +
118A THR* 1.3 97.3 - - + +
120A PRO* 1.3 77.4 - - + +
121A THR* 3.1 11.3 + - - +
----------------------------------------------------------
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