Contacts of the helix formed by residues 96 - 115 (chain A) in PDB entry 1TKK
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 96 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR 5.9 0.6 + - - -
57A ASP* 3.2 20.9 + - - +
61A SER* 4.3 13.0 + - - +
65A ALA* 4.1 9.6 - - - +
93A LEU* 3.3 33.9 - - + +
94A THR 2.8 24.0 + - - -
95A GLY* 1.3 71.0 - - - +
97A MET* 1.3 64.6 + - - +
98A SER 3.3 2.7 - - - -
99A ALA* 3.2 12.8 + - + +
100A LYS* 3.0 22.5 + - - +
52F LEU* 4.5 2.2 - - - +
56F GLY* 3.1 28.3 + - - +
61F SER* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 5.5 3.4 - - - -
57A ASP* 3.5 5.8 + - - +
90A GLN* 3.9 15.0 - - - +
95A GLY* 3.6 26.0 - - - +
96A ASN* 1.3 74.1 - - - +
98A SER* 1.3 64.9 + - - +
100A LYS* 3.4 12.1 + - - +
101A ALA* 3.0 21.0 + - - +
248A PHE* 4.7 10.3 - - + -
249A THR* 4.1 22.0 - - + -
270A MET 3.2 17.9 - - - +
271A LYS* 3.5 26.9 - - - +
272A ALA 3.6 19.5 - - - +
273A GLY* 3.2 13.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ALA* 3.1 20.6 - - - +
49A PRO 4.1 3.5 + - - -
51A THR* 3.9 4.9 + - - -
55A THR* 3.2 20.4 + - - +
57A ASP* 2.9 33.9 + - - +
62A ILE* 4.1 12.1 - - - -
97A MET* 1.3 79.0 - - - +
99A ALA* 1.3 60.9 + - - +
101A ALA* 3.5 2.1 + - - +
102A ALA 3.4 10.9 + - - -
270A MET* 3.6 26.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
48A ALA* 4.8 0.2 - - - -
57A ASP* 4.5 0.6 + - - +
62A ILE* 3.8 33.6 - - + +
65A ALA* 3.8 29.2 - - + -
66A ILE* 4.2 6.1 - - + +
70A LEU* 4.3 4.7 - - + -
96A ASN* 3.2 13.8 + - + +
98A SER* 1.3 75.9 - - - +
100A LYS* 1.3 65.5 + - - +
101A ALA 3.3 0.7 + - - -
102A ALA* 3.3 12.0 + - - +
103A VAL* 3.5 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 4.1 8.1 - - + -
89A ILE* 3.3 36.7 - - + +
90A GLN* 3.0 31.3 + - - +
93A LEU* 2.8 38.7 + - + -
94A THR* 4.0 0.8 - - - +
95A GLY 2.7 33.0 + - - +
96A ASN 3.0 13.6 + - - +
97A MET* 3.7 19.8 - - - +
99A ALA* 1.3 76.2 - - - +
101A ALA* 1.3 57.3 + - - +
103A VAL* 3.5 4.0 + - - +
104A GLU* 3.1 29.8 + - - +
273A GLY* 3.6 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A MET 3.0 14.5 + - - +
98A SER 3.7 0.9 - - - +
99A ALA 3.2 0.2 - - - -
100A LYS* 1.3 75.2 - - - +
102A ALA* 1.3 62.1 + - - +
104A GLU* 3.2 2.4 + - - +
105A MET* 2.9 33.6 + - - +
269A LEU* 3.1 30.3 - - + +
270A MET* 3.6 21.8 - - + -
273A GLY 3.4 10.1 - - - -
274A GLY* 3.4 8.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL 5.1 0.4 - - - +
34A VAL* 3.9 23.8 - - + +
46A GLY* 3.6 8.1 - - - -
47A GLU 3.6 35.4 + - - +
48A ALA* 3.9 10.3 - - + -
62A ILE* 5.5 0.2 - - + -
66A ILE* 4.7 3.8 - - + -
98A SER 3.4 1.8 + - - -
99A ALA 3.3 9.7 + - - +
101A ALA* 1.3 78.6 - - - +
103A VAL* 1.3 61.9 + - - +
105A MET* 3.5 6.6 + - - +
106A ALA* 3.4 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 5.8 4.0 - - + -
34A VAL* 4.9 7.2 - - + -
36A ILE* 4.1 9.3 - - + +
66A ILE* 4.0 21.3 - - + -
70A LEU* 3.7 25.4 - - + -
74A LEU* 3.6 32.5 - - + -
89A ILE* 4.0 13.7 - - + -
99A ALA 3.5 13.1 + - - +
100A LYS 3.8 7.0 - - - +
101A ALA 3.2 0.2 - - - -
102A ALA* 1.3 75.1 - - - +
104A GLU* 1.3 65.5 + - - +
106A ALA* 3.3 6.8 + - - +
107A LEU* 3.1 21.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.0 17.5 - - + +
89A ILE* 4.3 9.9 - - + +
90A GLN* 2.9 24.7 + - - +
100A LYS 3.1 18.4 + - - +
101A ALA 3.2 7.6 + - - +
103A VAL* 1.3 77.4 - - - +
105A MET* 1.3 63.1 + - - +
107A LEU* 3.2 6.8 + - - +
108A TYR* 2.9 37.3 + - + -
273A GLY 3.4 11.9 - - - +
274A GLY* 3.7 7.4 - - - -
275A ILE* 2.8 28.4 + - - +
276A SER* 2.8 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TRP 3.3 13.3 - - - +
46A GLY* 3.8 2.2 - - - -
47A GLU 3.4 27.6 - - - +
101A ALA 2.9 15.9 + - - +
102A ALA* 3.5 6.5 - - - +
103A VAL 3.3 0.4 - - - -
104A GLU* 1.3 75.7 - - - +
106A ALA* 1.3 56.3 + - - +
108A TYR* 4.0 1.9 - - - +
109A ASP* 3.1 28.9 + - - +
269A LEU* 4.3 22.4 - - + -
270A MET* 3.3 34.1 - - + -
274A GLY* 5.6 0.4 - - - -
275A ILE* 4.7 8.7 - - - +
299A GLU* 4.1 12.1 - - - +
302A LEU* 4.8 1.3 - - - +
303A GLY* 4.1 17.3 - - - +
306A ALA* 3.6 25.6 - - + -
352A LEU* 3.9 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 4.2 6.7 - - + -
36A ILE* 3.4 29.8 - - + -
38A TYR* 2.6 21.4 + - - -
44A GLY* 3.4 29.2 - - - +
45A TRP 3.2 19.5 - - - +
46A GLY 4.1 1.1 - - - +
102A ALA 3.4 8.0 + - - +
103A VAL 3.3 3.5 + - - +
104A GLU 3.2 0.6 - - - -
105A MET* 1.3 77.3 - - - +
107A LEU* 1.3 53.3 + - - +
109A ASP* 4.1 1.1 - - - -
110A GLY 3.4 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.8 29.6 - - + -
36A ILE* 4.1 3.1 - - + +
38A TYR* 3.3 10.8 + - - +
74A LEU* 4.3 9.6 - - + -
79A LEU* 3.9 16.8 - - + +
82A TYR* 4.9 12.1 - - + -
85A ILE* 3.9 24.5 - - + -
86A LEU* 3.7 30.7 - - + -
89A ILE* 4.6 4.0 - - + -
103A VAL* 3.1 17.4 + - + +
104A GLU* 3.6 4.9 - - - +
105A MET 3.2 0.2 - - - -
106A ALA* 1.3 77.7 - - - +
108A TYR* 1.3 61.3 + - + +
109A ASP 3.3 0.2 - - - -
110A GLY* 3.3 1.7 + - - -
111A TRP* 2.9 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 4.4 12.9 - + - -
86A LEU* 3.9 24.9 - - + +
104A GLU* 2.9 47.7 + - + +
105A MET 4.0 1.8 - - - +
107A LEU* 1.3 75.7 - - + +
109A ASP* 1.3 61.0 + - - +
111A TRP* 3.5 29.6 - + + +
112A ALA* 2.8 32.1 + - - +
119A LEU* 3.6 23.5 - - + +
123A LEU* 4.0 18.6 - - + -
275A ILE* 3.6 34.6 - - + +
276A SER* 3.5 23.0 - - - -
279A GLU* 4.3 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL 3.6 5.2 - - - +
44A GLY* 3.4 7.8 - - - -
45A TRP* 3.2 26.0 + - - +
105A MET 3.1 17.0 + - - +
106A ALA 3.7 8.1 - - - +
108A TYR* 1.3 75.0 - - - +
110A GLY* 1.3 62.1 + - - +
112A ALA 3.2 0.2 + - - -
113A GLN* 2.6 47.3 + - - +
119A LEU* 4.7 0.4 - - - +
351A GLY* 3.1 6.8 - - - -
352A LEU* 2.9 46.9 + - + +
353A GLY 4.5 1.7 + - - -
354A ILE 5.3 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.8 5.6 - - - +
38A TYR* 3.7 29.1 - - - -
79A LEU* 3.7 7.7 - - - +
106A ALA 3.4 4.9 + - - -
107A LEU 3.3 6.1 + - - -
108A TYR 3.3 0.4 - - - -
109A ASP* 1.3 80.5 - - - +
111A TRP* 1.3 60.5 + - - +
113A GLN* 3.4 10.0 + - - +
114A MET* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 3.6 16.0 + - + +
82A TYR* 3.4 48.2 - + + -
107A LEU* 2.9 18.6 + - + +
108A TYR* 3.5 28.5 - + + +
109A ASP 3.2 0.2 - - - -
110A GLY* 1.3 76.3 - - - +
112A ALA* 1.3 62.7 + - - +
114A MET* 3.4 36.2 + - + +
115A CYS* 3.5 15.2 + - - +
119A LEU* 4.7 2.0 - - + -
122A MET* 3.1 45.0 - - + +
123A LEU* 4.3 17.0 - - + -
82B TYR* 5.8 0.2 - - - -
111B TRP* 4.4 8.3 - + - -
121B GLN 4.9 2.0 + - - -
122B MET* 3.3 36.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TYR 2.8 17.0 + - - +
109A ASP 3.2 0.2 + - - -
111A TRP* 1.3 78.2 - - - +
113A GLN* 1.3 60.0 + - - +
115A CYS* 3.2 4.9 + - - +
116A GLY 3.2 14.6 + - - -
117A LEU* 3.1 29.6 + - - +
119A LEU* 3.7 23.1 - - + -
122A MET* 4.3 14.1 - - + -
351A GLY* 3.6 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.3 8.2 - - + +
42A ALA* 3.2 27.2 - - + +
43A VAL 3.3 18.2 + - - +
109A ASP* 2.6 48.5 + - - +
110A GLY* 3.8 7.3 - - - +
112A ALA* 1.3 74.0 - - - +
114A MET* 1.3 65.4 + - - +
116A GLY* 3.1 13.7 + - - -
349A LYS* 6.0 3.4 - - - -
350A PRO* 3.9 19.7 + - + +
351A GLY* 3.8 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.9 44.4 - - + +
79A LEU* 4.0 23.1 - - + +
80A ALA* 5.0 2.2 - - - -
110A GLY 3.1 16.8 + - - +
111A TRP* 3.6 35.9 - - + +
112A ALA 3.3 0.2 - - - -
113A GLN* 1.3 76.4 - - - +
115A CYS* 1.3 59.3 + - - +
116A GLY 3.4 0.8 + - - -
115B CYS 4.6 4.9 - - - +
117B LEU* 3.8 34.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
111A TRP* 3.5 9.8 + - - +
112A ALA 3.2 2.9 + - - +
113A GLN 3.1 0.6 - - - -
114A MET* 1.3 82.7 - - - +
116A GLY* 1.3 62.7 + - - -
117A LEU* 3.2 12.9 + - - +
122A MET* 3.7 27.6 - - + -
114B MET 4.8 2.6 - - - +
115B CYS* 3.3 39.7 - - + -
117B LEU* 3.9 13.2 - - - -
122B MET* 3.6 23.8 - - - -
----------------------------------------------------------
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