Contacts of the helix formed by residues 83 - 101 (chain A) in PDB entry 3QTH
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 SER 83 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU* 3.5 16.4 - - - -
40A LEU* 3.5 8.7 - - - +
80A ASP* 2.6 24.2 + - - -
81A ILE 3.4 0.8 - - - -
82A ASP* 1.3 77.1 - - - +
84A PHE* 1.3 60.4 + - - +
85A CYS* 3.9 7.0 + - - +
86A GLY 3.2 12.1 + - - -
87A LEU* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 4.1 17.8 - - + +
29A VAL* 3.7 35.9 - - + -
30A GLU* 3.7 48.7 - - + +
34A LEU* 5.2 5.6 - - + -
36A GLU* 2.9 47.7 + - + +
39A LEU* 4.1 18.2 - - + -
40A LEU* 3.7 24.9 - - + +
51A PHE* 4.8 4.0 - + - -
83A SER* 1.3 71.3 - - - +
85A CYS* 1.4 57.6 + - - +
87A LEU* 3.5 3.1 + - - +
88A LYS* 3.0 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 4.1 15.3 - - - -
36A GLU* 4.6 1.5 + - - -
83A SER* 3.3 6.8 + - - +
84A PHE* 1.4 79.0 - - - +
86A GLY* 1.3 55.4 + - - +
88A LYS* 3.7 14.0 - - - +
89A THR* 2.9 32.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
79A GLY* 5.8 0.2 - - - -
80A ASP* 2.9 30.6 + - - +
83A SER* 3.2 16.7 + - - -
85A CYS* 1.3 76.5 - - - +
87A LEU* 1.4 58.6 + - - +
89A THR* 3.4 7.4 + - - -
90A TYR* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 3.9 25.6 - - + -
40A LEU* 3.9 23.1 - - + -
51A PHE* 4.0 15.7 - - + -
52A ASN* 3.9 25.8 - - + +
55A ALA* 3.9 14.1 - - + -
56A LYS* 4.7 3.1 - - - +
80A ASP 3.3 4.3 + - - -
81A ILE* 3.9 24.9 - - + +
83A SER 3.0 17.7 + - - +
84A PHE* 4.0 4.5 - - - +
86A GLY* 1.4 72.3 - - - +
88A LYS* 1.3 64.8 + - - +
90A TYR* 3.3 9.6 - - + +
91A VAL* 3.1 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A HIS* 4.0 21.7 + - + +
26A ILE* 3.6 22.4 - - + -
27A GLU* 3.8 30.6 + - + +
30A GLU* 2.8 34.1 + - - +
84A PHE 3.0 24.6 + - - +
85A CYS* 3.7 14.7 - - - +
87A LEU* 1.3 73.6 - - - +
89A THR* 1.4 58.4 - - - +
91A VAL* 3.2 6.8 + - - +
92A VAL* 2.9 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A CYS 2.9 19.4 + - - -
86A GLY* 3.6 8.5 - - - -
88A LYS* 1.4 73.8 - - - +
90A TYR* 1.3 51.8 + - - +
92A VAL* 3.3 6.8 + - - +
93A THR* 2.8 49.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LYS* 3.4 28.8 - - + +
59A THR* 3.9 20.4 - - + -
60A ASN* 2.7 32.8 + - - -
77A LEU* 2.7 75.4 + - + +
78A GLU 3.9 15.0 - - - -
79A GLY* 4.1 10.8 - - - -
81A ILE* 3.8 22.0 - - + -
86A GLY 2.9 14.7 + - - +
87A LEU* 3.3 16.6 - - + +
89A THR* 1.3 76.1 - - - +
91A VAL* 1.4 62.7 + - + +
93A THR* 3.5 2.8 + - - -
94A ALA* 3.3 7.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
19A LEU* 3.4 34.5 - - + +
22A LEU* 3.9 12.3 - - + -
23A HIS* 4.0 12.8 - - + +
26A ILE* 3.8 21.8 - - + -
55A ALA 5.1 0.9 - - - +
59A THR* 3.8 21.5 - - - +
87A LEU* 3.1 18.6 + - + +
88A LYS 3.2 6.0 + - - +
90A TYR* 1.4 73.4 - - + +
92A VAL* 1.4 60.3 + - - +
94A ALA* 3.1 4.9 + - - +
95A ILE* 3.0 34.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
23A HIS* 3.5 34.1 - - + +
88A LYS 2.9 20.3 + - - +
89A THR* 3.8 6.5 - - - +
91A VAL* 1.4 71.2 - - - +
93A THR* 1.4 61.0 + - - +
95A ILE* 3.3 10.7 + - + +
96A ASP* 2.9 48.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 3.7 26.2 - - + -
89A THR* 2.8 38.2 + - - +
90A TYR* 3.6 7.4 - - - -
92A VAL* 1.4 73.8 - - - +
94A ALA* 1.3 56.3 + - - +
96A ASP* 4.0 4.5 - - - +
97A TYR* 3.0 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.3 9.9 - - + -
59A THR* 3.3 34.1 - - + -
63A LEU* 4.1 23.3 - - + -
77A LEU* 4.2 4.7 - - + +
90A TYR 3.3 3.3 + - - +
91A VAL 3.1 6.5 + - - +
93A THR* 1.3 75.0 - - - +
95A ILE* 1.4 58.8 + - - +
97A TYR* 3.4 3.3 + - - +
98A ILE* 2.9 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.7 17.1 - - + +
19A LEU* 3.7 45.3 - - + +
20A GLU* 3.9 20.9 - - + +
23A HIS* 4.4 8.5 - - + -
91A VAL* 3.0 27.2 + - + +
92A VAL* 3.3 12.3 + - + +
94A ALA* 1.4 76.8 - - - +
96A ASP* 1.4 64.1 + - - +
98A ILE 3.3 0.2 + - - -
99A ASN* 2.9 47.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 2.9 39.8 + - - +
93A THR* 4.0 4.6 - - - +
95A ILE* 1.4 77.4 - - - +
97A TYR* 1.3 62.5 + - - +
99A ASN* 3.5 7.8 + - - +
100A LYS* 3.1 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.7 19.1 - - + -
66A CYS* 6.2 0.2 - - + -
67A CYS* 3.5 33.5 - - - -
72A LYS* 3.8 25.3 - - - +
93A THR* 3.0 23.9 + - + +
94A ALA* 3.6 3.8 - - - +
96A ASP* 1.3 75.4 - - - +
98A ILE* 1.4 67.1 + - + +
100A LYS* 3.2 7.3 + - + +
101A LEU* 3.2 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 3.9 27.5 - - + +
15A PHE* 5.3 2.7 - - + -
16A LEU* 3.7 23.8 - - + -
19A LEU* 3.8 25.8 - - + -
62A ALA* 4.0 26.2 - - + +
63A LEU* 4.1 16.2 - - + -
66A CYS* 4.0 21.5 - - + -
94A ALA 2.9 23.7 + - - +
95A ILE 3.7 3.1 - - - +
97A TYR* 1.4 71.9 - - + +
99A ASN* 1.4 62.3 + - - +
101A LEU* 3.2 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 6.1 0.4 - - - +
16A LEU* 3.5 25.2 - - - +
95A ILE* 2.9 39.1 + - - +
96A ASP* 3.7 9.7 + - - +
97A TYR 3.4 0.2 - - - -
98A ILE* 1.4 76.1 - - - +
100A LYS* 1.3 61.3 + - + +
101A LEU 3.4 4.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
96A ASP* 3.1 30.5 + - + +
97A TYR* 3.2 5.8 + - + +
99A ASN* 1.3 77.5 - - + +
101A LEU* 1.4 67.0 + - - +
102A SER* 3.5 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 4.8 7.9 - - - +
66A CYS* 3.7 41.3 - - + +
67A CYS* 5.2 0.4 - - - -
70A SER* 3.6 26.7 - - - +
72A LYS* 4.4 12.6 - - + -
97A TYR* 3.2 47.9 + - + +
98A ILE* 3.2 23.2 + - + +
99A ASN 4.3 4.9 - - - +
100A LYS* 1.4 78.8 - - - +
102A SER* 1.3 63.7 + - - +
103A GLU* 3.8 1.2 + - - -
----------------------------------------------------------
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