Contacts of the helix formed by residues 83 - 101 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLU* 3.5 16.4 - - - -
40B LEU* 3.7 8.9 - - - +
80B ASP* 2.7 23.6 + - - -
81B ILE 3.4 1.0 + - - -
82B ASP* 1.3 77.3 - - - +
84B PHE* 1.3 60.0 + - - +
85B CYS* 3.9 6.5 + - - +
86B GLY 3.2 11.8 + - - -
87B LEU* 3.0 30.5 + - - +
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Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 4.0 19.2 - - + +
29B VAL* 3.7 23.8 - - + -
30B GLU* 3.6 47.1 - - + +
34B LEU 5.1 3.1 - - - -
36B GLU* 2.9 47.5 + - + +
39B LEU* 3.7 33.0 - - + -
40B LEU* 3.9 23.8 - - + +
51B PHE* 4.8 4.9 - + - -
83B SER* 1.3 70.0 - - - +
85B CYS* 1.3 57.4 + - - +
87B LEU* 3.9 3.6 - - - +
88B LYS* 3.0 37.4 + - - +
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Residues in contact with CYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLU* 4.4 5.1 + - - +
36B GLU* 4.6 1.2 + - - -
83B SER* 3.3 7.8 - - - +
84B PHE* 1.3 77.9 - - - +
86B GLY* 1.3 57.1 + - - +
88B LYS* 3.7 15.5 - - - +
89B THR* 2.9 35.4 + - - -
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Residues in contact with GLY 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLY* 5.8 0.2 - - - -
80B ASP* 2.9 31.5 + - - +
83B SER* 3.2 15.3 + - - -
85B CYS* 1.3 78.7 - - - +
87B LEU* 1.3 59.1 + - - +
89B THR* 3.4 7.5 + - - -
90B TYR* 2.9 25.5 + - - +
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 3.9 26.7 - - + -
40B LEU* 3.8 22.9 - - + -
51B PHE* 4.1 16.2 - - + -
52B ASN* 3.9 22.7 - - - +
55B ALA* 3.9 16.6 - - + -
56B LYS* 4.6 3.6 - - - +
80B ASP 3.3 4.3 + - - -
81B ILE* 3.9 25.1 - - + +
83B SER 3.0 17.9 + - - +
84B PHE* 4.0 4.0 - - - +
86B GLY* 1.3 72.1 - - - +
88B LYS* 1.4 64.7 + - - +
90B TYR* 3.3 9.2 - - + +
91B VAL* 3.1 28.8 + - + +
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Residues in contact with LYS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B HIS* 3.7 25.8 + - + +
26B ILE* 3.6 22.2 - - + -
27B GLU* 3.8 30.4 + - + +
30B GLU* 2.8 34.7 + - - +
84B PHE 3.0 24.4 + - - +
85B CYS* 3.7 12.8 - - - +
87B LEU* 1.4 74.1 - - - +
89B THR* 1.4 58.4 + - - +
91B VAL* 3.2 5.9 + - - -
92B VAL* 2.9 33.6 + - - +
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Residues in contact with THR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B CYS* 2.9 25.0 + - - -
86B GLY* 3.6 8.3 - - - +
88B LYS* 1.4 73.9 - - - +
90B TYR* 1.3 52.6 + - - +
92B VAL* 3.3 8.0 + - + +
93B THR* 2.8 49.3 + - - +
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Residues in contact with TYR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LYS* 3.5 45.7 - - + -
59B THR* 3.9 28.5 - - + -
60B ASN* 2.9 24.9 + - - -
63B LEU* 5.5 3.1 - - + +
78B GLU* 3.9 38.2 + - - -
79B GLY* 4.1 10.8 - - - -
81B ILE* 3.9 17.5 - - + -
86B GLY 2.9 13.6 + - - +
87B LEU* 3.3 16.8 - - + +
89B THR* 1.3 76.4 - - - +
91B VAL* 1.3 62.5 + - + +
93B THR* 3.5 7.7 + - - -
94B ALA* 3.3 19.2 + - - +
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 3.3 36.6 - - + +
22B LEU* 3.9 16.8 - - + -
23B HIS* 4.0 13.2 - - + +
26B ILE* 3.9 14.4 - - + -
55B ALA 5.2 0.7 - - - +
59B THR* 3.8 22.0 - - - +
87B LEU* 3.1 19.9 + - + +
88B LYS* 3.7 6.3 - - - +
90B TYR* 1.3 73.3 - - + +
92B VAL* 1.4 61.2 - - - +
94B ALA* 3.2 4.9 + - - +
95B ILE* 3.0 35.5 + - + +
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B HIS* 3.4 30.5 - - + +
88B LYS 2.9 19.7 + - - +
89B THR* 3.8 7.4 - - + +
91B VAL* 1.4 71.3 - - - +
93B THR* 1.4 60.3 + - - +
95B ILE* 3.3 11.1 + - + +
96B ASP* 2.9 49.4 + - - +
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Residues in contact with THR 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU 5.8 3.4 - - - +
89B THR* 2.8 38.5 + - - +
90B TYR* 3.6 8.2 - - - -
92B VAL* 1.4 73.9 - - - +
94B ALA* 1.3 56.6 + - - +
96B ASP* 3.6 5.2 + - - +
97B TYR* 3.0 32.5 + - + +
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.3 10.3 - - + -
59B THR* 3.4 33.4 - - + -
63B LEU* 4.0 26.0 - - + -
90B TYR 3.3 4.1 + - - +
91B VAL 3.2 7.4 + - - +
93B THR* 1.3 76.4 - - - +
95B ILE* 1.4 58.4 + - - +
97B TYR* 3.3 2.2 + - - +
98B ILE* 2.9 37.4 + - - +
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Residues in contact with ILE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.8 15.6 - - + +
19B LEU* 3.7 36.6 - - + +
20B GLU* 3.8 36.6 - - + +
23B HIS* 4.6 6.3 - - + -
91B VAL* 3.0 28.6 + - + +
92B VAL* 3.3 13.9 + - + +
94B ALA* 1.4 75.1 - - - +
96B ASP* 1.4 64.6 + - - +
98B ILE* 3.3 2.3 + - - +
99B ASN* 2.9 50.2 + - - +
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Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 2.9 36.2 + - - +
93B THR* 4.0 5.3 - - - +
95B ILE* 1.4 80.6 - - - +
97B TYR* 1.3 63.3 + - - +
99B ASN* 3.4 9.4 + - - +
100B LYS* 3.1 23.2 + - - +
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Residues in contact with TYR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 3.7 23.1 - - + -
66B CYS* 6.3 0.2 - - + -
67B CYS* 4.0 27.9 - - + +
93B THR* 3.0 21.9 + - + +
94B ALA* 3.6 5.2 - - - +
96B ASP* 1.3 76.6 - - - +
98B ILE* 1.3 68.7 + - + +
100B LYS* 3.0 53.7 + - + +
101B LEU* 3.4 26.7 + - + +
182B GOL 5.3 0.7 + - - -
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ARG* 3.9 27.0 - - + +
15B PHE* 5.3 2.0 - - + -
16B LEU* 3.7 26.2 - - + -
19B LEU* 3.8 26.2 - - + -
62B ALA* 4.1 25.6 - - + +
63B LEU* 4.2 14.4 - - + -
66B CYS* 4.0 21.5 - - + -
94B ALA 2.9 25.7 + - - +
95B ILE 3.8 3.4 - - - +
97B TYR* 1.3 72.9 - - + +
99B ASN* 1.3 61.2 + - - +
101B LEU* 3.1 27.6 + - + +
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Residues in contact with ASN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 6.3 0.2 - - - +
16B LEU* 3.4 25.6 - - - +
20B GLU* 5.4 2.4 + - - -
95B ILE* 2.9 40.0 + - - +
96B ASP* 3.7 9.4 + - - +
98B ILE* 1.3 75.8 - - - +
100B LYS* 1.3 60.4 + - - +
101B LEU 3.5 5.2 + - - +
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Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ASP 3.1 12.8 + - - +
97B TYR* 3.0 51.9 + - + +
99B ASN* 1.3 76.3 - - - +
101B LEU* 1.4 67.1 + - + +
102B SER* 3.7 1.9 + - - -
182B GOL 3.4 32.1 - - - -
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B TYR* 4.5 7.4 - - - +
12B ARG* 4.8 10.3 + - - -
66B CYS* 3.5 38.6 - - + +
67B CYS* 5.1 5.4 - - - +
97B TYR* 3.5 31.6 - - + +
98B ILE* 3.1 26.9 + - + +
99B ASN 4.0 5.9 - - - +
100B LYS* 1.4 91.9 - - + +
102B SER* 1.3 69.0 + - - +
103B GLU 4.0 0.2 + - - -
182B GOL 3.6 25.4 - - - +
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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) + - + + + + + -
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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