Contacts of the helix formed by residues 66 - 81 (chain B) in PDB entry 5TQB
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 HIS 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LYS* 3.6 30.6 - - + +
34B LEU* 3.9 19.7 - - + -
60B ILE* 3.9 15.9 - - + +
64B GLY 3.3 0.6 - - - -
65B ARG* 1.3 110.5 - - - +
67B ALA* 1.3 58.0 + - - +
68B GLY 3.3 3.1 + - - -
69B ALA* 3.4 1.4 + - + -
70B ALA* 2.9 28.8 + - - +
106B GLU* 2.7 45.4 + - - -
107B LEU* 3.4 15.3 - - + +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TYR* 4.5 4.3 - - + -
60B ILE* 3.7 8.8 - - - +
61B GLY 3.3 23.3 - - - +
62B GLU* 3.5 16.6 - - - +
64B GLY 3.4 12.7 + - - +
65B ARG 3.3 3.0 + - - -
66B HIS* 1.3 76.5 - - - +
68B GLY* 1.3 57.8 + - - +
70B ALA* 3.3 2.7 + - - +
71B LEU* 2.9 38.2 + - - +
97B VAL* 3.9 14.4 - - + -
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Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ARG 4.9 0.6 + - - -
66B HIS 3.3 0.6 - - - -
67B ALA* 1.3 80.4 - - - +
69B ALA* 1.3 52.2 + - - +
71B LEU 3.9 0.2 - - - -
72B THR* 2.7 37.2 + - - -
94B ALA* 3.9 14.0 - - - +
97B VAL* 3.9 15.5 - - - +
98B ASP* 5.5 0.4 - - - -
103B LEU* 6.1 0.2 - - - +
107B LEU 3.7 3.0 + - - -
108B GLY* 3.4 24.0 - - - -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LYS* 6.1 0.4 - - - +
34B LEU* 4.6 8.0 - - + +
66B HIS* 3.4 10.3 + - + +
68B GLY* 1.3 75.6 - - - +
70B ALA* 1.3 57.6 + - - +
72B THR* 3.4 2.8 + - - -
73B LEU* 3.0 28.6 + - - +
105B GLU 4.5 0.9 - - - +
106B GLU 3.4 20.2 - - - +
107B LEU 3.0 20.5 + - - +
108B GLY 3.5 0.8 - - - -
109B GLY* 3.8 15.7 - - - +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 3.9 27.0 - - + +
53B ALA* 5.5 0.9 - - - +
57B TYR* 3.8 24.7 - - + -
60B ILE* 4.0 9.6 - - + -
66B HIS 2.9 18.9 + - - +
67B ALA 3.6 3.8 - - - +
69B ALA* 1.3 75.8 - - - +
71B LEU* 1.3 60.4 + - - +
73B LEU* 3.3 4.6 + - - +
74B LEU* 3.0 32.5 + - - +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TYR* 3.7 40.4 - - + +
62B GLU* 5.9 0.2 - - + -
67B ALA 2.9 21.3 + - - +
70B ALA* 1.3 71.9 - - - +
72B THR* 1.3 66.9 + - - +
74B LEU* 3.4 4.1 + - + -
75B GLY* 2.9 18.2 + - - -
90B TYR* 3.6 46.8 - - + +
93B ALA* 3.7 40.6 - - + +
94B ALA* 3.7 9.4 - - + +
97B VAL* 4.0 14.1 - - + -
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLY 2.7 23.7 + - - -
69B ALA* 3.5 7.0 - - - +
70B ALA 3.3 0.2 - - - -
71B LEU* 1.3 75.6 - - - +
73B LEU* 1.3 58.2 + - - +
75B GLY* 2.9 4.3 + - - -
76B GLN* 2.9 46.5 + - - +
91B TYR* 3.6 16.5 - - + -
94B ALA* 4.1 8.7 - - - +
108B GLY 4.0 2.3 + - - -
109B GLY* 3.5 26.4 - - - +
112B GLU* 4.1 17.3 - - + +
113B LYS* 4.3 8.0 - - - +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ILE* 5.6 0.2 - - + -
34B LEU* 3.8 40.2 - - + +
37B ALA* 3.8 18.4 - - + -
38B THR* 3.9 19.3 - - + +
41B LEU* 4.1 15.7 - - + -
53B ALA* 4.2 6.3 - - + -
69B ALA 3.0 17.2 + - - +
70B ALA* 3.6 4.9 - - - +
72B THR* 1.3 77.4 - - - +
74B LEU* 1.3 63.2 + - - +
75B GLY 3.2 0.2 + - - -
76B GLN* 3.2 25.0 + - - +
77B ILE* 3.0 37.5 + - + +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ALA 4.3 4.9 - - - +
53B ALA* 3.7 26.9 - - + +
54B ARG* 4.0 19.1 - - + +
57B TYR* 4.0 29.6 - - + -
70B ALA 3.0 21.0 + - - +
71B LEU* 3.7 7.2 - - + +
73B LEU* 1.3 75.6 - - - +
75B GLY* 1.3 60.8 + - - +
77B ILE* 3.6 6.5 + - + -
78B HIS* 2.8 50.9 + - + -
90B TYR* 3.7 37.8 - - + +
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Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU 2.9 15.0 + - - -
72B THR 2.9 5.1 + - - -
74B LEU* 1.3 75.1 - - - +
76B GLN* 1.3 64.2 + - - +
77B ILE 3.3 0.2 + - - -
78B HIS 3.3 1.4 + - - -
79B VAL* 3.0 26.3 + - - +
87B ALA* 3.7 6.0 - - - +
90B TYR* 3.9 13.7 - - - +
91B TYR* 3.5 21.5 - - - -
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Residues in contact with GLN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A HIS* 4.0 20.4 - - + -
114A ILE* 3.8 16.3 - - - +
41B LEU* 3.8 8.9 - - + +
72B THR* 2.9 25.7 + - - +
73B LEU* 3.6 26.6 - - - +
75B GLY* 1.3 74.8 - - - +
77B ILE* 1.3 62.7 + - - +
79B VAL* 3.2 6.7 + - - +
80B GLU* 3.0 29.0 + - - +
91B TYR* 3.1 8.4 + - - +
112B GLU* 3.0 42.7 + - - +
401B PEG 3.5 12.7 + - - -
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ALA* 5.0 1.1 - - + +
41B LEU* 4.0 28.0 - - + -
46B ILE* 3.8 17.6 - - + +
49B ALA* 3.7 16.8 - - + +
50B ALA* 3.7 26.9 - - + +
53B ALA* 3.5 30.7 - - + -
73B LEU* 3.0 32.1 + - + +
74B LEU* 3.9 7.2 - - + +
75B GLY 3.2 0.2 - - - -
76B GLN* 1.3 77.1 - - - +
78B HIS* 1.3 61.3 + - - +
80B GLU* 3.2 5.2 + - - +
81B LEU* 3.0 29.4 + - + +
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Residues in contact with HIS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ALA* 4.7 16.9 - - + +
74B LEU* 2.8 40.6 + - + +
75B GLY 4.1 1.3 - - - +
77B ILE* 1.3 76.5 - - + +
79B VAL* 1.3 61.9 + - - +
81B LEU* 3.4 17.8 + - + +
82B GLY 3.2 1.9 + - - -
83B ASP* 2.9 53.2 + - + +
86B ALA* 3.6 22.0 - - + +
87B ALA* 3.9 11.4 - - - +
90B TYR* 3.5 24.4 + + - -
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Residues in contact with VAL 79 (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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44A ALA* 4.1 8.1 + - - +
107A TRP* 4.9 8.6 - - + +
109A LYS* 6.0 1.3 - - + -
111A HIS* 4.1 8.3 - - + +
75B GLY 3.0 16.6 + - - +
76B GLN* 3.4 11.0 - - - +
78B HIS* 1.3 77.4 - - - +
80B GLU* 1.3 61.0 + - + +
82B GLY* 3.0 19.5 + - - -
83B ASP 4.9 0.7 - - - +
84B ILE* 5.0 10.6 - - + +
87B ALA* 3.7 17.5 - - + -
91B TYR* 4.0 13.9 - - + -
116B TRP* 3.6 44.2 - - + -
120B LEU* 4.5 4.9 - - + -
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Residues in contact with GLU 80 (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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38A HIS* 2.4 48.6 + - - +
44A ALA* 3.7 9.9 - - - +
109A LYS* 5.6 4.7 - - - +
111A HIS* 2.7 32.9 + - + +
114A ILE* 4.6 1.9 - - - +
115A ASN* 5.7 1.4 + - - +
118A GLN* 3.0 22.3 + - - +
41B LEU* 4.4 11.0 - - + +
46B ILE* 3.8 19.8 - - + +
76B GLN 3.0 17.6 + - - +
77B ILE* 3.6 7.6 - - - +
79B VAL* 1.3 77.7 - - + +
81B LEU* 1.3 59.9 + - - +
82B GLY 3.6 0.2 + - - -
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA* 4.2 3.2 - - - +
45A LYS* 3.9 14.7 - - - +
46B ILE* 3.3 25.4 - - + +
47B GLU* 3.5 30.7 - - - +
50B ALA* 4.6 9.6 - - + -
77B ILE* 3.0 31.5 + - + +
78B HIS* 3.7 26.9 - - + +
79B VAL 3.1 0.4 - - - -
80B GLU* 1.3 78.3 - - - +
82B GLY* 1.3 59.3 + - - +
83B ASP* 3.2 7.0 + - + +
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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
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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