Contacts of the helix formed by residues 65 - 83 (chain B) in PDB entry 2L0T
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 VAL 65 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLU* 3.0 35.7 - - + +
63B HIS* 3.3 24.9 + - + +
64B LYS* 1.3 79.6 - - + +
66B PRO* 1.3 67.5 - - + +
67B HIS* 3.0 23.8 + - + +
68B VAL 3.4 4.3 + - - -
69B ALA 3.9 0.3 + - - -
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Residues in contact with PRO 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B HIS 4.9 1.3 - - - +
64B LYS 3.4 9.6 - - - +
65B VAL* 1.3 87.1 - - + +
67B HIS* 1.3 64.4 + - - +
68B VAL 3.3 0.2 - - - -
69B ALA* 3.5 12.8 - - + +
70B LEU* 2.9 31.7 + - + +
109B HIS* 3.5 50.3 - - + +
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Residues in contact with HIS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASN 4.0 0.2 - - - -
26B GLU* 3.2 34.1 + - - +
28B ASN* 2.8 28.7 + - - +
29B THR 5.8 1.1 - - - -
65B VAL* 3.0 16.9 + - + -
66B PRO* 1.3 83.3 - - - +
68B VAL* 1.3 62.0 + - - +
70B LEU* 3.2 21.4 + - + +
71B GLN* 2.9 42.0 + - - +
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 3.2 30.3 - - - +
26B GLU* 3.3 40.8 - - + +
60B ARG* 3.6 39.9 - - + +
63B HIS* 3.4 22.0 - - + +
65B VAL 3.4 1.2 + - - -
66B PRO 3.3 0.2 - - - -
67B HIS* 1.3 72.6 - - - +
69B ALA* 1.3 60.6 + - - +
71B GLN* 3.4 9.3 + - - +
72B ALA* 3.0 26.0 + - - +
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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
----------------------------------------------------------
60B ARG 3.5 13.1 + - - +
61B VAL* 3.7 28.5 - - + +
63B HIS* 4.8 3.8 - - + +
65B VAL 3.9 2.6 + - - +
66B PRO* 3.2 20.5 + - + +
67B HIS 3.2 0.4 - - - -
68B VAL* 1.3 80.3 - - - +
70B LEU* 1.3 59.6 + - - +
72B ALA* 3.2 15.5 - - - +
73B LEU* 3.3 15.3 + - - +
112B VAL* 4.2 14.5 - - + +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PRO* 2.9 31.3 + - + +
67B HIS* 3.2 16.4 + - + +
69B ALA* 1.3 74.3 - - - +
71B GLN* 1.3 65.6 + - + +
73B LEU* 3.1 28.7 + - + +
74B THR* 3.2 11.8 + - - -
109B HIS* 4.7 3.6 - - + +
111B LYS* 4.0 38.4 - - + +
112B VAL* 3.6 22.7 - - + -
115B LYS* 6.3 0.2 - - + -
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Residues in contact with GLN 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA 3.2 23.0 + - - +
24B THR* 3.3 15.0 - - + +
25B ASN 2.8 33.3 + - - +
28B ASN* 3.1 33.9 - - - +
36B ILE* 4.9 8.4 - - + +
67B HIS* 2.9 35.5 + - - +
68B VAL* 3.7 7.7 - - - +
69B ALA 3.3 0.2 - - - -
70B LEU* 1.3 78.8 - - + +
72B ALA* 1.3 61.8 + - - +
74B THR* 3.1 12.4 + - - -
75B LEU* 3.0 21.7 + - - +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 4.0 8.0 - - - +
57B ILE* 3.8 10.5 - - + +
60B ARG* 3.7 23.3 - - + -
61B VAL* 3.7 19.3 - - + +
68B VAL 3.0 13.5 + - - +
69B ALA 3.2 11.9 - - - +
71B GLN* 1.3 77.1 - - - +
73B LEU* 1.3 57.4 + - - +
75B LEU* 3.3 6.6 + - - +
76B LEU* 3.0 29.8 + - - +
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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
----------------------------------------------------------
61B VAL* 4.8 13.5 - - + -
69B ALA 3.3 10.5 - - - +
70B LEU* 3.1 27.1 + - + +
72B ALA* 1.3 77.9 - - - +
74B THR* 1.3 61.3 + - - +
76B LEU* 3.4 9.7 + - + +
77B GLY* 3.1 21.5 + - - -
112B VAL* 3.9 45.5 - - + +
115B LYS* 4.0 29.2 - - + +
116B LEU* 4.5 22.4 - - + +
119B LEU* 4.6 10.9 - - + +
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Residues in contact with THR 74 (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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31B GLU* 5.2 11.4 - - + +
33B TRP* 3.6 29.4 + - + +
36B ILE* 4.7 8.7 - - + -
70B LEU 3.2 13.7 + - - -
71B GLN* 3.1 11.0 + - - -
73B LEU* 1.3 77.5 - - - +
75B LEU* 1.3 60.7 + - - +
77B GLY* 4.1 0.7 - - - -
78B ALA* 3.1 25.5 + - - +
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Residues in contact with LEU 75 (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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20B VAL* 4.2 20.4 - - + -
23B ALA* 5.6 0.7 - - + -
24B THR* 4.8 9.4 - - + -
36B ILE* 3.6 49.5 - - + +
39B ILE* 4.1 29.2 - - + -
53B CYS* 4.8 0.7 - - - -
57B ILE* 3.9 26.7 - - + -
60B ARG* 6.2 0.2 - - + -
71B GLN 3.0 11.9 + - - +
72B ALA* 3.5 9.2 - - - +
74B THR* 1.3 75.5 - - - +
76B LEU* 1.3 65.2 + - - +
78B ALA* 3.5 2.3 + - - +
79B CYS* 3.1 37.9 + - - -
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 4.1 17.5 - - + -
57B ILE* 3.9 29.8 - - + +
58B MET* 6.1 1.6 - - - -
72B ALA 3.0 15.9 + - - +
73B LEU* 3.7 10.5 - - + +
74B THR 3.4 0.2 - - - -
75B LEU* 1.3 77.5 - - - +
77B GLY* 1.3 63.2 + - - +
79B CYS* 3.2 6.6 + - - +
80B VAL* 3.1 25.0 + - + +
87B PHE* 3.8 23.2 - - + -
91B VAL* 5.7 2.2 - - + -
96B PHE* 4.1 26.5 - - + -
116B LEU* 5.1 9.0 - - + -
119B LEU* 5.1 7.0 - - + -
123B TRP* 4.3 17.3 - - + -
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Residues in contact with GLY 77 (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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73B LEU 3.1 13.4 + - - -
74B THR* 4.2 0.9 - - - -
76B LEU* 1.3 79.3 - - - +
78B ALA* 1.3 62.0 + - - +
80B VAL* 3.3 11.6 + - - +
81B ALA* 3.5 11.8 + - - +
119B LEU* 5.0 8.3 - - - +
123B TRP* 4.1 22.2 + - - -
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLY* 4.6 4.3 - - - -
33B TRP* 4.4 20.9 - - + -
36B ILE* 4.4 10.3 - - + -
37B MET* 4.3 20.6 - - + -
40B CYS* 4.3 0.2 - - - -
74B THR 3.1 20.4 + - - +
75B LEU 3.6 5.6 - - - +
76B LEU 3.2 0.2 - - - -
77B GLY* 1.3 78.4 - - - +
79B CYS* 1.3 53.0 + - - +
81B ALA* 3.3 2.4 + - - +
82B ASN* 2.8 39.2 + - - +
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Residues in contact with CYS 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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40B CYS* 3.5 36.1 - - - -
43B VAL* 4.7 0.4 - - - -
53B CYS* 4.7 8.7 - - - -
57B ILE* 5.2 0.2 - - - -
75B LEU* 3.1 34.3 - - - -
76B LEU* 3.2 7.7 + - - +
78B ALA* 1.3 77.8 - - - +
80B VAL* 1.3 59.8 + - - +
83B CYS* 2.9 41.2 + - - +
84B GLY 3.7 0.7 + - - -
87B PHE* 3.7 28.9 - - + +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 3.1 19.9 + - + +
77B GLY 3.6 5.8 - - - +
78B ALA 3.2 0.6 - - - -
79B CYS* 1.3 77.8 - - - +
81B ALA* 1.3 58.7 + - + +
84B GLY* 3.9 6.1 + - - +
87B PHE* 3.8 21.3 - - + -
88B HIS* 2.9 48.4 + - + +
91B VAL* 4.1 15.5 - - + -
123B TRP* 3.7 45.5 - - + +
127B PHE* 4.7 8.3 - - + -
133B PHE* 5.0 1.3 - - + -
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Residues in contact with ALA 81 (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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46A ALA 3.2 27.6 - - - +
47A GLY* 3.2 15.6 - - - +
48A LYS* 3.7 9.4 + - + +
49A GLN 5.0 0.2 + - - -
77B GLY 3.5 6.7 + - - +
78B ALA 3.3 3.8 + - - +
80B VAL* 1.3 78.5 - - + +
82B ASN* 1.3 64.3 + - - +
84B GLY* 4.3 4.9 + - - -
127B PHE* 6.0 4.5 - - + -
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Residues in contact with ASN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 2.8 27.5 + - - -
44A ILE* 3.4 30.7 - - - +
47A GLY* 2.8 23.2 + - - +
49A GLN* 5.3 8.2 + - - +
33B TRP* 5.2 0.2 - - - -
37B MET* 3.6 19.7 - - + +
40B CYS* 3.3 16.0 - - - -
78B ALA 2.8 18.9 + - - +
81B ALA* 1.3 79.3 - - - +
83B CYS* 1.3 66.5 + - - +
84B GLY* 3.4 0.7 + - - -
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Residues in contact with CYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B CYS* 3.1 43.1 - - - -
43B VAL* 3.6 21.5 - - + -
44B GLY* 4.5 2.7 - - - +
79B CYS* 2.9 23.6 + - - +
82B ASN* 1.3 76.6 - - - +
84B GLY* 1.3 59.9 + - - +
85B LYS 4.2 0.2 + - - -
86B ILE* 3.4 28.2 - - + +
87B PHE* 3.8 13.5 - - + -
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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