Contacts of the helix formed by residues 61 - 80 (chain B) in PDB entry 3E20
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 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ILE* 2.9 23.4 + - - +
60B LYS* 1.3 74.6 - - - +
62B ARG* 1.3 58.8 + - - +
63B VAL 3.1 2.7 - - - -
64B ASN* 2.6 24.8 + - - +
65B ARG* 2.4 33.7 + - - -
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Residues in contact with ARG 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS 3.3 9.1 + - - +
61B SER* 1.3 70.7 - - - +
63B VAL* 1.3 76.8 + - + +
65B ARG* 4.5 9.6 - - - +
66B LEU* 3.1 66.4 + - + +
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B SER* 2.9 2.4 + - - -
62B ARG* 1.3 89.0 - - + +
64B ASN* 1.3 61.6 + - - +
66B LEU* 4.4 3.1 - - - +
67B SER* 3.6 17.3 + - - -
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Residues in contact with ASN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASN 4.3 2.1 - - - +
28B GLY* 3.3 36.4 - - - +
29B THR* 4.1 16.0 + - - +
59B ILE* 4.2 19.4 - - - +
61B SER* 2.6 27.2 + - - -
63B VAL* 1.3 74.6 - - - +
65B ARG* 1.3 67.3 + - - +
67B SER* 2.9 16.7 + - - -
68B VAL* 3.0 18.1 + - - +
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Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA 3.3 26.0 - - - +
57B SER* 3.0 33.6 + - - +
59B ILE* 3.4 27.7 - - + +
60B LYS 4.9 2.7 - - - +
61B SER 2.4 27.7 + - - +
62B ARG* 4.1 8.8 - - - +
64B ASN* 1.3 70.7 - - - +
66B LEU* 1.3 77.8 + - - +
68B VAL* 2.8 16.1 + - - +
69B LEU* 3.0 44.2 + - - +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 3.1 44.6 + - - +
63B VAL* 4.4 3.8 - - - +
65B ARG* 1.3 97.5 - - - +
67B SER* 1.3 60.2 + - - +
69B LEU* 3.5 13.5 + - + +
70B SER* 3.2 24.8 + - - -
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Residues in contact with SER 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASN 5.1 3.6 + - - -
30B SER* 3.0 25.6 + - - -
63B VAL 3.6 13.3 + - - -
64B ASN* 2.9 15.9 + - - -
65B ARG 2.8 1.0 + - - -
66B LEU* 1.3 76.4 - - - +
68B VAL* 1.3 64.8 + - - -
69B LEU 3.4 0.2 + - - -
70B SER* 3.4 5.6 + - - -
71B ALA* 3.1 21.7 + - - +
96B GLU* 4.4 19.2 + - - +
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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
----------------------------------------------------------
29B THR* 3.3 23.3 - - - +
30B SER* 4.3 6.7 - - - -
32B ILE* 5.5 0.2 - - + -
56B ALA* 3.9 12.6 - - + -
59B ILE* 3.7 23.6 - - + -
64B ASN* 3.2 19.7 - - - +
65B ARG 2.8 7.9 + - - +
67B SER* 1.3 71.6 - - - +
69B LEU* 1.3 63.5 + - - +
71B ALA* 3.2 3.9 + - + +
72B ILE* 2.9 48.7 + - + +
124B CYS* 4.0 21.3 - - - -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 3.8 53.7 - - + +
56B ALA* 4.2 13.7 - - + -
57B SER* 4.3 5.8 - - - +
65B ARG* 3.0 55.3 + - - +
66B LEU* 3.6 16.6 - - + +
68B VAL* 1.3 77.7 - - - +
70B SER* 1.3 56.5 + - - +
72B ILE* 3.3 3.8 + - - +
73B THR* 2.9 33.3 + - - -
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Residues in contact with SER 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU 3.2 13.8 + - - -
67B SER* 4.0 4.3 - - - -
69B LEU* 1.3 78.1 - - - +
71B ALA* 1.3 56.7 + - - +
73B THR* 4.0 7.7 - - - +
74B SER* 3.0 15.8 + - - -
96B GLU* 6.1 0.9 - - - -
106B LYS* 2.6 46.1 + - - -
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B SER* 3.8 24.7 - - - +
32B ILE* 4.1 13.7 - - + -
67B SER 3.1 16.1 + - - +
68B VAL* 3.6 6.3 - - - +
69B LEU 3.1 0.8 - - - -
70B SER* 1.3 78.0 - - - +
72B ILE* 1.3 59.6 + - - +
74B SER* 3.2 5.5 + - - -
75B THR* 2.9 33.8 + - - -
94B CYS* 4.0 2.1 - - - -
95B GLY* 4.6 10.5 - - - +
106B LYS* 4.4 4.0 - - - +
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE* 4.1 20.0 - - + -
49B LEU* 3.4 38.2 - - + +
52B GLU* 3.6 33.4 - - + +
53B TYR* 4.0 14.6 - - + -
56B ALA* 3.7 17.0 - - + -
68B VAL* 2.9 26.0 + - + +
69B LEU* 3.8 4.3 - - - +
71B ALA* 1.3 75.4 - - - +
73B THR* 1.3 62.8 + - - +
75B THR* 3.4 6.1 + - - -
76B ARG* 2.9 24.5 + - + +
122B TYR* 4.2 5.4 - - - +
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 3.2 22.1 + - - -
69B LEU 2.9 19.6 + - - -
70B SER* 4.0 8.5 - - - +
72B ILE* 1.3 79.2 - - - +
74B SER* 1.3 63.8 + - - +
76B ARG* 3.1 16.8 + - - +
77B GLU* 3.2 25.2 + - + +
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Residues in contact with SER 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B SER 3.0 19.4 + - - -
71B ALA 3.2 5.4 + - - -
73B THR* 1.3 80.9 - - - +
75B THR* 1.3 60.8 + - - +
77B GLU* 5.5 0.4 - - - +
78B ARG* 3.3 12.6 + - - +
94B CYS* 3.8 10.1 - - - -
106B LYS* 2.9 28.7 + - - +
108B ASN* 3.3 21.6 + - - +
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Residues in contact with THR 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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32B ILE* 3.4 31.2 - - + +
34B LEU* 4.0 17.5 - - + -
49B LEU* 3.7 18.2 - - + -
71B ALA 2.9 18.0 + - - -
72B ILE* 3.6 5.4 - - - -
74B SER* 1.3 75.1 - - - +
76B ARG* 1.3 55.2 + - - +
78B ARG* 3.0 9.0 + - - +
79B LEU* 2.8 32.6 + - + +
92B ILE* 4.1 15.3 - - + -
94B CYS* 3.5 15.1 - - - +
108B ASN* 4.7 0.7 - - - -
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Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER* 3.3 46.0 + - - +
47B ASN* 3.9 5.7 - - - +
49B LEU* 3.5 17.3 - - + -
50B ALA* 3.6 29.5 - - - +
53B TYR* 6.4 2.2 - - - -
72B ILE* 2.9 19.7 + - - +
73B THR* 3.1 8.0 + - - +
75B THR* 1.3 76.2 - - - +
77B GLU* 1.3 61.8 + - + +
79B LEU* 3.0 7.1 + - - +
80B LYS* 2.8 65.0 + - - +
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Residues in contact with GLU 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 THR* 3.2 21.3 + - + +
74B SER* 4.6 0.7 - - - +
76B ARG* 1.3 80.6 + - + +
78B ARG* 1.3 62.1 + - - +
80B LYS* 2.9 49.1 + - + +
81B LEU* 3.9 13.5 - - - +
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Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B SER 3.3 17.1 + - - +
75B THR 3.0 10.3 + - - +
77B GLU* 1.3 76.5 - - - +
79B LEU* 1.3 66.2 + - - +
80B LYS 3.1 1.3 - - - -
81B LEU* 3.0 40.4 + - - +
82B TYR* 4.2 3.9 + - - -
92B ILE* 4.1 16.8 - - + -
108B ASN* 3.2 53.6 + - - +
110B ASP* 3.2 39.9 + - - -
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.2 4.7 - - + -
36B ILE* 3.7 23.6 - - + -
42B ILE* 4.1 21.7 - - + +
45B TYR* 4.0 13.2 - - + -
46B SER* 3.6 37.2 - - - +
49B LEU* 4.3 11.7 - - + -
75B THR 2.8 12.8 + - - +
76B ARG* 3.2 8.7 - - - +
78B ARG* 1.3 78.3 - - - +
80B LYS* 1.3 61.0 + - - +
82B TYR* 3.1 27.3 + - + +
90B LEU* 4.1 8.7 - - + -
92B ILE* 3.9 23.8 - - + -
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Residues in contact with LYS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 5.1 5.6 - - + -
46B SER* 4.2 13.5 - - - +
76B ARG* 2.8 54.0 + - - +
77B GLU* 2.9 50.8 + - + +
78B ARG 3.1 0.2 - - - -
79B LEU* 1.3 77.3 - - - +
81B LEU* 1.3 62.6 + - - +
82B TYR 3.1 10.5 + - - +
83B ASN* 4.5 4.0 - - - +
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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
------------------------------------------------------------
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