Contacts of the helix formed by residues 47 - 64 (chain B) in PDB entry 4V2G
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 ASN 47 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASP* 5.3 7.3 + - - +
27B THR* 4.4 14.6 - - - -
45B VAL* 3.4 5.9 - - - +
46B LYS* 1.3 91.3 + - - +
48B LYS* 1.3 64.5 + - - +
49B ARG* 3.0 21.8 + - - +
50B ALA* 3.0 16.2 + - - +
51B LEU* 3.3 19.1 + - - +
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Residues in contact with LYS 48 (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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22B ILE* 2.9 30.5 + - - +
23B ASP* 4.3 10.5 + - - +
25B LEU* 3.2 28.0 + - + +
26B THR* 5.2 8.0 - - + +
27B THR* 4.2 13.2 - - + +
47B ASN* 1.3 73.9 - - - +
49B ARG* 1.3 65.0 + - - +
51B LEU* 3.2 14.7 + - + +
52B LEU* 3.0 50.9 + - + +
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A GLU* 5.4 7.3 + - - +
154A ALA* 4.2 21.5 - - - +
157A ASP* 3.9 48.2 - - + +
158A ARG* 4.1 13.4 - - + +
47B ASN* 3.0 9.8 + - - +
48B LYS* 1.3 76.8 - - - +
50B ALA* 1.3 58.3 + - - +
52B LEU* 3.2 39.2 + - - +
53B ASP* 2.8 68.1 + - - +
99B VAL 4.4 6.5 + - - -
101B LEU 4.9 7.6 + - - -
103B THR* 4.0 16.2 - - - +
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 5.3 2.5 - - + -
46B LYS* 4.7 11.4 - - + +
47B ASN* 3.0 26.9 + - - +
48B LYS 3.3 0.2 - - - -
49B ARG* 1.3 76.6 - - - +
51B LEU* 1.3 62.9 + - - +
53B ASP* 3.5 9.4 + - - +
54B ALA* 3.3 21.7 + - - +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 4.6 9.9 - - + -
10B ILE* 5.4 4.0 - - + -
13B ALA* 3.9 23.1 - - + -
25B LEU* 4.2 29.6 - - + -
26B THR 5.7 3.4 - - - +
27B THR* 5.7 5.8 - - + -
30B LEU* 4.2 24.5 - - + -
45B VAL* 4.3 18.5 - - + +
47B ASN 3.3 9.8 + - - +
48B LYS* 3.2 17.7 + - + +
49B ARG 3.2 0.2 - - - -
50B ALA* 1.3 77.6 - - - +
52B LEU* 1.3 67.0 + - + +
54B ALA* 3.2 7.6 + - + +
55B LEU* 3.0 33.7 + - + +
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 4.2 30.1 - - + -
25B LEU* 4.3 19.7 - - + -
48B LYS* 3.0 41.6 + - + +
49B ARG* 3.6 37.1 + - - +
51B LEU* 1.3 78.0 - - + +
53B ASP* 1.3 64.4 + - - +
55B LEU* 3.1 8.0 + - + +
56B ALA* 3.0 24.4 + - - +
99B VAL* 4.0 25.2 - - + +
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Residues in contact with ASP 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ARG* 2.9 42.7 + - - +
49B ARG* 2.8 46.5 + - - +
50B ALA* 3.8 7.8 - - - +
51B LEU 3.3 0.2 - - - -
52B LEU* 1.3 77.7 - - - +
54B ALA* 1.3 61.0 + - - +
56B ALA* 3.5 7.0 - - - +
57B VAL* 3.3 26.4 + - + +
103B THR* 4.1 5.8 - - - +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ARG* 4.3 23.6 + - - +
10B ILE* 4.4 13.9 - - + -
50B ALA 3.3 10.2 + - - +
51B LEU* 3.2 11.1 + - + +
52B LEU 3.1 0.4 - - - -
53B ASP* 1.3 79.1 - - - +
55B LEU* 1.3 61.0 + - - +
57B VAL* 3.4 7.6 + - - +
58B GLU* 2.9 33.5 + - - +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 4.1 19.3 - - + -
13B ALA* 3.9 29.2 - - + +
14B LEU* 3.4 29.2 - - + -
17B LEU* 4.9 9.6 - - + -
25B LEU* 4.2 25.6 - - + -
51B LEU* 3.0 25.8 + - + +
52B LEU* 3.1 13.0 + - + +
54B ALA* 1.3 72.6 - - - +
56B ALA* 1.3 66.9 + - - +
58B GLU* 3.1 3.3 + - - +
59B ILE* 2.8 34.2 + - + +
99B VAL* 4.1 10.1 - - + -
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU 3.0 11.9 + - - +
53B ASP 3.5 10.8 - - - +
55B LEU* 1.3 79.1 - - - +
57B VAL* 1.3 64.2 + - + +
59B ILE* 3.6 4.5 + - - +
60B LEU* 3.5 24.8 + - - +
99B VAL* 3.9 16.2 - - + +
100B HIS* 4.4 12.6 + - - +
103B THR* 3.8 30.5 - - + +
109B GLN* 5.4 0.2 - - - -
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ARG* 5.4 2.5 - - - +
53B ASP 3.3 17.4 + - - +
54B ALA* 3.7 8.7 - - - +
55B LEU 3.2 0.6 - - - -
56B ALA* 1.3 78.3 - - + +
58B GLU* 1.3 62.3 + - - +
60B LEU* 3.5 3.5 + - - +
61B ALA* 2.9 27.1 + - + +
104B ARG 5.9 1.3 - - - +
106B ASP* 3.6 41.7 - - + +
108B LYS* 4.4 23.6 - - + +
109B GLN* 4.1 21.9 + - + +
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ARG* 3.6 18.9 + - - +
10B ILE* 4.0 34.8 - - + -
14B LEU* 5.3 3.8 - - + -
54B ALA 2.9 20.6 + - - +
55B LEU* 3.8 3.6 - - - +
57B VAL* 1.3 76.2 - - + +
59B ILE* 1.3 67.5 + - - +
60B LEU 3.2 1.3 - - - -
61B ALA* 3.7 10.9 - - - +
62B ARG* 2.9 60.2 + - - +
108B LYS* 4.4 13.5 - - - -
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Residues in contact with ILE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 4.5 12.1 - - + -
17B LEU* 5.0 5.6 - - + -
55B LEU* 2.8 33.3 + - + +
56B ALA* 4.0 4.7 - - - +
58B GLU* 1.3 72.3 - - - +
60B LEU* 1.3 64.0 + - + +
62B ARG* 5.6 0.9 - - - +
63B HIS* 3.0 38.3 + - + +
89B ALA* 3.5 31.8 - - + +
90B LEU* 4.8 6.7 - - + +
93B TYR* 3.8 29.4 - - + -
96B GLY* 4.8 13.2 - - - +
99B VAL* 4.3 20.0 - - + -
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Residues in contact with LEU 60 (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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56B ALA 3.5 11.2 + - - +
57B VAL 3.5 7.0 + - - +
58B GLU 3.2 0.2 - - - -
59B ILE* 1.3 79.3 - - + +
61B ALA* 1.3 66.4 + - - +
64B HIS* 2.9 54.9 + - + +
86B PHE* 4.0 26.9 - - + -
89B ALA* 4.1 12.1 - - + -
90B LEU* 5.0 5.8 - - + -
100B HIS* 4.1 25.6 - - + +
109B GLN* 3.9 21.3 - - - +
222B CTC 4.2 18.8 - - - +
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Residues in contact with ALA 61 (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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57B VAL* 2.9 22.1 + - + +
58B GLU* 3.2 18.6 + - - +
60B LEU* 1.3 77.4 - - - +
62B ARG* 1.3 61.4 + - + +
64B HIS 5.4 0.9 - - - +
108B LYS* 5.7 5.8 - - + -
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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
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7B GLU* 4.3 13.3 + - - +
10B ILE* 3.7 21.6 - - - +
11B ASP* 2.9 30.9 + - - +
14B LEU* 3.6 24.6 - - - +
58B GLU* 2.9 38.6 + - - +
59B ILE* 5.6 0.2 - - - +
61B ALA* 1.3 81.0 - - + +
63B HIS* 1.3 87.6 + - + +
64B HIS 3.9 0.2 - - - -
65B ASP* 5.7 1.6 - - - +
93B TYR* 4.6 4.0 + - - -
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Residues in contact with HIS 63 (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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59B ILE* 3.0 26.2 + - + +
62B ARG* 1.3 101.2 + - + +
64B HIS* 1.3 61.4 + - - +
65B ASP* 3.4 16.9 + - - +
85B SER* 4.4 4.5 + - - +
88B ARG* 5.4 5.4 + - - +
89B ALA* 3.9 22.8 + - + +
92B ARG* 3.4 39.0 + - + -
93B TYR* 3.1 39.8 + + - -
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Residues in contact with HIS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 2.9 47.2 + - + +
61B ALA 5.4 1.1 - - - +
62B ARG 3.9 0.6 - - - -
63B HIS* 1.3 73.9 - - - +
65B ASP* 1.3 58.8 + - - +
66B TYR 3.7 7.6 + - - -
67B SER* 3.9 14.1 + - - -
82B ASN* 3.4 34.0 + - - -
85B SER* 2.7 27.3 + - - -
86B PHE* 3.5 14.7 + + + +
89B ALA* 4.1 5.3 - - + +
222B CTC 2.9 47.2 + - + -
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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