Contacts of the helix formed by residues 49 - 64 (chain B) in PDB entry 1Z0X
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 49 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASP* 5.4 4.8 + - - -
164A TYR* 4.2 21.0 - - - +
29B MSE 3.9 12.5 - - - +
44B TYR* 4.0 11.2 - - + +
47B PHE* 3.3 1.6 - - - +
48B LYS* 1.3 84.6 + - - +
50B LYS* 1.3 64.2 + - - +
51B GLN* 2.9 32.0 + - - +
52B ALA* 2.9 27.3 + - - +
53B LEU 3.3 7.6 + - - -
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Residues in contact with LYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 2.8 26.6 + - - +
25B GLU* 3.4 23.8 + - - +
27B LEU* 2.7 34.2 + - - +
28B SER* 5.2 2.2 - - - -
29B MSE 3.9 27.5 - - + +
44B TYR* 5.2 0.4 + - - -
49B ASN* 1.3 75.7 - - - +
51B GLN* 1.3 58.2 + - - +
53B LEU* 3.1 8.5 + - + +
54B LEU* 2.8 57.7 + - + +
101B GLN* 5.9 0.7 - - - -
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Residues in contact with GLN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 5.1 4.2 - - - +
157A GLN* 5.4 3.6 + - - +
162A ASP* 6.1 1.3 - - - +
164A TYR* 3.8 20.9 - - + -
165A LEU* 4.0 27.3 - - + +
49B ASN* 2.9 16.4 + - - +
50B LYS* 1.3 79.0 - - - +
52B ALA* 1.3 54.1 + - - +
54B LEU* 3.2 15.7 + - - +
55B GLN* 2.9 56.7 + - - +
101B GLN* 3.0 22.9 + - - +
102B THR* 4.0 1.7 - - - +
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TYR* 3.2 35.1 + - + +
47B PHE* 3.5 11.7 - - + -
48B LYS* 4.0 21.3 - - + +
49B ASN* 2.9 17.8 + - - +
51B GLN* 1.3 76.5 - - - +
53B LEU* 1.3 61.2 + - - +
55B GLN* 3.5 2.6 + - - +
56B SER* 3.3 24.4 + - - -
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Residues in contact with LEU 53 (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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10B ILE* 4.1 13.2 - - + -
11B ILE* 4.5 5.4 - - + -
14B ALA* 4.3 12.1 - - + -
27B LEU* 4.2 24.0 - - + -
28B SER 6.1 0.2 - - - -
29B MSE 4.1 21.3 - - + +
32B VAL* 4.3 12.6 - - + -
47B PHE* 3.6 36.7 - - + -
49B ASN 3.3 7.8 + - - +
50B LYS* 3.1 14.9 + - + +
52B ALA* 1.3 79.9 - - - +
54B LEU* 1.3 58.0 + - + +
56B SER* 3.2 3.5 + - - -
57B MSE 2.9 46.7 + - + +
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.8 29.2 - - + -
27B LEU* 4.5 3.1 - - + -
50B LYS* 2.8 41.1 + - + +
51B GLN* 3.2 23.3 + - - +
53B LEU* 1.3 74.8 - - + +
55B GLN* 1.3 64.5 + - - +
57B MSE 3.2 17.7 + - - +
58B ALA* 2.9 25.6 + - - +
98B ILE* 4.0 6.9 - - + +
101B GLN* 3.9 30.7 - - + +
102B THR* 3.7 13.8 - - + +
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Residues in contact with GLN 55 (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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164A TYR* 3.4 28.9 - - + +
165A LEU* 4.5 1.4 - - - +
168A GLN* 4.6 10.6 + - + +
51B GLN* 2.9 47.4 + - - +
52B ALA 3.7 1.8 - - - +
53B LEU 3.3 0.2 - - - -
54B LEU* 1.3 75.9 - - - +
56B SER* 1.3 60.0 + - - +
58B ALA* 3.4 2.9 + - - +
59B GLU* 3.0 27.8 + - - +
102B THR* 3.2 25.4 - - - +
103B VAL* 3.0 35.6 + - - +
105B ALA* 4.7 6.4 - - - +
106B TYR* 4.6 8.4 - - + -
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LYS* 4.0 11.8 - - - +
11B ILE* 3.6 26.0 - - - +
47B PHE* 3.2 25.4 - - - -
52B ALA 3.3 3.8 + - - -
53B LEU 3.2 8.3 + - - -
55B GLN* 1.3 75.9 - - - +
57B MSE 1.3 61.7 + - - +
59B GLU* 3.3 12.9 + - - +
60B ALA* 2.9 27.0 + - - +
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Residues in contact with MSE 57 (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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11B ILE* 4.1 16.4 - - + -
14B ALA* 3.7 29.4 - - + -
15B PHE* 3.6 30.8 - - + +
18B LEU* 3.6 31.6 - - + -
24B LEU* 5.2 0.2 - - + -
27B LEU* 3.8 15.3 - - + -
53B LEU* 2.9 30.4 + - + +
54B LEU* 3.2 17.7 + - - +
56B SER* 1.3 72.3 - - - +
58B ALA* 1.3 66.9 + - - +
60B ALA* 2.9 19.3 + - - +
61B ILE* 2.9 17.0 + - - +
98B ILE* 4.2 10.3 - - + -
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Residues in contact with ALA 58 (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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54B LEU 2.9 16.6 + - - +
55B GLN 3.6 4.9 - - - +
57B MSE 1.3 74.9 - - - +
59B GLU* 1.3 62.9 + - - +
61B ILE* 3.2 8.5 + - - +
62B GLU* 3.1 17.3 + - - +
98B ILE* 3.6 21.9 - - + +
99B GLU* 4.6 5.2 - - - +
102B THR* 3.6 15.5 - - + +
106B TYR* 3.3 29.6 + - + +
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLN 3.0 16.9 + - - +
56B SER* 3.6 12.5 + - - +
58B ALA* 1.3 77.1 - - - +
60B ALA* 1.3 62.1 + - - +
62B GLU* 3.3 3.5 + - - +
63B GLU* 3.2 38.7 + - - +
106B TYR* 3.6 41.7 - - + +
107B PRO* 5.5 4.4 - - - +
108B GLN* 5.4 8.5 - - + +
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Residues in contact with ALA 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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11B ILE* 4.1 20.4 - - + -
15B PHE* 4.1 7.2 - - + -
56B SER 2.9 14.5 + - - +
57B MSE 2.9 15.9 + - - +
59B GLU* 1.3 77.4 - - - +
61B ILE* 1.3 60.4 + - - +
63B GLU* 3.4 17.6 + - - +
64B HIS* 3.5 20.0 + - + -
92B PHE* 4.6 2.6 - - + -
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Residues in contact with ILE 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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15B PHE* 3.7 14.8 - - + -
57B MSE 2.9 16.2 + - - +
58B ALA* 3.6 6.3 - - - +
60B ALA* 1.3 72.8 - - - +
62B GLU* 1.3 67.9 + - - +
64B HIS* 2.8 21.1 + - - +
88B LEU* 3.5 31.6 - - + +
89B TYR* 4.7 6.7 - - + -
92B PHE* 3.8 25.6 - - + -
95B ALA* 3.9 32.1 - - + +
98B ILE* 4.0 26.9 - - + -
99B GLU* 4.1 13.9 - - - +
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Residues in contact with GLU 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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58B ALA 3.1 3.0 + - - -
59B GLU 3.3 9.4 + - - +
61B ILE* 1.3 77.5 - - - +
63B GLU* 1.3 53.9 + - - +
65B PHE* 2.8 35.4 + - - +
85B TYR* 2.9 20.1 + - - -
88B LEU* 4.4 5.1 - - - +
99B GLU* 4.3 3.1 - - - +
106B TYR* 3.8 16.6 + - + -
108B GLN* 3.6 13.0 - - + -
109B ARG* 2.9 59.8 + - + +
112B HIS* 2.7 30.2 + - + -
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Residues in contact with GLU 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 GLU* 3.2 33.2 + - - +
60B ALA* 3.5 15.1 - - - +
61B ILE 3.0 1.0 + - - -
62B GLU* 1.3 77.0 - - - +
64B HIS* 1.3 64.7 + - + +
65B PHE 3.3 5.3 + - - +
108B GLN* 4.7 18.1 - - + +
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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
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60B ALA* 3.5 15.3 + - + -
61B ILE 2.8 15.5 + - - +
63B GLU* 1.3 76.2 - - + +
65B PHE* 1.3 66.8 + - - +
66B GLN* 3.3 19.8 + - - +
88B LEU* 3.6 17.1 - - + +
91B GLN* 4.4 12.3 + - - +
92B PHE* 3.5 25.5 - + + -
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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
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Atomic class I II III IV V VI VII VIII
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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