Contacts of the helix formed by residues 57 - 71 (chain N) in PDB entry 5GJQ
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 ARG 57 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24N LEU* 4.4 2.5 - - - -
48N LEU* 3.2 19.7 - - + +
49N TYR* 2.8 50.1 + - + +
50N GLU 4.7 0.2 - - - -
51N ASP 2.9 23.1 + - - -
52N GLU* 3.4 25.9 + - - +
54N PHE* 3.0 35.1 + - + -
55N ARG* 2.6 21.9 + - - +
56N SER* 1.3 70.2 - - - +
58N GLN* 1.3 54.1 + - + +
59N PHE 3.0 0.9 - - - +
60N ALA* 2.8 11.3 + - + +
61N ALA* 2.6 33.4 + - - +
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Residues in contact with GLN 58 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49N TYR* 4.5 10.1 - - + -
55N ARG 4.9 5.6 - - - +
56N SER 2.5 6.9 + - - +
57N ARG* 1.3 75.1 - - + +
59N PHE* 1.3 55.8 + - - +
61N ALA* 3.5 9.3 - - - +
62N LEU* 2.8 34.7 + - - +
83N GLY 3.1 26.0 - - - +
84N ALA* 3.5 18.3 - - - +
86N ASP* 3.6 17.3 - - - +
87N LEU* 3.5 4.4 - - - +
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Residues in contact with PHE 59 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N LEU* 3.3 46.2 - - + -
25N HIS* 4.2 6.1 - + - -
28N ASN* 4.1 18.4 - - + +
56N SER* 2.3 37.4 + - - +
58N GLN* 1.3 67.6 - - - +
60N ALA* 1.3 50.7 + - - +
62N LEU* 3.1 1.6 + - - +
63N VAL* 2.4 38.7 + - + +
87N LEU* 3.3 19.0 - - + +
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Residues in contact with ALA 60 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N LEU* 3.7 26.0 - - + +
45N ILE* 3.5 29.8 - - + +
48N LEU* 4.7 6.7 - - + -
49N TYR* 5.3 0.4 - - + +
57N ARG* 2.8 14.4 + - + +
59N PHE* 1.3 77.0 - - - +
61N ALA* 1.3 51.4 + - - +
63N VAL* 3.2 11.8 - - - +
64N ALA* 2.3 39.5 + - - +
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Residues in contact with ALA 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45N ILE* 5.6 0.2 - - - -
49N TYR* 3.8 23.9 - - + +
57N ARG 2.6 17.3 + - - +
58N GLN* 3.5 14.4 - - - +
60N ALA* 1.3 72.7 - - - +
62N LEU* 1.3 52.4 + - - +
64N ALA* 3.0 3.4 + - - +
65N SER* 2.7 35.2 + - - -
80N TYR* 3.0 39.8 - - + +
84N ALA 4.6 0.4 - - - +
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Residues in contact with LEU 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N ASN* 5.1 5.4 - - - +
58N GLN 2.8 19.8 + - - +
59N PHE 3.7 2.0 - - - +
61N ALA* 1.3 69.3 - - - +
63N VAL* 1.3 55.6 + - - +
65N SER* 2.9 19.5 + - - -
66N LYS* 2.6 53.5 + - + +
80N TYR 3.6 3.2 + - - -
81N ALA* 4.0 16.8 - - + -
84N ALA* 3.8 11.0 - - + -
87N LEU* 3.3 39.3 - - + +
88N PHE* 3.8 6.3 - - + +
96N TYR* 6.2 0.9 - - + -
97N VAL* 6.1 4.9 - - + -
100N ILE* 4.2 15.9 - - + -
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Residues in contact with VAL 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N LEU* 4.4 7.0 - - + +
27N LEU* 4.9 0.4 - - + -
28N ASN* 3.2 34.1 - - + +
31N VAL* 3.5 22.8 - - + +
45N ILE* 5.7 2.5 - - + -
59N PHE* 2.4 37.9 + - + +
60N ALA* 3.2 12.6 - - - +
62N LEU* 1.3 71.2 - - - +
64N ALA* 1.3 62.0 + - - +
66N LYS* 2.9 13.9 + - - +
67N VAL* 2.8 26.3 + - + +
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Residues in contact with ALA 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42N VAL* 5.6 6.5 - - + -
45N ILE* 4.2 16.9 - - + +
46N GLU* 4.6 9.2 - - - +
60N ALA 2.3 31.6 + - - +
61N ALA* 3.3 6.7 - - - +
63N VAL* 1.3 67.0 - - - +
65N SER* 1.3 51.1 + - - +
67N VAL* 2.9 13.7 + - - +
68N PHE* 2.5 44.2 + - + -
80N TYR* 4.2 16.8 - - + -
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Residues in contact with SER 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61N ALA 2.7 15.7 + - - -
62N LEU* 2.9 26.4 + - - -
64N ALA* 1.3 72.3 - - - +
66N LYS* 1.3 55.3 + - - +
69N TYR* 2.8 31.4 + - - +
77N SER* 2.4 47.3 + - - +
80N TYR* 3.2 2.1 - - - +
81N ALA* 2.8 15.1 + - - -
100N ILE* 5.0 6.4 - - - +
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Residues in contact with LYS 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N ASN* 2.4 60.1 + - - +
29N ALA* 4.5 2.0 - - - +
31N VAL* 3.5 25.1 - - + -
32N ASN* 4.5 18.2 - - - -
62N LEU* 2.6 33.7 + - + +
63N VAL* 3.1 8.5 - - - +
65N SER* 1.3 73.3 - - - +
67N VAL* 1.3 62.7 + - - +
69N TYR* 3.5 2.1 + - - +
70N HIS* 2.9 31.3 + - + -
96N TYR* 5.0 19.7 - - + -
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Residues in contact with VAL 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31N VAL* 4.1 4.5 - - + -
35N TRP* 3.4 31.6 - - + -
38N ILE* 4.7 12.6 - - + -
39N SER* 3.3 34.5 - - - +
42N VAL* 4.2 9.9 - - + -
45N ILE* 5.6 1.6 - - + -
63N VAL* 2.8 26.5 + - + +
64N ALA* 3.2 12.6 - - - +
66N LYS* 1.3 71.5 - - - +
68N PHE* 1.3 50.0 + - + +
70N HIS* 2.9 4.6 - - - +
71N LEU* 2.3 54.0 + - + +
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Residues in contact with PHE 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46N GLU* 6.1 0.4 - - - -
64N ALA* 2.5 37.0 + - + +
65N SER 3.0 0.2 + - - -
67N VAL* 1.3 72.2 - - + +
69N TYR* 1.3 54.1 + - - +
71N LEU* 2.8 12.7 - - + +
72N GLY 2.4 14.0 + - - -
73N ALA* 2.3 60.4 + - + +
76N GLU* 3.9 14.4 - - + -
77N SER* 3.5 15.0 - - - -
80N TYR* 5.2 2.7 - + - -
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Residues in contact with TYR 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N SER 2.8 18.1 + - - +
66N LYS 3.9 2.7 - - - +
68N PHE* 1.3 71.1 - - - +
70N HIS* 1.3 65.4 + + - +
72N GLY* 2.4 27.7 + - - +
73N ALA 3.2 6.5 + - - -
74N PHE* 5.3 8.1 - + + -
77N SER* 4.2 1.3 - - - -
96N TYR* 4.9 16.2 - + + -
99N THR* 3.6 34.1 - - + -
100N ILE* 4.5 15.0 - - + -
236S ARG* 2.7 43.2 + - + -
239S THR* 1.9 37.1 + - - -
240S LEU* 3.8 10.7 - - + +
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Residues in contact with HIS 70 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N ASN* 4.5 5.2 - - - -
35N TRP* 3.2 43.3 - + + -
66N LYS* 2.9 24.3 + - + +
67N VAL 2.9 4.9 - - - +
69N TYR* 1.3 88.0 - + - +
71N LEU* 1.3 47.6 - - - +
72N GLY 3.4 0.2 - - - -
236S ARG* 4.7 9.4 - - + -
273S LYS* 2.0 48.3 + - - +
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Residues in contact with LEU 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N TRP* 3.5 7.6 - - + -
39N SER* 3.8 16.8 - - - +
42N VAL* 4.9 7.6 - - + -
67N VAL* 2.3 50.3 + - + +
68N PHE* 2.8 16.3 + - + +
70N HIS* 1.3 71.2 - - - +
72N GLY* 1.3 55.7 + - - +
73N ALA* 3.0 11.8 + - + +
269S LYS* 4.3 6.5 - - + +
272S SER* 5.8 1.1 - - - -
273S LYS* 2.8 55.6 - - + +
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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