Contacts of the helix formed by residues 72 - 87 (chain A) in PDB entry 4N9W
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 GLY 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A LYS 4.6 4.8 + - - -
58A VAL* 5.8 2.3 - - - +
70A ARG* 3.7 5.8 + - - -
71A PHE* 1.3 73.5 - - - +
73A PRO* 1.4 75.6 - - - +
74A ALA* 3.2 3.8 - - - -
75A THR* 3.0 17.5 + - - -
76A HIS* 3.2 14.9 - - - -
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Residues in contact with PRO 73 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A GLY* 1.4 83.1 - - - +
74A ALA* 1.3 62.8 + - - +
76A HIS* 3.2 15.9 + - + +
77A ARG* 3.1 43.3 + - + +
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLY* 3.2 2.1 - - - -
73A PRO* 1.3 79.4 - - - +
75A THR* 1.3 56.9 + - - +
77A ARG* 3.4 30.9 + - - +
78A LYS* 2.9 29.3 + - - +
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Residues in contact with THR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLY 2.7 28.4 + - - +
55A GLY* 4.1 5.7 - - - -
56A LYS 4.5 1.7 + - - -
71A PHE* 3.5 32.1 - - + +
72A GLY 3.0 14.7 + - - -
74A ALA* 1.3 75.6 - - - +
76A HIS* 1.3 62.7 + - - +
78A LYS* 3.1 3.9 + - - +
79A VAL* 2.8 36.0 + - + +
101A LEU* 3.7 27.4 - - + -
104A LEU* 3.9 7.0 - - + -
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Residues in contact with HIS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A PHE 3.9 12.5 + - - -
72A GLY 3.2 28.7 - - - -
73A PRO* 3.2 12.1 + - + +
75A THR* 1.3 77.8 - - - +
77A ARG* 1.3 61.7 + - + +
79A VAL* 3.5 6.7 + - - +
80A LYS* 3.2 28.0 + - - +
104A LEU* 3.7 39.2 - - + +
107A GLN* 5.6 0.9 - - - -
108A ALA* 5.8 0.2 - - - +
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Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PRO* 3.1 22.8 + - + +
74A ALA* 3.6 38.9 - - - +
76A HIS* 1.3 74.0 - - + +
78A LYS* 1.3 65.5 + - - +
80A LYS* 3.4 6.8 + - - +
81A LYS* 3.0 24.7 + - - +
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 5.6 2.5 - - + -
52A VAL* 6.4 0.4 - - + -
53A SER 4.7 14.8 - - - +
54A GLY* 4.7 9.0 - - - +
74A ALA 2.9 18.0 + - - +
75A THR* 3.5 8.3 - - - +
77A ARG* 1.3 76.1 - - - +
79A VAL* 1.3 58.4 + - - +
81A LYS* 3.4 8.0 + - - +
82A TRP* 2.9 31.9 + - - +
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.0 15.9 - - + -
54A GLY* 5.7 0.4 - - - -
75A THR* 2.8 24.8 + - + +
76A HIS* 3.7 7.0 - - - +
78A LYS* 1.3 76.7 - - + +
80A LYS* 1.3 62.8 + - - +
82A TRP* 3.4 7.7 + - + +
83A ILE* 3.1 28.7 + - + +
101A LEU* 3.9 27.6 - - + -
104A LEU* 4.2 10.3 - - + +
105A ALA* 3.9 22.4 - - + +
108A ALA* 3.8 24.7 - - + -
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A HIS 3.2 16.6 + - - +
77A ARG* 3.8 6.5 - - - +
78A LYS 3.3 0.2 - - - -
79A VAL* 1.3 76.9 - - - +
81A LYS* 1.3 58.0 + - - +
83A ILE* 3.4 2.8 + - - -
84A ALA* 2.9 30.3 + - - +
108A ALA* 4.3 17.7 - - + -
372A VAL* 3.7 33.5 - - + +
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Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ARG 3.0 16.8 + - - +
78A LYS* 3.7 7.0 - - - +
80A LYS* 1.3 77.6 - - - +
82A TRP* 1.3 57.0 + - - +
84A ALA* 3.7 5.3 - - - -
85A GLU* 2.9 72.7 + - + +
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Residues in contact with TRP 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLY* 3.9 0.2 - - - -
5A MET 3.7 20.2 - - - -
6A VAL* 3.7 23.6 - - + -
36A SER* 2.9 40.3 + - - -
38A LEU* 3.8 30.4 - - + +
52A VAL* 4.1 26.5 - - + +
78A LYS 2.9 19.3 + - - +
79A VAL* 3.6 5.2 - - + +
81A LYS* 1.3 76.4 - - - +
83A ILE* 1.3 77.7 + - + +
85A GLU* 3.8 3.1 - - - +
86A GLY* 3.0 28.8 + - - -
88A PHE* 3.5 27.7 - + - -
91A LEU* 3.7 22.4 - - + -
105A ALA* 5.2 2.2 - - + -
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A VAL* 3.1 24.3 + - + +
80A LYS* 3.7 7.0 - - - +
82A TRP* 1.3 91.5 - - + +
84A ALA* 1.3 64.7 + - - +
85A GLU 3.2 0.5 + - - -
86A GLY* 3.2 8.7 + - - -
87A ASP* 3.8 6.8 + - - -
88A PHE* 4.2 10.3 - - + -
91A LEU* 5.2 2.9 - - + -
105A ALA* 4.2 4.3 - - + +
108A ALA* 3.9 24.0 - - + +
109A ALA* 3.7 23.1 - - + -
370A VAL* 4.1 22.4 - - + +
371A GLN* 3.7 32.8 - - - +
372A VAL* 3.8 5.8 - - + +
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LYS 2.9 20.8 + - - +
81A LYS* 3.2 7.4 + - - +
83A ILE* 1.3 74.6 - - - +
85A GLU* 1.3 64.0 + - + +
86A GLY 3.7 0.3 + - - -
87A ASP* 4.3 4.5 + - - +
371A GLN* 6.3 0.7 - - - +
372A VAL* 4.2 14.1 - - + +
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Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ARG* 4.8 3.1 + - - -
81A LYS* 2.9 59.8 + - + +
82A TRP* 3.8 2.6 - - - +
84A ALA* 1.3 81.6 - - + +
86A GLY* 1.3 62.2 + - - +
87A ASP* 3.4 3.9 - - - +
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Residues in contact with GLY 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ARG* 2.8 29.4 + - - -
82A TRP 3.0 17.1 + - - -
83A ILE 3.2 1.6 + - - -
85A GLU* 1.3 78.5 - - - +
87A ASP* 1.3 68.6 + - - +
88A PHE* 3.2 26.0 + - - -
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ARG* 3.4 17.0 + - - +
83A ILE 3.8 7.0 + - - -
84A ALA 4.3 4.2 + - - +
85A GLU 3.4 4.4 - - - +
86A GLY* 1.3 79.6 - - - +
88A PHE* 1.3 60.1 + - - +
369A LYS* 3.0 56.2 + - - +
370A VAL 5.2 4.3 - - - -
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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