Contacts of the helix formed by residues 72 - 88 (chain A) in PDB entry 5J1T
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 GLN 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 3.9 20.2 + - + -
70A PHE 3.2 10.3 + - - +
71A GLY* 1.4 90.3 + - - +
73A HIS* 1.3 64.4 + - - +
74A LEU 3.2 3.7 + - - -
75A ALA* 3.2 9.1 + - + -
76A LYS* 3.0 26.7 + - - +
106A THR* 3.0 33.9 + - - +
268A PRO 4.1 2.8 - - - +
269A PHE* 3.5 19.0 - - + -
270A LEU* 2.9 51.2 + - - +
272A LEU* 4.1 4.9 - - - +
401A ATP 3.9 3.8 - - - +
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Residues in contact with HIS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLY 3.8 0.8 - - - -
72A GLN* 1.3 75.7 - - - +
74A LEU* 1.3 87.0 + - + +
76A LYS* 3.6 14.5 + - - +
77A LYS* 3.5 19.1 + - - +
228A ARG* 3.0 32.1 + - - +
229A GLU* 3.6 37.3 + - + +
231A ILE* 3.0 25.5 + - + -
270A LEU* 3.8 24.9 - - + +
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Residues in contact with LEU 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 GLN 3.2 0.8 - - - -
73A HIS* 1.3 94.3 + - + +
75A ALA* 1.3 68.6 + - - +
77A LYS* 3.3 4.9 + - - +
78A ILE* 3.1 33.8 + - + +
231A ILE* 3.4 41.5 - - + +
232A LYS* 4.2 6.5 - - + -
233A LEU* 4.0 18.4 - - + +
236A ILE* 4.2 10.5 - - + -
268A PRO* 4.0 30.1 - - + +
270A LEU* 5.0 10.0 - - + +
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Residues in contact with ALA 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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69A LEU* 4.7 5.2 - - + -
72A GLN* 3.2 18.1 + - + +
74A LEU* 1.3 78.2 - - - +
76A LYS* 1.3 65.3 + - - +
79A ILE* 2.9 32.9 + - + +
111A VAL* 5.5 0.2 - - + -
267A VAL* 3.6 27.4 - - + -
268A PRO 3.9 11.0 + - - +
269A PHE* 3.8 22.7 - - + -
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Residues in contact with LYS 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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65A LEU* 3.6 39.6 - - + +
66A ASP* 3.1 35.6 + - - +
69A LEU* 3.6 31.5 + - + +
72A GLN 3.0 22.4 + - - +
73A HIS* 4.0 13.9 - - - +
74A LEU 3.2 0.2 - - - -
75A ALA* 1.3 76.4 - - - +
77A LYS* 1.3 59.1 + - - +
79A ILE* 4.8 0.7 - - - -
80A LEU* 3.0 31.4 + - - +
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A HIS 3.5 11.8 + - - +
74A LEU* 3.3 5.5 + - - +
75A ALA 3.2 0.4 - - - -
76A LYS* 1.3 80.3 - - + +
78A ILE* 1.3 67.0 + - + +
80A LEU* 3.8 5.2 - - + +
81A ASN* 3.2 45.1 + - - +
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Residues in contact with ILE 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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74A LEU* 3.1 24.6 + - + +
75A ALA 4.0 2.2 - - - +
77A LYS* 1.3 80.8 - - + +
79A ILE* 1.3 63.0 - - - +
81A ASN* 4.0 2.3 - - - +
82A ALA* 3.0 24.1 + - + +
233A LEU* 4.3 21.5 - - + -
265A TYR* 4.0 28.8 - - + -
266A PHE 4.2 7.2 - - - +
267A VAL* 3.8 24.9 - - + -
268A PRO* 4.0 26.9 - - + -
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Residues in contact with ILE 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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61A LEU* 5.2 2.9 - - + -
65A LEU* 4.3 17.3 - - + -
69A LEU* 6.6 0.2 - - + -
75A ALA* 2.9 22.9 + - + +
76A LYS* 4.0 2.9 - - - +
78A ILE* 1.3 76.8 - - - +
80A LEU* 1.3 64.0 + - - +
82A ALA* 4.7 1.6 - - - -
83A VAL* 2.9 28.4 + - + +
98A LEU* 3.9 27.1 - - + -
100A LEU* 4.3 7.2 - - + -
111A VAL* 4.2 16.8 - - + -
115A ILE* 3.8 32.8 - - + -
267A VAL* 4.0 28.3 - - + -
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Residues in contact with LEU 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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58A ARG* 3.6 49.1 + - + +
61A LEU* 4.0 16.8 - - + +
62A GLN* 3.7 55.4 - - + +
65A LEU* 4.3 7.9 - - + -
76A LYS 3.0 19.2 + - - +
77A LYS* 3.8 7.4 - - + +
79A ILE* 1.3 75.6 - - - +
81A ASN* 1.3 61.9 + - - +
84A PHE* 3.0 33.7 + - + +
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Residues in contact with ASN 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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58A ARG* 2.9 33.3 + - - +
77A LYS* 3.2 42.9 + - - +
78A ILE* 4.2 2.2 - - - +
80A LEU* 1.3 77.6 - - - +
82A ALA* 1.3 64.8 + - - +
84A PHE* 4.5 2.0 - - - +
85A GLY* 3.1 20.6 + - - -
265A TYR* 5.7 0.7 - - - -
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Residues in contact with ALA 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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78A ILE* 3.0 20.1 + - + +
79A ILE* 4.1 2.7 - - - +
81A ASN* 1.3 78.3 - - - +
83A VAL* 1.3 63.9 + - + +
85A GLY* 4.1 0.3 - - - -
86A PHE* 3.2 25.1 + - - +
96A LEU* 3.6 6.5 - - + +
98A LEU* 4.1 15.9 - - + -
265A TYR* 3.6 43.4 - - + -
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 4.3 5.6 - - + -
61A LEU* 4.1 19.1 - - + -
79A ILE* 2.9 33.6 + - + +
82A ALA* 1.3 72.8 - - - +
84A PHE* 1.3 67.5 + - - +
86A PHE* 3.2 1.4 + - - -
87A ILE* 3.1 28.7 + - + +
96A LEU* 4.2 8.1 - - + -
98A LEU* 4.2 22.4 - - + -
115A ILE* 4.2 16.8 - - + -
119A ILE* 4.1 26.0 - - + -
202A MET* 4.6 3.6 - - + -
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Residues in contact with PHE 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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56A LEU* 3.9 25.8 - - + +
57A SER* 4.1 6.7 - - - -
58A ARG* 3.3 63.0 - - + -
61A LEU* 4.6 2.6 - - + +
80A LEU* 3.0 21.0 + - + +
81A ASN* 4.5 2.2 - - - +
83A VAL* 1.3 79.0 - - - +
85A GLY* 1.3 65.3 + - - +
88A ASN* 3.1 62.1 + - + +
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Residues in contact with GLY 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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81A ASN 3.1 18.7 + - - -
82A ALA 4.1 0.7 - - - -
83A VAL 3.2 0.2 - - - -
84A PHE* 1.3 82.8 - - - +
86A PHE* 1.3 61.4 + - - +
88A ASN* 4.1 2.6 - - - +
89A ASN* 3.3 22.7 + - - +
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Residues in contact with PHE 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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82A ALA 3.2 17.4 + - - +
83A VAL 3.2 1.1 + - - +
84A PHE 3.2 0.6 - - - -
85A GLY* 1.3 78.3 - - - +
87A ILE* 1.3 82.0 + - + +
89A ASN* 3.2 22.4 + - - +
92A PRO* 3.5 15.9 - - + +
94A LYS 3.4 15.7 - - - -
96A LEU* 3.4 37.2 - - + -
164A ARG* 3.4 14.2 + - - -
199A GLN 3.3 23.8 - - - -
200A LYS 3.5 16.4 - - - -
201A ALA 3.0 30.7 - - - -
202A MET* 4.1 5.6 - - + -
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Residues in contact with ILE 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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56A LEU* 3.8 29.8 - - + -
83A VAL* 3.1 17.3 + - + +
86A PHE* 1.3 87.5 - - + +
88A ASN* 1.3 59.4 - - - +
89A ASN 3.2 1.4 + - - -
119A ILE* 4.0 33.2 - - + -
164A ARG* 3.8 31.4 + - + +
166A ILE* 5.8 1.3 - - + -
202A MET* 3.8 25.4 - - + -
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Residues in contact with ASN 88 (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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56A LEU* 5.5 0.4 - - - +
84A PHE* 3.1 54.5 + - + +
85A GLY* 4.1 3.8 - - - +
87A ILE* 1.3 74.2 - - - +
89A ASN* 1.3 58.6 + - - +
90A PRO* 3.5 10.7 - - - +
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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