Contacts of the helix formed by residues 72 - 86 (chain A) in PDB entry 1JTF
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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69A SER 2.7 20.1 + - - -
71A PRO* 1.3 77.8 - - - +
73A THR* 1.3 65.9 + - - +
74A HIS* 3.2 2.7 - - - -
75A ILE* 3.2 29.1 + - - +
76A ARG 3.9 0.5 + - - -
103A LEU* 3.3 13.9 - - - +
400A SAH 3.2 18.3 + - - -
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Residues in contact with THR 73 (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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39A GLN* 3.5 14.5 + - + -
71A PRO* 3.3 12.5 - - - +
72A GLY* 1.3 76.2 - - - +
74A HIS* 1.3 63.0 + - - +
75A ILE 3.2 0.7 + - - -
76A ARG* 3.3 19.8 + - - +
100A ASP* 2.6 33.6 + - - +
102A ILE* 3.5 16.1 - - + +
293A PHE* 3.7 13.9 - - + +
294A LEU* 4.8 8.1 - - + -
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Residues in contact with HIS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN* 2.6 53.1 + - + +
42A LEU* 3.8 9.4 - - + +
43A LEU* 3.7 31.6 - - + +
46A GLU* 2.7 32.2 + - - -
66A TYR* 3.5 9.6 - - - -
72A GLY* 4.1 0.2 - - - -
73A THR* 1.3 78.6 - - - +
75A ILE* 1.3 80.0 + - + +
77A TYR* 3.1 16.3 + - - +
78A LEU* 3.3 12.3 + - + +
293A PHE* 4.2 10.8 - - - -
294A LEU* 4.5 2.7 - - + -
400A SAH 2.8 24.3 + - - -
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU* 4.5 0.4 - - - +
66A TYR* 3.7 20.2 - - + -
69A SER* 3.6 32.8 - - - +
72A GLY* 3.2 25.7 + - - +
74A HIS* 1.3 105.0 - - + +
76A ARG* 1.3 50.0 + - - +
78A LEU* 3.0 8.7 - - - +
79A ARG* 2.7 34.7 + - + +
91A TRP* 4.2 19.5 - - + -
93A LEU* 3.7 31.9 - - + -
103A LEU* 4.1 6.3 - - + -
109A VAL* 6.3 0.4 - - + -
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Residues in contact with ARG 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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72A GLY 3.9 0.8 + - - -
73A THR 3.3 13.8 + - - +
74A HIS 3.1 0.2 - - - -
75A ILE* 1.3 76.1 - - - +
77A TYR* 1.3 65.7 + - - +
79A ARG* 3.2 14.9 + - - +
80A ASP* 2.8 62.3 + - - +
102A ILE* 2.6 60.6 + - + +
103A LEU* 4.3 10.5 - - + +
104A ASN 4.7 1.2 + - - -
106A LEU* 3.3 39.5 - - - +
293A PHE* 4.1 7.9 - - + -
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Residues in contact with TYR 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.7 21.1 - - + -
47A LEU* 4.4 8.7 - - + -
74A HIS 3.1 9.8 + - - +
76A ARG* 1.3 78.3 - - - +
78A LEU* 1.3 60.0 + - - +
80A ASP* 3.3 11.1 + - + +
81A HIS* 2.9 43.1 + - + +
286A LEU* 4.1 13.6 - - + +
289A SER* 3.0 34.1 + - - -
290A ILE* 3.5 31.6 - - + +
293A PHE* 3.6 46.4 - + + -
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Residues in contact with LEU 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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43A LEU* 3.7 13.2 - - + -
46A GLU* 3.2 38.6 - - + +
47A LEU* 4.0 37.5 - - + -
50A LEU* 4.1 4.5 - - + -
74A HIS* 3.3 7.3 + - + +
75A ILE* 3.0 14.1 + - + +
77A TYR* 1.3 82.8 - - - +
79A ARG* 1.3 62.2 + - - +
81A HIS* 3.2 10.8 + - - +
82A PHE* 3.3 38.0 + - + -
91A TRP* 3.9 25.4 - - + -
136A ILE* 5.7 0.2 - - + -
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Residues in contact with ARG 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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75A ILE* 2.7 22.0 + - + +
76A ARG* 3.5 19.0 - - - +
78A LEU* 1.3 74.9 - - - +
80A ASP* 1.3 89.6 + - - +
82A PHE* 3.7 1.0 + - - +
83A TYR* 2.9 66.5 + - - +
91A TRP* 3.8 32.0 + - + +
103A LEU* 5.6 0.4 - - + -
106A LEU* 3.6 31.7 - - - +
107A ARG 5.5 0.2 - - - +
108A ASP* 2.9 33.2 + - - +
109A VAL* 3.5 21.8 - - + -
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Residues in contact with ASP 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 ARG* 2.8 42.7 + - - +
77A TYR* 3.7 10.5 - - + +
79A ARG* 1.3 98.8 + - - +
81A HIS* 1.3 57.1 + - - +
83A TYR* 3.2 5.7 + - - +
84A ASN* 2.7 53.5 + - - +
293A PHE* 4.9 5.4 - - - -
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Residues in contact with HIS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.0 11.6 - - + +
77A TYR* 2.9 33.7 + + + +
78A LEU* 3.2 7.2 + - - +
80A ASP* 1.3 77.4 - - - +
82A PHE* 1.3 84.7 + + + +
84A ASN* 3.6 5.4 + - - +
85A LEU* 3.2 38.5 + - + +
270A VAL* 3.6 21.2 - - + +
271A TYR 2.9 30.3 + - - -
272A CYS* 4.8 4.9 - - - -
286A LEU* 4.1 14.5 - - + +
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Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.5 3.4 - - + -
50A LEU* 3.5 37.2 - - + -
51A SER* 4.0 15.5 - - - -
54A GLN* 3.0 28.9 - - - -
59A LEU* 3.6 14.8 - - + -
78A LEU* 3.3 33.4 + - + +
79A ARG 4.6 1.3 - - - +
80A ASP 3.3 0.2 - - - -
81A HIS* 1.3 96.4 - + - +
83A TYR* 1.3 60.3 + - - +
85A LEU* 3.2 8.4 + - + +
86A GLY 3.1 8.0 + - - -
87A VAL* 2.9 37.1 + - + -
89A ILE* 3.4 31.6 - - + -
91A TRP* 4.7 4.3 - + + -
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Residues in contact with TYR 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 ARG* 2.9 59.6 + - - +
80A ASP* 3.4 5.2 - - + +
82A PHE* 1.3 78.1 - - - +
84A ASN* 1.3 76.7 + - - +
86A GLY* 3.3 12.8 + - - -
87A VAL 4.0 9.4 - - - +
89A ILE* 5.5 0.2 - - - +
107A ARG* 5.4 5.9 + - - -
108A ASP* 3.7 16.8 - - - +
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Residues in contact with ASN 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 ASP* 2.7 37.2 + - - +
81A HIS* 4.0 5.1 + - - +
83A TYR* 1.3 86.9 - - - +
85A LEU* 1.3 60.9 + - - +
86A GLY* 3.0 6.2 + - - -
273A ASN* 3.3 20.4 + - - +
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Residues in contact with LEU 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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54A GLN* 4.1 16.2 - - - +
81A HIS* 3.2 48.0 + - + +
82A PHE* 3.2 20.4 + - + +
84A ASN* 1.3 77.0 - - + +
86A GLY* 1.3 60.0 + - - +
87A VAL* 3.4 8.5 - - + +
271A TYR* 3.6 14.1 - - + +
272A CYS* 3.8 31.9 - - - +
273A ASN* 4.0 19.0 - - - +
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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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60A ASP* 4.0 5.4 - - - +
82A PHE 3.1 2.2 + - - -
83A TYR 3.3 9.5 + - - -
84A ASN 3.0 5.4 - - - -
85A LEU* 1.3 79.2 - - - +
87A VAL* 1.3 66.1 + - - +
88A ILE* 3.5 13.0 + - - +
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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