Contacts of the helix formed by residues 100 - 114 (chain A) in PDB entry 1JAT
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ARG* 3.7 11.0 - - - +
11A GLU* 3.3 20.6 + - - +
14A LYS* 6.2 2.2 - - - +
62A TYR* 3.9 2.7 - - - -
95A TRP* 4.0 6.1 - - - -
98A ALA 5.0 4.5 - - - +
99A LEU* 1.3 78.4 - - - +
101A ILE* 1.3 69.1 + - - +
102A ARG* 4.0 24.1 - - + +
103A THR* 3.0 34.6 + - - +
104A VAL* 3.3 8.5 + - - +
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Residues in contact with ILE 101 (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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8A ILE 5.9 0.4 - - - +
11A GLU* 2.9 38.4 + - + +
12A THR* 5.6 0.4 - - - +
15A LEU* 3.8 27.4 - - + -
35A PHE* 4.9 8.7 - - + -
56A LEU* 4.0 20.2 - - + -
58A LEU* 3.8 39.9 - - + -
62A TYR* 3.5 11.8 + - + +
67A PRO* 4.8 5.2 - - + -
100A GLN* 1.3 70.2 - - - +
102A ARG* 1.3 63.4 + - - +
104A VAL* 3.0 11.4 + - - +
105A LEU* 2.9 34.8 + - + +
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Residues in contact with ARG 102 (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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11A GLU* 4.4 0.8 + - - -
14A LYS* 3.2 42.8 + - - +
15A LEU* 4.1 20.2 - - + +
18A ASP* 2.8 41.4 + - - -
19A PRO 4.3 0.8 + - - -
20A VAL* 3.5 34.9 - - + +
100A GLN* 3.2 24.5 - - + +
101A ILE* 1.3 79.9 - - - +
103A THR* 1.3 61.7 + - - +
105A LEU* 3.3 6.8 + - - +
106A LEU* 3.0 37.5 + - + +
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Residues in contact with THR 103 (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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90A VAL* 5.2 8.5 - - + -
99A LEU* 3.9 28.9 - - + +
100A GLN* 3.0 34.8 + - - +
102A ARG* 1.3 77.6 - - - +
104A VAL* 1.3 59.6 + - - +
106A LEU* 3.5 8.7 + - - +
107A SER* 3.0 38.9 + - - +
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Residues in contact with VAL 104 (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* 5.2 3.6 - - + -
67A PRO* 4.1 11.2 - - + -
69A VAL* 4.5 5.4 - - + -
88A LEU* 4.7 1.1 - - + -
90A VAL* 4.6 10.8 - - + -
91A LEU* 3.6 35.0 - - + -
95A TRP* 3.8 23.6 - - + -
100A GLN 3.7 11.4 - - - +
101A ILE* 3.0 9.1 + - + +
103A THR* 1.3 82.4 - - - +
105A LEU* 1.3 67.1 + - + +
107A SER* 3.2 6.8 + - - -
108A ILE* 3.0 39.6 + - + +
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Residues in contact with LEU 105 (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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15A LEU* 4.2 18.4 - - + -
20A VAL* 5.6 3.6 - - + -
23A ILE* 3.6 33.8 - - + +
25A ALA* 4.2 12.8 - - + -
37A VAL* 4.0 22.7 - - + -
39A ILE* 4.0 5.4 - - + +
54A LEU* 5.6 0.2 - - + -
56A LEU* 4.4 18.2 - - + -
69A VAL* 5.6 2.2 - - + -
101A ILE* 2.9 35.8 + - + +
102A ARG* 3.3 5.8 + - - +
104A VAL* 1.3 76.6 - - + +
106A LEU* 1.3 62.7 + - - +
108A ILE* 3.3 18.3 + - + +
109A GLN* 3.0 22.5 + - - +
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Residues in contact with LEU 106 (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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20A VAL* 3.7 22.4 - - + -
23A ILE* 4.6 0.2 - - - -
102A ARG* 3.0 36.8 + - + +
103A THR* 3.7 6.7 - - - +
105A LEU* 1.3 76.2 - - - +
107A SER* 1.3 57.8 - - - +
109A GLN* 3.3 28.0 + - - +
110A ALA* 2.9 29.0 + - - +
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Residues in contact with SER 107 (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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88A LEU* 3.5 31.3 - - - +
90A VAL* 4.4 8.7 - - - +
103A THR* 3.0 24.7 + - - +
104A VAL* 3.2 6.5 + - - -
106A LEU* 1.3 76.2 - - - +
108A ILE* 1.3 58.4 + - - +
110A ALA* 3.3 7.7 + - - +
111A LEU* 2.9 28.2 + - - +
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Residues in contact with ILE 108 (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 ILE* 3.7 17.7 - - + -
54A LEU* 4.1 5.4 - - + -
69A VAL* 4.1 15.9 - - + -
71A PHE* 3.7 31.2 - - + -
80A ILE* 5.5 0.7 - - + -
86A ILE* 3.8 28.5 - - + -
88A LEU* 4.2 12.8 - - + -
91A LEU* 4.8 0.4 - - + -
104A VAL* 3.0 31.9 + - + +
105A LEU* 3.7 12.3 - - + +
107A SER* 1.3 75.2 - - - +
109A GLN* 1.3 64.6 + - - +
111A LEU* 3.1 18.4 + - + +
112A LEU* 3.1 14.6 + - + +
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Residues in contact with GLN 109 (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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20A VAL* 4.1 4.0 - - - +
21A PRO 3.0 21.4 + - - +
22A GLY* 4.1 5.5 - - - -
23A ILE* 3.7 19.9 - - + +
39A ILE* 4.2 20.3 - - + +
40A GLU* 4.9 3.8 - - - +
42A PRO* 3.6 15.8 - - + +
105A LEU 3.0 12.1 + - - +
106A LEU* 3.4 34.6 + - - +
108A ILE* 1.3 76.9 - - - +
110A ALA* 1.3 61.2 + - - +
112A LEU* 3.3 15.0 + - - +
113A ALA* 3.4 8.5 + - - +
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Residues in contact with ALA 110 (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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106A LEU 2.9 16.8 + - - +
107A SER* 3.6 8.1 - - - +
109A GLN* 1.3 74.0 - - - +
111A LEU* 1.3 59.7 + - - +
113A ALA* 3.1 8.5 + - - +
114A SER* 2.9 31.7 + - - -
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Residues in contact with LEU 111 (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 HIS* 2.8 28.2 - - + +
79A ASN* 3.7 40.2 - - + +
80A ILE* 4.4 10.3 - - + -
86A ILE* 3.8 28.7 - - + -
87A CYS 4.1 8.7 - - - +
88A LEU* 5.0 10.5 - - + -
107A SER 2.9 14.2 + - - +
108A ILE* 3.1 11.9 + - + +
110A ALA* 1.3 76.9 - - - +
112A LEU* 1.3 62.3 + - + +
114A SER 3.3 22.5 - - - +
116A ASN* 5.0 3.1 - - + +
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Residues in contact with LEU 112 (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 ILE* 4.0 27.1 - - + -
40A GLU 4.5 1.6 - - - +
41A GLY* 4.8 0.2 - - - -
42A PRO* 3.6 20.6 - - + -
45A SER* 4.1 3.5 - - - -
46A PRO* 4.9 0.3 - - - +
47A TYR* 3.5 30.7 - - + -
52A PHE* 4.5 12.8 - - + -
71A PHE* 4.1 17.5 - - + -
75A ILE* 3.6 31.0 - - + -
77A HIS* 3.9 7.6 - - - +
80A ILE* 4.0 16.4 - - + -
108A ILE* 3.1 18.7 + - + +
109A GLN* 3.5 6.5 - - - +
110A ALA 3.2 0.4 - - - -
111A LEU* 1.3 77.9 - - - +
113A ALA* 1.3 60.3 + - - +
115A PRO* 3.8 4.9 - - - +
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Residues in contact with ALA 113 (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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42A PRO* 3.7 26.9 - - + +
43A GLU 6.0 0.2 - - - +
45A SER* 4.4 10.6 - - - -
109A GLN 3.4 4.5 + - - +
110A ALA* 3.1 11.7 + - - +
112A LEU* 1.3 80.0 - - - +
114A SER* 1.3 65.7 + - - +
115A PRO* 3.6 5.4 - - - +
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Residues in contact with SER 114 (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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110A ALA 2.9 13.5 + - - +
111A LEU* 3.3 15.7 - - - +
113A ALA* 1.3 85.6 + - - +
115A PRO* 1.3 67.6 - - - +
116A ASN* 3.6 4.9 + - - +
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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