Contacts of the helix formed by residues 92 - 110 (chain A) in PDB entry 1IJZ
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 VAL 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 5.2 12.6 - - + +
29A CYS* 4.6 18.2 - - + +
32A SER* 3.3 27.2 + - - +
34A VAL* 3.9 25.8 - - + -
51A LEU* 5.3 9.4 - - + -
54A VAL* 4.4 9.9 - - + -
60A ILE* 5.2 7.9 - - + -
90A ILE 3.5 0.6 + - - -
91A GLU* 1.3 71.6 - - - +
93A ALA* 1.3 67.1 + - - +
95A PHE* 2.8 21.7 + - + -
96A VAL* 2.9 31.6 + - + +
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Residues in contact with ALA 93 (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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24A GLN* 4.5 19.7 - - - +
27A PRO* 5.4 16.8 - - + +
28A LEU* 6.0 3.1 - - - +
91A GLU* 3.1 10.9 - - + +
92A VAL* 1.3 79.3 - - - +
94A GLN* 1.3 63.1 + - + +
96A VAL* 3.7 5.5 + - - +
97A LYS* 3.2 35.8 + - - +
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Residues in contact with GLN 94 (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 ILE* 4.1 21.1 - - + +
91A GLU* 2.9 27.5 + - + +
93A ALA* 1.3 77.2 - - + +
95A PHE* 1.3 61.7 + - - +
97A LYS* 4.4 7.9 - - + -
98A ASP* 2.8 47.1 + - - +
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Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.6 32.3 - - + -
35A TRP 4.4 6.1 - - - -
36A SER* 5.5 0.7 - - - -
37A ILE* 4.2 24.0 - - + -
39A LEU* 6.4 0.4 - - + -
47A ALA* 3.7 33.4 - - + -
50A SER* 4.3 14.6 - - - -
51A LEU* 4.3 24.0 - - + -
90A ILE* 4.1 15.4 - - + +
91A GLU 3.1 5.9 + - - +
92A VAL* 2.8 10.6 + - + +
94A GLN* 1.3 78.9 - - - +
96A VAL* 1.3 72.9 + - + +
98A ASP* 3.8 3.9 - - - +
99A LEU* 3.0 41.7 + - + +
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Residues in contact with VAL 96 (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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17A LEU* 4.7 24.7 - - + +
20A ILE* 6.0 0.9 - - + -
21A THR* 3.6 31.6 - - + -
28A LEU* 5.1 8.7 - - + -
51A LEU* 6.1 1.6 - - + -
60A ILE* 5.7 4.5 - - + -
92A VAL* 2.9 33.9 + - + +
93A ALA* 4.0 5.8 - - - +
95A PHE* 1.3 85.0 - - + +
97A LYS* 1.3 60.7 + - - +
99A LEU* 3.2 8.8 + - + +
100A LEU* 2.8 29.3 + - + +
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Residues in contact with LYS 97 (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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21A THR* 5.3 12.7 + - + -
24A GLN* 4.5 17.6 - - - +
93A ALA* 3.2 26.1 + - - +
94A GLN* 3.8 8.3 - - + +
96A VAL* 1.3 79.1 - - + +
98A ASP* 1.3 67.4 + - - +
100A LEU* 2.9 21.7 + - + +
101A LEU* 3.2 20.4 - - + +
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Residues in contact with ASP 98 (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 LEU* 5.4 10.8 - - + -
90A ILE* 4.2 13.9 - - + +
94A GLN* 2.8 34.4 + - - +
95A PHE* 3.8 4.3 - - + +
97A LYS* 1.3 76.1 - - - +
99A LEU* 1.3 63.9 + - - +
101A LEU* 3.4 13.7 + - - +
102A HIS* 3.7 18.8 + - + -
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Residues in contact with LEU 99 (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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17A LEU* 5.0 7.0 - - + -
39A LEU* 4.1 25.1 - - + +
43A MET* 4.7 15.0 - - + +
44A TYR* 5.8 1.8 - - + +
47A ALA* 4.7 12.8 - - + -
51A LEU* 6.1 0.2 - - + -
63A THR* 6.2 2.0 - - + -
67A LEU* 4.6 22.2 - - + -
95A PHE* 3.0 37.9 + - + +
96A VAL* 3.5 7.2 - - + +
98A ASP* 1.3 79.2 - - - +
100A LEU* 1.3 63.8 + - - +
102A HIS* 3.0 7.6 + - + +
103A LEU* 2.9 50.6 + - + +
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Residues in contact with LEU 100 (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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14A ILE* 3.7 36.6 - - + +
17A LEU* 5.4 6.5 - - + +
18A VAL* 3.7 25.4 - - + -
21A THR* 5.5 3.4 - - - +
96A VAL* 2.8 16.4 + - + +
97A LYS* 2.9 16.8 + - + +
99A LEU* 1.3 76.2 - - - +
101A LEU* 1.3 72.6 + - + +
103A LEU* 3.2 19.0 + - + +
104A LYS* 3.3 19.7 + - + +
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Residues in contact with LEU 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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97A LYS* 3.2 19.3 - - + +
98A ASP* 3.8 9.2 - - - +
99A LEU 3.2 1.2 - - - -
100A LEU* 1.3 84.8 - - + +
102A HIS* 1.3 69.0 + - + +
104A LYS* 3.4 31.9 - - - +
105A LYS* 3.2 22.0 + - - +
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Residues in contact with HIS 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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39A LEU* 3.1 54.1 + - + +
40A THR* 5.4 0.6 + - - -
43A MET* 3.7 26.1 - - + +
98A ASP 3.8 10.3 - - - +
99A LEU* 3.0 8.7 + - + +
101A LEU* 1.3 80.2 - - + +
103A LEU* 1.3 69.1 + - - +
105A LYS* 3.1 36.5 + - + +
106A LEU* 3.3 15.2 + - - +
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Residues in contact with LEU 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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10A LEU* 3.4 26.3 - - + +
13A LEU* 4.5 5.8 - - + -
14A ILE* 3.7 23.3 - - + -
17A LEU* 3.4 33.0 - - + -
43A MET* 5.3 4.0 - - + -
44A TYR* 3.4 38.1 - - + +
67A LEU* 5.7 0.2 - - + -
99A LEU* 2.9 43.3 + - + +
100A LEU* 3.2 13.9 + - + +
102A HIS* 1.3 80.4 - - - +
104A LYS* 1.3 63.9 + - - +
106A LEU* 3.4 7.3 + - - +
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Residues in contact with LYS 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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14A ILE* 3.7 24.1 - - + +
100A LEU* 3.3 14.9 + - + +
101A LEU* 3.4 44.5 - - - +
103A LEU* 1.3 79.4 - - - +
105A LYS* 1.3 68.2 + - - +
107A PHE* 3.2 20.8 + - + +
108A ARG* 3.6 18.5 + - - +
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Residues in contact with LYS 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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101A LEU 3.2 16.4 + - - +
102A HIS* 3.1 37.0 + - + +
103A LEU 3.0 0.6 - - - -
104A LYS* 1.3 79.3 - - - +
106A LEU* 1.3 71.6 + - + +
107A PHE 3.1 0.7 + - - -
108A ARG* 3.2 23.7 + - + +
109A GLU* 3.8 14.0 + - - +
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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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10A LEU* 4.8 7.2 - - + -
40A THR 5.2 6.7 - - - +
43A MET* 4.3 20.0 - - + -
44A TYR* 5.9 4.9 - - + +
102A HIS* 3.3 18.4 + - + +
103A LEU 3.4 6.3 + - - +
105A LYS* 1.3 89.1 - - + +
107A PHE* 1.3 63.8 + - - +
109A GLU* 3.0 21.6 + - - +
110A GLY* 2.9 17.8 + - - -
111A ARG* 3.2 35.1 + - + +
112A PHE* 4.4 4.6 - - + -
113A ASN 5.5 3.6 - - - +
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Residues in contact with PHE 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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7A SER* 4.7 7.0 - - - -
10A LEU* 4.3 9.3 - - + +
11A ARG* 3.8 49.4 - - + -
14A ILE* 5.3 3.1 - - + -
103A LEU 3.7 2.6 + - - -
104A LYS* 3.2 22.2 + - + +
105A LYS 3.1 1.0 - - - -
106A LEU* 1.3 79.1 - - - +
108A ARG* 1.3 69.9 + - + +
110A GLY* 3.0 12.8 + - - -
112A PHE* 4.1 27.1 - + - -
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Residues in contact with ARG 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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104A LYS* 3.9 17.1 + - - +
105A LYS* 3.2 16.3 + - - +
106A LEU 3.1 0.4 - - - -
107A PHE* 1.3 85.7 - - + +
109A GLU* 1.3 63.2 + - + +
110A GLY 3.2 0.6 + - - -
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Residues in contact with GLU 109 (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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105A LYS* 4.4 16.9 - - + +
106A LEU* 3.0 24.3 + - - +
108A ARG* 1.3 80.1 - - + +
110A GLY* 1.3 53.4 + - - +
111A ARG* 2.6 48.8 + - + +
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Residues in contact with GLY 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 5.2 + - - -
107A PHE 3.0 9.6 + - - -
108A ARG 3.2 0.8 + - - -
109A GLU* 1.3 77.4 - - - +
111A ARG* 1.3 58.7 + - - +
112A PHE* 2.9 42.6 + - - -
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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