Contacts of the helix formed by residues 106 - 123 (chain A) in PDB entry 2K2V
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 ASP 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A GLU* 6.1 3.3 - - + +
105A VAL* 1.3 83.7 - - + +
107A ASP* 1.3 84.8 + - - +
108A ASP* 3.3 11.7 + - + +
109A THR* 3.2 11.6 + - - +
110A GLN* 3.0 20.2 + - - +
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Residues in contact with ASP 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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106A ASP* 1.3 83.6 + - - +
108A ASP* 1.3 60.2 + - - +
110A GLN* 3.3 7.3 + - - +
111A GLU* 2.9 45.0 + - - +
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Residues in contact with ASP 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 THR* 3.2 45.9 - - - +
41A GLU* 6.2 1.3 - - + -
106A ASP* 3.3 10.0 - - + +
107A ASP* 1.3 79.2 - - - +
109A THR* 1.3 66.5 + - - +
111A GLU* 3.3 8.0 + - - +
112A ALA 3.1 18.7 + - - -
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Residues in contact with THR 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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39A THR 3.9 4.0 + - - -
40A LEU* 3.5 28.0 - - + +
41A GLU* 3.1 28.6 + - - +
44A PHE* 3.7 20.4 - - + -
105A VAL* 3.5 28.9 - - + +
106A ASP* 3.2 14.7 + - - +
108A ASP* 1.3 77.6 - - - +
110A GLN* 1.3 60.8 + - - +
112A ALA 3.3 2.3 + - - -
113A ILE* 3.3 28.9 + - + +
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Residues in contact with GLN 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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101A GLU* 2.8 34.4 + - - +
102A ALA* 3.6 20.0 - - - +
103A ILE* 5.5 0.2 - - - -
104A ASP 5.8 0.3 + - - -
105A VAL* 3.7 13.4 + - + +
106A ASP 3.0 16.8 + - - +
107A ASP* 3.7 7.2 - - - +
109A THR* 1.3 76.2 - - - +
111A GLU* 1.3 58.4 + - + +
113A ILE* 3.3 11.1 + - - +
114A ALA* 2.9 34.1 + - + +
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Residues in contact with GLU 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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10A ARG* 2.8 37.1 + - - +
39A THR* 5.8 0.4 - - + -
107A ASP* 2.9 36.9 + - - +
108A ASP* 3.7 11.0 - - - +
109A THR 3.3 0.2 - - - -
110A GLN* 1.3 74.9 - - + +
112A ALA* 1.3 59.4 + - - +
114A ALA* 3.8 9.6 - - - +
115A ASP* 2.8 33.8 + - - +
118A TYR* 5.7 0.5 + - - -
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Residues in contact with ALA 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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36A LEU* 4.6 21.3 - - + +
39A THR* 3.8 21.5 - - + +
40A LEU* 3.8 19.7 - - + -
97A LEU* 5.7 0.9 - - - -
108A ASP 3.1 12.9 + - - +
109A THR 3.3 8.5 + - - +
111A GLU* 1.3 75.2 - - - +
113A ILE* 1.3 57.3 + - - +
115A ASP* 3.7 6.1 - - - +
116A TRP* 3.0 28.8 + - - +
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Residues in contact with ILE 113 (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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40A LEU* 3.8 11.9 - - + -
44A PHE* 3.8 19.1 - - + -
97A LEU* 4.4 20.0 - - + +
100A ILE* 3.8 20.4 - - + +
101A GLU* 3.4 23.3 - - - +
102A ALA* 3.4 32.1 - - + +
109A THR* 3.3 21.7 + - + +
110A GLN* 3.6 6.7 - - - +
111A GLU 3.2 0.2 - - - -
112A ALA* 1.3 74.1 - - - +
114A ALA* 1.3 59.0 + - - +
116A TRP* 3.1 7.9 + - - +
117A LEU* 2.9 37.9 + - + +
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Residues in contact with ALA 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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101A GLU* 5.8 0.9 - - - +
110A GLN* 2.9 24.4 + - + +
111A GLU* 3.8 13.2 - - - +
113A ILE* 1.3 75.5 - - - +
115A ASP* 1.3 57.5 + - - +
117A LEU* 3.1 12.6 + - - +
118A TYR* 2.9 57.1 + - + +
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Residues in contact with ASP 115 (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 ARG* 2.8 43.0 + - - +
14A ILE* 4.2 10.7 - - - +
18A ILE* 5.2 2.4 - - - +
32A TRP* 3.6 28.2 - - - -
36A LEU* 5.6 1.4 - - + +
111A GLU 2.8 23.0 + - - +
112A ALA* 3.7 6.3 - - - +
114A ALA* 1.3 72.2 - - - +
116A TRP* 1.3 57.9 + - - +
118A TYR* 3.3 13.4 + - - +
119A TRP* 3.0 25.5 + - - +
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Residues in contact with TRP 116 (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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32A TRP* 3.7 37.9 - + - -
36A LEU* 3.8 8.7 - - + -
77A ASP* 3.5 7.2 - - - -
78A MET* 3.4 32.9 - - + +
97A LEU* 3.9 24.5 - - + -
98A SER* 2.9 39.8 + - - +
112A ALA 3.0 18.5 + - - +
113A ILE 3.1 4.9 + - - +
115A ASP* 1.3 76.8 + - - +
117A LEU* 1.3 59.2 + - + +
119A TRP* 3.2 36.7 + + - +
120A LEU* 2.8 29.6 + - + +
124A TYR* 3.3 28.3 - + - -
126A PHE* 4.3 9.9 - + - -
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Residues in contact with LEU 117 (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 LEU 4.6 1.6 - - - +
98A SER* 3.8 28.3 - - - +
99A ASP 6.0 0.2 - - - -
100A ILE 4.2 13.7 - - - +
101A GLU* 4.0 22.4 - - + +
113A ILE* 2.9 31.0 + - + +
114A ALA* 3.1 11.4 + - - +
116A TRP* 1.3 72.7 - - + +
118A TYR* 1.3 63.4 + - + +
120A LEU* 3.5 15.4 + - + +
121A ALA* 3.0 28.4 + - - +
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Residues in contact with TYR 118 (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 VAL* 3.4 49.5 - - + +
10A ARG* 3.8 40.9 + - - -
111A GLU* 5.7 0.5 + - - -
114A ALA* 2.9 40.5 + - + +
115A ASP* 3.5 13.7 - - - +
117A LEU* 1.3 75.6 - - + +
119A TRP* 1.3 52.7 + - - +
121A ALA* 3.1 2.8 + - + -
122A ARG* 2.8 32.9 + - - +
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Residues in contact with TRP 119 (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* 5.2 9.4 - - + -
19A ILE* 5.5 3.6 - - + -
28A ARG* 5.1 3.4 - - - -
32A TRP* 3.2 44.9 - + + -
115A ASP 3.0 12.7 + - - +
116A TRP* 3.2 41.7 + + + +
118A TYR* 1.3 74.3 - - - +
120A LEU* 1.3 65.5 + - - +
122A ARG* 3.2 10.7 + - + +
123A GLY 3.2 17.3 + - - -
124A TYR* 3.1 45.6 + + - -
125A LYS* 3.1 56.8 - - + -
126A PHE* 3.4 25.4 - + + -
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Residues in contact with LEU 120 (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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98A SER* 3.4 45.5 - - - +
116A TRP* 2.8 21.1 + - - +
117A LEU* 3.5 21.1 - - + +
118A TYR 3.2 0.2 - - - -
119A TRP* 1.3 72.9 - - + +
121A ALA* 1.3 63.1 + - - +
123A GLY* 3.3 13.9 + - - -
124A TYR* 3.8 27.6 - - + +
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Residues in contact with ALA 121 (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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1A MET 4.5 2.1 - - - +
2A ALA* 3.4 16.7 + - + +
4A VAL* 4.1 20.6 - - + -
117A LEU 3.0 17.0 + - - +
118A TYR 3.6 4.0 - - - +
120A LEU* 1.3 77.4 - - - +
122A ARG* 1.3 61.4 + - - +
123A GLY* 3.3 1.2 + - - -
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Residues in contact with ARG 122 (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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1A MET* 2.9 52.2 + - - +
2A ALA* 2.8 45.4 + - - +
3A SER* 4.4 1.2 - - - +
4A VAL* 4.1 13.6 + - - +
5A GLU* 2.7 47.9 + - - +
10A ARG* 6.2 0.4 - - - +
11A GLU* 2.7 34.1 + - - +
118A TYR 2.8 20.6 + - - +
119A TRP* 3.2 14.6 + - + +
121A ALA* 1.3 72.3 - - - +
123A GLY* 1.3 58.5 + - - +
124A TYR* 4.6 2.1 - - - +
125A LYS* 4.4 22.5 - - + +
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Residues in contact with GLY 123 (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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1A MET 4.9 2.7 - - - -
119A TRP 3.2 2.6 + - - -
120A LEU 3.3 8.2 + - - -
121A ALA 3.2 4.7 - - - -
122A ARG* 1.3 76.4 - - - +
124A TYR* 1.3 77.5 + - - +
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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