Contacts of the helix formed by residues 97 - 115 (chain A) in PDB entry 2KWI
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 GLU 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A SER* 4.4 4.8 - - - -
25A VAL* 3.6 25.1 + - - +
94A SER* 3.0 20.6 + - - +
96A THR* 1.3 89.6 - - - +
98A HIS* 1.3 64.0 + - - +
99A GLU* 4.1 4.7 - - + +
100A SER* 2.8 43.4 + - - +
101A PHE* 3.5 9.4 + - - +
138A VAL* 3.9 4.1 - - - +
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Residues in contact with HIS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A THR 3.9 4.4 + - - -
97A GLU* 1.3 70.8 - - - +
99A GLU* 1.3 67.1 + - + +
100A SER 3.4 0.2 - - - -
101A PHE* 3.3 16.5 - + - +
102A THR* 3.1 42.5 + - - -
137A GLN* 4.4 20.3 - - + +
138A VAL* 4.0 27.1 - - + +
139A PRO* 5.6 0.7 - - + -
142A GLU* 4.7 7.6 + - - -
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Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 5.3 4.3 - - - +
97A GLU* 3.1 5.4 - - + -
98A HIS* 1.3 81.1 - - + +
100A SER* 1.3 58.3 + - - +
102A THR* 3.2 8.6 + - - -
103A ALA* 2.9 27.0 + - - +
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Residues in contact with SER 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 3.4 31.6 + - - -
93A PHE* 3.5 23.2 - - - +
94A SER 4.0 0.5 + - - -
97A GLU* 2.8 36.3 + - - +
99A GLU* 1.3 76.0 - - - +
101A PHE* 1.3 65.0 + - - +
103A ALA* 3.3 10.2 + - - +
104A THR* 3.2 24.6 + - - +
107A PHE* 4.3 3.9 - - - -
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Residues in contact with PHE 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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93A PHE* 3.7 33.3 - + + -
97A GLU 3.5 10.4 + - - +
98A HIS* 3.3 23.3 + + - +
100A SER* 1.3 81.3 + - - +
102A THR* 1.3 61.4 + - - +
104A THR* 2.6 32.5 + - + +
138A VAL* 3.6 19.5 - - + -
142A GLU* 3.4 36.8 - - + -
143A ALA* 3.7 25.8 - - + -
146A LYS* 3.8 31.9 - - + -
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Residues in contact with THR 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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98A HIS* 3.1 32.8 + - - -
99A GLU* 3.6 8.9 - - - -
101A PHE* 1.3 81.6 - - - +
103A ALA* 1.3 61.7 + - - +
104A THR* 3.2 1.2 + - - -
105A ALA* 3.5 17.3 + - - +
106A GLU* 4.2 2.3 + - - +
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Residues in contact with ALA 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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22A SER* 5.2 3.1 - - - +
99A GLU 2.9 17.3 + - - +
100A SER* 3.6 10.8 - - - +
101A PHE 3.2 0.2 - - - -
102A THR* 1.3 75.6 - - - +
104A THR* 1.3 64.9 + - - +
105A ALA 3.2 0.4 - - - -
106A GLU* 2.9 13.9 + - + +
107A PHE* 2.9 46.7 + - + -
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Residues in contact with THR 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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91A LEU* 4.3 13.7 - - + +
93A PHE* 4.0 27.1 - - + -
100A SER 3.2 16.7 + - - +
101A PHE* 2.6 23.6 + - + +
102A THR 4.3 0.2 + - - -
103A ALA* 1.3 76.3 - - - +
105A ALA* 1.3 58.8 + - - +
107A PHE* 3.4 18.3 + - + +
108A ARG* 2.9 27.9 + - - +
125A VAL* 4.7 8.5 - - + -
146A LYS* 5.8 2.1 - - - +
150A TRP* 3.7 23.4 - - - -
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Residues in contact with ALA 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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102A THR 3.5 10.2 + - - +
103A ALA 3.2 0.4 - - - -
104A THR* 1.3 79.3 + - - +
106A GLU* 1.3 60.6 + - - +
108A ARG* 3.3 10.0 + - - +
109A GLU* 3.0 39.9 + - - +
150A TRP* 4.3 13.9 - - + -
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Residues in contact with GLU 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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102A THR 4.2 2.1 + - - +
103A ALA* 2.9 20.0 + - + +
105A ALA* 1.3 76.2 - - - +
107A PHE* 1.3 64.3 + - + +
109A GLU* 3.3 11.2 + - - +
110A GLN* 2.9 54.7 + - - +
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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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20A VAL* 4.3 15.5 - - + -
21A GLY* 3.2 37.9 - - - -
22A SER* 4.0 8.3 - - - -
79A ARG* 4.9 20.2 - - - -
83A PHE* 5.0 3.9 - + + -
91A LEU* 3.9 24.0 - - + -
92A VAL 5.7 2.0 - - - -
93A PHE* 6.1 1.1 - - + -
100A SER* 4.3 7.4 - - - -
103A ALA* 2.9 44.5 + - + -
104A THR* 3.6 16.2 - - + +
106A GLU* 1.3 79.1 - - + +
108A ARG* 1.3 64.6 + - - +
110A GLN* 3.2 10.2 + - + +
111A ILE* 3.0 29.5 + - + +
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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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91A LEU* 4.9 3.8 - - + +
104A THR 2.9 14.7 + - - +
105A ALA* 3.4 11.9 - - - +
107A PHE* 1.3 76.8 - - - +
109A GLU* 1.3 59.9 + - + +
111A ILE* 3.1 13.2 + - - +
112A LEU* 3.0 41.3 + - + +
123A LEU* 4.0 29.0 - - + +
149A GLU* 5.1 0.8 + - - -
150A TRP* 3.4 70.6 + - + +
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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 ALA* 3.0 24.6 + - - +
106A GLU* 3.9 11.8 - - - +
108A ARG* 1.3 77.8 - - + +
110A GLN* 1.3 61.9 + - - +
112A LEU* 3.1 11.1 + - + +
113A ARG* 2.8 41.8 + - + +
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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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79A ARG* 4.7 10.9 + - - +
80A ASP* 3.4 25.7 + - - +
83A PHE* 4.2 15.1 - - + -
106A GLU* 2.9 42.2 + - - +
107A PHE* 3.2 14.3 + - + +
109A GLU* 1.3 78.1 - - - +
111A ILE* 1.3 62.1 + - - +
113A ARG* 3.4 41.5 + - - +
114A VAL* 3.6 16.6 + - - +
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Residues in contact with ILE 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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20A VAL* 5.4 1.6 - - + -
83A PHE* 4.2 16.8 - - + -
89A PHE* 3.6 66.6 - - + -
91A LEU* 4.6 8.1 - - + -
107A PHE* 3.0 19.4 + - + +
108A ARG* 3.3 7.9 - - - +
110A GLN* 1.3 75.0 - - - +
112A LEU* 1.3 61.3 + - + +
114A VAL* 3.1 11.3 + - + +
115A LYS* 2.8 36.5 + - + +
121A ILE* 4.1 12.1 - - + -
123A LEU* 4.2 11.9 - - + -
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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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108A ARG* 3.0 40.7 + - + +
109A GLU* 3.1 16.5 + - + +
111A ILE* 1.3 80.6 - - + +
113A ARG* 1.3 61.5 + - + +
115A LYS 3.0 27.3 + - - +
116A ALA* 3.8 18.4 - - + +
121A ILE* 4.3 17.7 - - + -
123A LEU* 5.4 5.4 - - + -
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Residues in contact with ARG 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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109A GLU* 2.8 26.9 + - + +
110A GLN* 3.5 34.3 - - - +
111A ILE 3.2 0.6 - - - -
112A LEU* 1.3 77.9 - - + +
114A VAL* 1.3 63.8 + - + +
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Residues in contact with VAL 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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80A ASP* 4.4 16.8 - - + +
83A PHE* 3.5 33.2 - - + -
84A ARG* 5.0 12.2 - - + +
110A GLN 3.6 13.5 - - - +
111A ILE 3.2 13.9 - - - +
113A ARG* 1.3 83.3 - - + +
115A LYS* 1.3 70.3 + - + +
116A ALA 4.3 0.4 - - - -
421B LYS* 5.7 8.7 - - - +
426B GLU* 5.6 7.0 - - - +
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Residues in contact with LYS 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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83A PHE 3.2 22.7 - - - +
84A ARG* 3.4 15.5 - - + +
86A GLY 2.6 21.4 + - - -
87A GLU* 3.4 13.5 + - - +
89A PHE* 3.4 21.9 - - - -
111A ILE* 2.8 13.2 + - - +
112A LEU* 3.0 17.2 + - - +
114A VAL* 1.3 92.2 - - + +
116A ALA* 1.3 60.8 + - - +
118A GLU* 2.6 45.2 + - - +
121A ILE* 3.3 25.6 - - + +
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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