Contacts of the helix formed by residues 106 - 122 (chain B) in PDB entry 2QVH
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 SER 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B GLN* 1.3 75.4 - - - +
107B GLU* 1.3 63.9 + - - +
108B ALA* 3.5 11.5 + - - +
109B ASN* 2.8 55.5 + - - +
110B ASP* 3.3 11.9 + - - +
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B SER* 1.3 71.4 - - - +
108B ALA* 1.3 65.5 + - - +
110B ASP* 3.0 17.5 + - - +
111B VAL* 3.0 26.7 + - + +
135B TRP* 4.7 8.0 + - + +
139B THR* 3.7 16.8 - - - +
142B ARG* 3.6 32.3 + - - -
143B MSE 3.8 28.0 - - + +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B SER* 3.1 10.6 + - - +
107B GLU* 1.3 80.0 - - - +
109B ASN* 1.3 62.7 + - - +
111B VAL* 3.4 9.0 + - - +
112B ALA* 3.0 23.4 + - - +
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Residues in contact with ASN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PRO* 5.9 1.0 - - - +
105B GLN* 3.9 13.5 - - - +
106B SER* 2.8 44.6 + - - +
108B ALA* 1.3 75.8 - - - +
110B ASP* 1.3 59.4 + - - +
112B ALA* 3.3 6.9 + - - +
113B ARG* 2.9 47.7 + - - +
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Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL* 3.3 16.8 - - + +
101B ALA* 3.1 33.2 + - - -
102B GLU 4.7 0.5 + - - -
105B GLN* 4.4 6.2 - - - +
106B SER 3.3 12.9 + - - +
107B GLU* 3.0 15.4 + - - +
109B ASN* 1.3 77.4 - - - +
111B VAL* 1.3 62.2 + - - +
113B ARG* 3.2 25.9 + - - +
114B VAL* 3.0 30.3 + - - +
135B TRP* 4.3 9.7 + - + -
143B MSE 6.3 1.8 - - - -
147B LEU* 4.3 9.9 - - + -
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLU* 3.0 16.7 + - + +
108B ALA* 3.7 9.6 - - - +
110B ASP* 1.3 76.3 - - + +
112B ALA* 1.3 58.4 + - - +
114B VAL* 4.0 1.6 - - - +
115B GLU* 3.0 31.3 + - + +
143B MSE 5.5 7.2 - - - -
146B LEU* 5.4 12.6 - - + -
147B LEU* 3.7 21.1 - - + -
149B ARG* 3.7 29.2 - - - +
150B PHE* 4.0 12.3 - - + -
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PRO* 3.7 21.6 - - + +
108B ALA 3.0 16.4 + - - +
109B ASN* 3.7 7.2 - - - +
110B ASP 3.3 0.2 - - - -
111B VAL* 1.3 77.4 - - - +
113B ARG* 1.3 57.5 + - - +
115B GLU* 3.7 11.3 - - - +
116B ALA* 3.1 27.9 + - - +
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B VAL* 4.3 1.8 - - + -
77B PRO 3.5 16.6 - - - -
78B ALA* 3.4 20.4 + - - +
79B VAL 2.7 28.6 + - - +
81B PRO* 4.6 9.6 - - + +
84B ALA* 3.9 13.9 - - + +
98B VAL* 3.5 24.5 - - + -
99B LYS 2.8 21.5 + - - -
100B VAL* 4.3 0.2 - - - +
102B GLU* 5.6 0.2 - - - +
105B GLN* 2.7 28.7 + - - +
109B ASN* 2.9 28.8 + - - +
110B ASP* 3.2 25.2 + - - +
111B VAL 3.2 0.2 - - - -
112B ALA* 1.3 75.0 - - - +
114B VAL* 1.3 65.7 + - - +
116B ALA* 3.2 3.8 + - - +
117B VAL* 3.1 26.5 + - - +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B VAL* 4.2 10.8 - - + -
100B VAL* 4.1 12.1 - - + -
110B ASP 3.0 20.3 + - - +
111B VAL 4.0 2.7 - - - +
113B ARG* 1.3 75.0 - - - +
115B GLU* 1.3 64.5 + - - +
117B VAL* 3.2 6.9 + - - +
118B ARG* 2.9 21.7 + - + +
127B VAL* 4.3 18.1 - - + +
129B ILE* 3.9 22.4 - - + -
147B LEU* 4.0 15.9 - - + +
150B PHE* 3.7 27.6 - - + -
152B LEU* 4.5 9.2 - - + -
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B VAL* 3.0 19.8 + - - +
112B ALA* 3.7 9.7 - - - +
114B VAL* 1.3 77.5 - - - +
116B ALA* 1.3 57.0 + - - +
118B ARG* 3.2 2.9 + - - +
119B ASP* 2.9 47.6 + - - +
149B ARG* 4.7 6.7 + - - -
150B PHE* 3.5 37.8 - - + -
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PRO* 3.3 36.1 - - + +
84B ALA* 4.9 0.2 - - + -
85B ALA* 3.9 11.4 - - + +
112B ALA 3.1 15.6 + - - +
113B ARG 3.2 5.1 + - - +
115B GLU* 1.3 80.1 - - - +
117B VAL* 1.3 57.4 + - - +
119B ASP* 3.4 9.8 + - - +
120B ALA* 3.0 27.4 + - - +
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 4.2 5.6 - - + -
84B ALA* 4.2 17.9 - - + +
85B ALA* 5.0 0.7 - - - +
88B VAL* 3.8 28.3 - - + -
96B ALA* 3.9 18.6 - - + -
98B VAL* 3.7 26.5 - - + -
113B ARG 3.1 14.8 + - - +
114B VAL 3.6 6.3 - - - +
116B ALA* 1.3 75.1 - - - +
118B ARG* 1.3 66.9 + - - +
120B ALA* 3.0 8.0 + - - +
121B LEU* 2.9 29.8 + - + +
127B VAL* 4.3 6.7 - - + -
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B VAL 2.9 12.7 + - - +
115B GLU 3.6 8.3 - - - +
117B VAL* 1.3 76.4 - - - +
119B ASP* 1.3 64.1 + - - +
121B LEU* 3.3 1.6 + - - +
122B GLY* 2.9 50.1 + - - +
123B PRO* 3.4 14.1 + - - +
125B GLY* 3.0 31.3 + - - -
127B VAL* 3.4 27.9 - - + +
150B PHE* 2.9 39.6 + - + +
151B GLU* 2.9 38.2 + - - +
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Residues in contact with ASP 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B GLU* 2.9 40.4 + - - +
116B ALA* 3.6 9.3 - - - +
118B ARG* 1.3 83.0 - - - +
120B ALA* 1.3 60.6 + - - +
122B GLY* 3.5 9.4 + - - +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ALA* 3.7 32.1 - - + +
88B VAL* 4.1 12.3 - - + +
89B ALA* 4.5 12.0 - - + +
116B ALA 3.0 15.4 + - - +
117B VAL 3.0 8.9 + - - +
119B ASP* 1.3 79.9 - - - +
121B LEU* 1.3 59.7 + - - +
122B GLY* 3.5 0.3 + - - -
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B VAL* 3.3 26.5 - - + +
93B CYS 3.4 22.0 - - - +
94B THR* 3.5 20.0 - - - +
95B THR 4.3 0.7 - - - +
96B ALA* 4.0 15.0 - - + -
117B VAL* 2.9 12.6 + - + +
118B ARG* 4.0 1.8 - - - +
120B ALA* 1.3 76.7 - - - +
122B GLY* 1.3 63.6 + - - +
124B ARG* 4.6 2.1 + - - +
125B GLY* 3.9 16.4 + - - -
126B ARG 3.5 27.6 - - - +
127B VAL* 3.7 18.6 - - + -
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Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ARG* 2.9 38.5 + - - +
119B ASP* 3.5 7.6 + - - -
120B ALA 3.3 3.4 + - - -
121B LEU* 1.3 85.3 - - - +
123B PRO* 1.3 68.8 - - - +
124B ARG 3.5 0.2 - - - -
125B GLY 3.6 0.5 + - - -
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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