Contacts of the helix formed by residues 109 - 122 (chain B) in PDB entry 2QNU
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 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A VAL 5.2 1.7 - - - +
164A THR* 5.2 0.5 - - - -
165A PRO* 3.5 24.3 - - - +
168A ARG* 2.9 26.5 + - - -
59B ARG* 3.3 22.1 + - - +
107B GLY 3.4 0.2 + - - -
108B ASP* 1.3 75.2 + - - +
110B GLY* 1.3 64.3 + - - +
111B TRP 3.4 0.9 - - - -
112B PHE* 3.1 13.4 + - - +
113B GLU* 3.0 42.0 + - - +
184B TRP* 4.5 1.0 + - - -
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Residues in contact with GLY 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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108B ASP* 2.7 25.1 + - - -
109B ASP* 1.3 71.1 - - - +
111B TRP* 1.3 55.5 + - - +
113B GLU* 3.3 12.8 + - - +
114B GLN* 2.9 41.9 + - - +
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Residues in contact with TRP 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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4B VAL* 4.3 13.9 - - + -
73B THR* 4.1 7.6 - - + -
74B GLY* 4.0 20.0 - - - -
91B VAL* 5.2 1.3 - - + -
92B ALA 5.2 0.4 - - - -
93B CYS* 4.0 24.2 - - + -
108B ASP* 4.4 4.4 + - - +
109B ASP 3.4 0.4 - - - -
110B GLY* 1.3 73.6 - - - +
112B PHE* 1.3 101.1 + + + +
114B GLN* 3.2 17.3 + - - +
115B VAL* 2.8 54.2 + - + +
139B LEU* 4.3 9.7 - - + +
140B PRO* 2.8 35.2 + - + -
141B ALA 4.0 2.7 - - - -
142B PRO* 3.7 38.5 - - + -
143B PRO* 4.4 12.1 - - + +
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Residues in contact with PHE 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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168A ARG* 6.4 0.2 - - - -
59B ARG* 3.8 33.0 - - + +
73B THR* 3.2 27.4 - - - -
74B GLY 3.6 20.0 - - - -
75B VAL* 4.0 3.6 - - + +
104B LEU* 4.0 33.0 - - + -
108B ASP 4.1 16.4 - - - -
109B ASP* 3.1 9.8 + - - +
111B TRP* 1.3 102.3 - + + +
113B GLU* 1.3 55.0 + - - +
115B VAL* 3.3 4.0 + - - +
116B GLU* 2.7 41.7 + - - +
184B TRP* 3.7 31.0 - + - -
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Residues in contact with GLU 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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59B ARG* 3.8 11.6 + - - +
109B ASP* 3.0 37.3 + - - +
110B GLY* 3.6 14.0 - - - +
112B PHE* 1.3 72.0 - - - +
114B GLN* 1.3 60.7 + - + +
116B GLU* 3.3 9.6 + - - +
117B SER* 2.9 30.0 + - - -
186B ARG* 3.1 32.7 + - - +
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Residues in contact with GLN 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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110B GLY* 2.9 28.6 + - - +
111B TRP* 3.4 16.4 - - + +
113B GLU* 1.3 76.6 - - + +
115B VAL* 1.3 61.9 + - - +
117B SER* 3.4 7.7 + - - +
118B LEU* 3.2 25.9 + - - +
139B LEU* 4.1 23.0 - - + +
140B PRO* 4.8 11.3 - - - +
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Residues in contact with VAL 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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75B VAL* 3.7 27.6 - - + +
91B VAL* 3.7 32.3 - - + -
111B TRP* 2.8 53.4 + - + +
112B PHE 3.7 4.7 - - - +
114B GLN* 1.3 75.7 - - - +
116B GLU* 1.3 63.7 + - - +
118B LEU* 3.0 17.8 + - - +
119B LEU* 3.1 14.2 + - + +
139B LEU* 3.9 19.1 - - + -
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Residues in contact with GLU 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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57B LEU* 4.2 31.6 - - + +
59B ARG* 2.7 37.1 + - - +
75B VAL* 3.9 18.6 - - + -
112B PHE 2.7 25.7 + - - +
113B GLU* 3.3 5.4 + - - +
115B VAL* 1.3 73.7 - - - +
117B SER* 1.3 62.7 + - - +
119B LEU* 3.4 4.3 + - - +
120B LEU* 2.9 36.3 + - + +
186B ARG* 2.8 37.3 + - - +
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Residues in contact with SER 117 (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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113B GLU 2.9 17.1 + - - -
114B GLN* 3.8 7.9 - - - -
115B VAL 3.2 0.4 - - - -
116B GLU* 1.3 76.2 - - - +
118B LEU* 1.3 67.4 + - - +
120B LEU* 3.4 10.5 + - - +
121B SER* 3.0 22.5 + - - -
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Residues in contact with LEU 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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91B VAL* 5.6 2.7 - - + -
114B GLN* 3.2 12.7 + - + +
115B VAL* 3.0 9.2 + - - +
117B SER* 1.3 81.3 - - - +
119B LEU* 1.3 62.2 + - + +
121B SER* 2.6 29.2 + - - +
122B THR 3.7 1.4 + - - -
132B PHE* 3.7 20.7 - - + -
135B ALA* 3.6 34.8 - - + -
136B VAL* 4.1 13.7 - - + +
139B LEU* 4.0 37.0 - - + -
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Residues in contact with LEU 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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57B LEU* 4.3 5.2 - - + -
75B VAL* 3.7 46.2 - - + +
77B MSE 3.4 34.3 - - + +
89B LEU* 3.6 39.0 - - + +
91B VAL* 3.6 25.6 - - + +
115B VAL* 3.1 16.6 + - + +
116B GLU* 3.7 5.8 - - - +
118B LEU* 1.3 77.3 - - - +
120B LEU* 1.3 61.5 + - - +
122B THR* 2.8 26.0 + - - -
132B PHE* 4.4 4.0 - - + -
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Residues in contact with LEU 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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57B LEU* 4.2 25.1 - - + -
77B MSE 4.2 3.8 - - - -
116B GLU* 2.9 35.6 + - + +
117B SER* 3.8 8.1 - - - +
118B LEU 3.2 0.2 - - - -
119B LEU* 1.3 72.3 - - - +
121B SER* 1.3 65.8 + - - +
123B LEU* 2.8 42.5 + - + +
124B GLU* 4.0 8.0 + - - +
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Residues in contact with SER 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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117B SER 3.0 13.0 + - - -
118B LEU* 2.6 28.4 + - - +
120B LEU* 1.3 75.1 - - - +
122B THR* 1.3 63.4 + - - +
123B LEU 3.2 1.6 + - - -
124B GLU* 3.4 31.0 + - - +
127B ALA* 3.2 24.1 - - - +
132B PHE* 4.4 8.7 - - - +
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Residues in contact with THR 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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10B LEU* 3.9 27.1 - - + +
11B ALA* 4.2 18.9 + - - +
12B GLY 5.6 0.3 + - - -
77B MSE 3.7 12.5 - - - +
79B SER* 5.0 1.0 + - - -
89B LEU* 3.8 8.0 - - + +
118B LEU 3.9 4.5 - - - +
119B LEU 2.8 16.4 + - - +
120B LEU 2.9 2.2 + - - -
121B SER* 1.3 76.5 - - - +
123B LEU* 1.3 62.2 + - - +
124B GLU 3.3 4.9 - - - +
127B ALA* 4.5 8.3 - - + +
132B PHE* 3.6 42.0 - - + -
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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