Contacts of the helix formed by residues 119 - 131 (chain B) in PDB entry 2QVS
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 THR 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B LYS* 1.3 76.4 - - - +
120B ASP* 1.3 65.2 + - - +
121B GLU* 3.3 8.4 + - - +
122B GLN* 3.1 39.3 + - - +
123B ARG* 2.9 22.8 + - - +
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Residues in contact with ASP 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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118B LYS 5.2 0.9 - - - +
119B THR* 1.3 74.0 - - - +
121B GLU* 1.3 58.5 + - + +
123B ARG* 3.9 6.7 - - - +
124B CYS* 2.8 34.0 + - - +
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Residues in contact with GLU 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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119B THR* 3.3 6.8 + - - +
120B ASP* 1.3 80.4 - - + +
122B GLN* 1.3 63.5 + - + +
124B CYS* 3.6 6.2 - - - +
125B ARG* 2.9 33.2 + - - +
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Residues in contact with GLN 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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117B PRO 4.4 1.2 + - - -
118B LYS* 3.5 16.1 - - + +
119B THR* 3.1 45.8 + - + +
121B GLU* 1.3 77.4 - - + +
123B ARG* 1.3 57.1 + - - +
125B ARG* 3.1 16.1 + - - +
126B LEU* 2.9 31.9 + - - +
153B GLU* 4.5 5.4 - - - +
176B GLU* 3.3 34.1 - - - +
226B TRP* 3.7 19.9 + - - +
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Residues in contact with ARG 123 (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 LYS* 3.4 35.7 - - + +
119B THR 2.9 20.8 + - - +
120B ASP* 3.9 6.5 - - - +
122B GLN* 1.3 74.3 - - - +
124B CYS* 1.3 62.8 + - - +
126B LEU* 3.1 11.2 + - - +
127B GLN* 2.9 28.0 + - - +
145B SER* 3.0 31.3 + - - +
148B LEU* 3.3 29.5 - - + +
149B ASP* 2.4 33.2 + - - +
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Residues in contact with CYS 124 (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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120B ASP 2.8 20.0 + - - +
121B GLU* 3.6 7.6 - - - +
123B ARG* 1.3 76.2 - - - +
125B ARG* 1.3 61.9 + - - +
127B GLN* 3.4 16.8 + - - +
128B GLU* 3.2 19.9 + - - +
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Residues in contact with ARG 125 (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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121B GLU* 2.9 21.4 + - - +
122B GLN* 3.4 17.5 - - - +
124B CYS* 1.3 76.7 - - - +
126B LEU* 1.3 64.8 + - - +
128B GLU* 3.4 8.3 + - + +
129B ALA* 3.0 23.4 + - + +
174B VAL* 5.5 0.6 - - - +
175B ILE 4.7 4.6 + - - +
176B GLU* 2.6 51.8 + - - +
198B ASN 5.1 5.5 + - - -
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Residues in contact with LEU 126 (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 LYS* 3.6 36.6 - - + -
122B GLN 2.9 12.5 + - - +
123B ARG* 3.4 9.0 - - - +
125B ARG* 1.3 75.3 - - - +
127B GLN* 1.3 66.4 + - - +
129B ALA* 3.2 3.0 + - - +
130B CYS* 3.1 29.7 + - - -
148B LEU* 4.1 15.3 - - + -
151B MET* 4.1 18.2 - - - -
174B VAL* 3.4 43.5 - - + -
226B TRP* 3.7 28.0 - - + -
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Residues in contact with GLN 127 (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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123B ARG 2.9 15.4 + - - +
124B CYS* 3.5 18.3 - - - +
125B ARG 3.3 0.2 - - - -
126B LEU* 1.3 77.9 - - - +
128B GLU* 1.3 62.7 - - - +
130B CYS* 3.0 15.8 + - - +
131B LYS* 3.1 16.5 + - - +
141B GLN* 5.8 5.5 + - - +
144B LEU* 3.4 30.5 - - + +
148B LEU* 3.7 18.5 - - + +
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Residues in contact with GLU 128 (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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124B CYS* 3.2 10.8 + - - +
125B ARG* 3.6 12.6 - - + +
127B GLN* 1.3 78.6 - - - +
129B ALA* 1.3 63.2 + - - +
130B CYS 3.1 1.4 + - - -
131B LYS* 2.6 65.4 + - - +
132B ASP 5.1 0.2 + - - -
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Residues in contact with ALA 129 (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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125B ARG* 3.0 17.9 + - + +
126B LEU 3.2 5.8 + - - +
128B GLU* 1.3 77.7 - - - +
130B CYS* 1.3 59.6 + - - +
131B LYS 3.6 0.2 - - - -
132B ASP 5.1 1.4 + - - -
133B ILE* 4.1 13.3 - - - +
174B VAL* 4.0 28.3 - - + -
200B GLY 5.1 7.2 - - - +
201B SER* 4.3 9.9 + - - -
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Residues in contact with CYS 130 (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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126B LEU* 3.1 25.4 + - - +
127B GLN* 3.0 8.0 + - - +
129B ALA* 1.3 81.0 - - - +
131B LYS* 1.3 66.1 + - - +
132B ASP 3.2 3.6 + - - -
133B ILE* 3.2 17.2 + - + +
136B PHE* 3.6 48.6 - - + +
137B LYS 4.3 0.2 + - - -
144B LEU* 5.2 5.2 - - + -
148B LEU* 4.8 9.0 - - - -
151B MET* 5.3 1.6 - - - -
172B PHE* 4.7 6.5 - - - -
174B VAL* 4.4 19.5 - - - -
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Residues in contact with LYS 131 (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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127B GLN 3.1 14.7 + - - +
128B GLU* 2.6 56.3 + - - +
129B ALA 3.6 0.2 - - - -
130B CYS* 1.3 77.5 - - - +
132B ASP* 1.3 59.0 + - + +
137B LYS* 3.4 29.2 + - - +
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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