Contacts of the helix formed by residues 117 - 130 (chain A) in PDB entry 1VHQ
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 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A PRO* 3.9 9.3 - - - +
46A LYS* 2.9 33.7 + - - +
81A LEU* 3.6 10.9 - - - +
104A LEU* 2.8 31.2 + - + +
105A SER* 4.3 1.4 - - - +
116A VAL* 1.3 73.1 - - - +
118A ARG* 1.3 64.7 + - - +
119A GLU* 3.0 19.8 + - - +
120A LEU* 2.9 32.0 + - + -
121A LYS* 2.9 19.9 + - - +
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Residues in contact with ARG 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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116A VAL 3.1 7.7 + - - +
117A ASP* 1.3 72.4 + - - +
119A GLU* 1.3 60.8 + - + +
121A LYS* 3.5 5.8 + - - +
122A ALA* 3.0 30.1 + - - +
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Residues in contact with GLU 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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44A PRO* 4.5 9.0 - - - +
45A ASP 5.1 2.1 + - - -
81A LEU* 3.7 25.7 + - + +
82A ALA* 3.2 40.9 + - - +
117A ASP* 3.0 10.0 + - - +
118A ARG* 1.3 75.5 - - + +
120A LEU* 1.3 68.1 + - - +
122A ALA* 3.3 5.4 + - - +
123A LEU* 2.9 25.9 + - - +
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Residues in contact with LEU 120 (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 ILE* 4.1 29.6 - - + -
81A LEU* 3.6 11.6 - - + +
92A LEU* 4.6 13.7 - - + -
94A VAL* 4.7 8.1 - - + -
104A LEU* 3.8 30.5 - - + +
116A VAL* 4.3 3.8 - - + -
117A ASP* 2.9 23.1 + - + +
119A GLU* 1.3 76.4 - - - +
121A LYS* 1.3 58.3 + - - +
123A LEU* 3.2 6.0 + - + +
124A ALA* 2.8 30.7 + - + +
136A PHE* 5.4 2.0 - - + -
143A MSE 3.8 31.9 - - + -
147A ILE* 5.1 6.1 - - + -
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Residues in contact with LYS 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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116A VAL* 4.0 21.3 - - + +
117A ASP 2.9 16.7 + - - +
118A ARG* 3.8 6.3 - - - +
120A LEU* 1.3 76.6 - - - +
122A ALA* 1.4 59.7 + - - +
124A ALA* 3.8 1.4 - - - +
125A GLN* 2.9 59.9 + - - +
146A LYS 2.8 29.3 + - - +
147A ILE* 3.7 18.6 + - + -
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Residues in contact with ALA 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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118A ARG 3.0 18.3 + - - +
119A GLU* 3.7 5.8 - - - +
120A LEU 3.2 0.2 - - - -
121A LYS* 1.4 79.5 - - - +
123A LEU* 1.3 56.8 + - - +
125A GLN* 3.4 9.9 + - - +
126A ALA* 3.0 29.3 + - - +
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Residues in contact with LEU 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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10A ILE* 4.2 11.0 - - + -
81A LEU* 4.2 7.4 - - + -
84A ALA* 3.8 35.2 - - + +
85A ASP 4.2 0.4 - - - -
86A ALA* 3.6 34.1 - - + +
89A LEU* 4.5 8.1 - - + -
92A LEU* 3.8 32.3 - - + -
119A GLU 2.9 18.1 + - - +
120A LEU* 3.7 5.6 - - + +
122A ALA* 1.3 72.5 - - - +
124A ALA* 1.3 67.1 + - - +
126A ALA* 3.2 4.8 + - - +
127A MSE 3.0 30.4 + - + +
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Residues in contact with ALA 124 (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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92A LEU* 4.2 17.6 - - + +
120A LEU* 2.8 18.2 + - + +
123A LEU* 1.3 76.8 - - - +
125A GLN* 1.3 61.8 + - - +
127A MSE 3.2 4.3 + - - +
128A HIS* 3.0 24.3 + - - +
134A LEU* 4.0 17.9 - - + +
136A PHE* 4.9 3.1 - - + -
147A ILE* 3.7 31.6 - - + -
148A PHE* 3.8 3.2 - - - -
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Residues in contact with GLN 125 (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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121A LYS* 2.9 40.1 + - - +
122A ALA* 3.7 8.1 - - - +
124A ALA* 1.3 74.1 - - - +
126A ALA* 1.3 58.0 + - - +
128A HIS* 3.3 2.1 + - - +
129A GLN* 2.8 38.5 + - + +
147A ILE* 2.8 34.4 + - + +
148A PHE* 4.2 15.1 - - + +
149A ASP* 5.5 2.2 - - - +
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Residues in contact with ALA 126 (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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86A ALA* 3.7 21.0 - - + +
122A ALA 3.0 17.6 + - - +
123A LEU* 3.2 6.9 + - - +
125A GLN* 1.3 76.3 - - - +
127A MSE 1.4 62.3 + - - +
129A GLN* 3.4 8.3 + - - +
130A ALA* 3.1 22.7 + - - +
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Residues in contact with MSE 127 (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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86A ALA* 3.6 35.0 - - + +
89A LEU* 4.0 12.8 - - + -
90A ASP 3.9 0.2 - - - -
91A ALA* 3.4 47.8 - - - +
92A LEU* 3.9 10.5 - - + +
123A LEU* 3.0 25.0 + - + +
124A ALA 3.6 6.3 - - - +
126A ALA* 1.4 76.8 - - - +
128A HIS* 1.3 60.3 + - - +
130A ALA* 3.1 10.3 + - - -
132A LYS* 2.9 48.4 + - + +
133A PRO 4.6 0.7 - - - +
134A LEU* 3.7 19.3 - - + -
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Residues in contact with HIS 128 (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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124A ALA 3.0 9.3 + - - +
125A GLN 3.8 2.3 + - - +
127A MSE 1.3 74.4 - - - +
129A GLN* 1.3 76.6 + - - +
131A GLY* 2.9 15.3 + - - -
132A LYS 4.3 7.6 - - - +
134A LEU* 4.8 4.4 - - + +
148A PHE* 3.5 36.3 - + + -
150A PHE* 3.6 25.5 - + - -
186A ASP 5.3 0.2 + - - -
187A ASN* 2.9 51.9 + - + -
189A ILE* 4.8 2.0 - - + -
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Residues in contact with GLN 129 (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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125A GLN* 2.8 30.7 + - + +
126A ALA* 3.6 8.3 - - - +
127A MSE 3.3 0.2 - - - -
128A HIS* 1.3 88.7 + - - +
130A ALA* 1.3 57.3 + - - +
131A GLY 3.6 0.5 + - - -
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Residues in contact with ALA 130 (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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86A ALA* 6.1 2.0 - - + -
126A ALA 3.1 11.5 + - - +
127A MSE 3.1 9.8 + - - +
129A GLN* 1.3 75.7 - - - +
131A GLY* 1.3 61.5 + - - +
132A LYS* 3.5 28.5 + - + +
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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