Contacts of the helix formed by residues 117 - 130 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B PRO* 3.8 9.1 - - - +
46B LYS* 2.9 35.3 + - - +
81B LEU* 3.5 10.2 - - + +
103B ASN 4.9 0.4 - - - -
104B LEU* 2.8 30.3 + - + +
105B SER* 4.4 0.6 - - - +
115B THR 4.3 0.2 + - - -
116B VAL* 1.3 72.4 - - - +
118B ARG* 1.3 60.1 + - - +
119B GLU* 2.9 20.5 + - - +
120B LEU* 2.9 32.2 + - + -
121B LYS* 2.9 24.9 + - - +
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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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116B VAL 3.0 9.7 + - - +
117B ASP* 1.3 71.0 + - - +
119B GLU* 1.3 67.4 + - + +
121B LYS* 3.8 7.4 - - + +
122B ALA* 3.0 26.3 + - - +
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Residues in contact with GLU 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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44B PRO* 4.7 7.3 - - - +
45B ASP 5.2 2.3 + - - -
81B LEU* 3.7 25.0 + - + +
82B ALA* 3.4 41.5 + - - +
117B ASP* 2.9 10.5 + - - +
118B ARG* 1.3 78.2 - - + +
120B LEU* 1.4 63.2 + - - +
122B ALA* 3.9 4.8 - - - +
123B LEU* 3.1 23.7 + - - +
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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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10B ILE* 4.3 26.5 - - + -
81B LEU* 3.6 12.4 - - + +
92B LEU* 4.5 15.5 - - + -
94B VAL* 4.7 8.7 - - + -
104B LEU* 3.9 28.0 - - + -
116B VAL* 4.4 5.8 - - + -
117B ASP* 2.9 22.4 + - + +
119B GLU* 1.4 77.3 - - - +
121B LYS* 1.3 57.1 + - - +
123B LEU* 3.2 7.4 + - + +
124B ALA* 2.9 32.1 + - + +
136B PHE* 5.2 3.1 - - + -
143B MSE 3.8 30.1 - - + -
147B ILE* 4.9 6.5 - - + -
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Residues in contact with LYS 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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116B VAL* 4.2 15.2 - - + +
117B ASP 2.9 16.5 + - - +
118B ARG* 3.8 8.7 - - + +
120B LEU* 1.3 75.0 - - - +
122B ALA* 1.3 58.6 + - - +
124B ALA* 3.5 0.5 + - - -
125B GLN* 3.0 63.3 + - - +
146B LYS 3.2 26.1 + - - +
147B ILE* 3.7 20.9 + - - +
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ARG 3.0 17.6 + - - +
119B GLU* 3.9 4.5 - - - +
121B LYS* 1.3 77.7 - - - +
123B LEU* 1.3 58.1 - - - +
125B GLN* 3.4 10.2 + - - +
126B ALA* 3.0 30.1 + - - +
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Residues in contact with LEU 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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10B ILE* 4.2 4.0 - - + -
81B LEU* 4.1 14.6 - - + -
84B ALA* 3.9 34.5 - - + +
85B ASP 4.3 0.7 - - - -
86B ALA* 3.7 33.2 - - + +
89B LEU* 4.7 5.6 - - + -
92B LEU* 3.9 33.9 - - + -
119B GLU 3.1 18.8 + - - +
120B LEU* 3.2 5.6 + - + +
122B ALA* 1.3 78.0 - - - +
124B ALA* 1.3 62.5 + - - +
126B ALA* 3.2 3.9 + - + +
127B MSE 3.0 30.9 + - + +
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Residues in contact with ALA 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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92B LEU* 4.3 13.2 - - + +
120B LEU* 2.9 21.8 + - + +
123B LEU* 1.3 73.1 - - - +
125B GLN* 1.3 63.3 + - - +
127B MSE 3.3 3.8 + - - +
128B HIS* 3.0 24.6 + - - +
134B LEU* 3.6 24.9 - - + +
136B PHE* 4.9 1.8 - - + -
147B ILE* 3.9 28.3 - - + -
148B PHE* 3.6 3.5 - - - -
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Residues in contact with GLN 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 LYS* 3.0 44.1 + - - +
122B ALA* 3.7 9.1 - - - +
124B ALA* 1.3 76.4 - - - +
126B ALA* 1.3 59.7 + - - +
128B HIS* 3.3 1.2 + - - +
129B GLN* 2.9 39.3 + - + +
147B ILE* 2.7 34.8 + - + +
148B PHE* 4.0 12.7 - - + -
149B ASP* 5.6 0.8 - - - +
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Residues in contact with ALA 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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86B ALA* 3.8 20.3 - - + +
122B ALA 3.0 17.6 + - - +
123B LEU* 3.2 6.3 + - - +
125B GLN* 1.3 75.7 - - - +
127B MSE 1.3 62.9 + - - +
129B GLN* 3.3 8.6 + - - +
130B ALA* 3.2 22.7 + - - +
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Residues in contact with MSE 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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86B ALA* 3.6 35.9 - - + +
89B LEU* 4.2 12.3 - - + +
90B ASP 4.1 0.2 - - - -
91B ALA* 3.6 37.0 - - - +
92B LEU* 3.9 9.0 - - + +
123B LEU* 3.0 25.4 + - + +
124B ALA* 3.5 7.0 - - - +
126B ALA* 1.3 76.0 - - - +
128B HIS* 1.3 62.8 + - - +
130B ALA* 3.1 10.2 + - - -
132B LYS* 3.1 55.5 + - + +
133B PRO 4.4 1.6 - - - +
134B LEU* 3.6 17.9 - - + -
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Residues in contact with HIS 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 ALA 3.0 8.3 + - - +
125B GLN 3.7 1.6 - - - +
127B MSE 1.3 74.9 - - - +
129B GLN* 1.3 85.2 + - - +
131B GLY* 3.1 13.7 + - - -
132B LYS 4.4 7.8 + - - -
134B LEU* 5.1 3.3 - - + +
148B PHE* 3.4 30.5 - + + -
150B PHE* 3.5 25.9 - + - -
186B ASP 5.2 0.2 + - - -
187B ASN* 2.8 53.0 + - + -
189B ILE* 4.9 2.7 - - + -
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Residues in contact with GLN 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 GLN* 2.9 33.5 + - + +
126B ALA* 3.8 7.6 - - - +
127B MSE 3.3 0.4 - - - -
128B HIS* 1.3 106.9 + - - +
130B ALA* 1.3 59.0 + - - +
131B GLY 3.2 1.0 + - - -
148B PHE* 4.8 3.8 - - - -
150B PHE* 5.3 2.4 - - - -
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Residues in contact with ALA 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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86B ALA* 6.1 2.0 - - + -
126B ALA 3.2 11.1 + - - +
127B MSE 3.1 10.3 + - - +
129B GLN* 1.3 76.2 - - - +
131B GLY* 1.3 61.2 + - - +
132B LYS* 3.5 28.2 + - + +
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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