Contacts of the helix formed by residues 118 - 129 (chain A) in PDB entry 2VDY
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 LEU 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A GLU 3.8 0.6 + - - +
117A LEU* 1.3 74.5 - - - +
119A GLU* 1.3 66.9 + - - +
120A SER* 3.3 8.7 - - - +
121A PHE* 3.3 4.1 + - + +
122A SER* 3.1 20.7 + - - -
310A SER 3.4 26.2 - - - +
311A ARG* 3.4 25.1 - - + +
312A ILE 3.1 10.7 + - - +
313A THR* 4.1 11.7 - - - +
314A GLN* 3.9 32.5 - - + +
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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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117A LEU 3.8 2.5 + - - -
118A LEU* 1.3 72.9 - - - +
120A SER* 1.3 60.9 + - - +
122A SER* 3.1 9.7 + - - -
123A ALA* 3.0 41.7 + - + +
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Residues in contact with SER 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 3.3 7.5 - - - +
119A GLU* 1.3 82.8 - - - +
121A PHE* 1.3 59.9 + - - +
123A ALA* 3.9 5.2 - - - +
124A ASP* 3.0 41.0 + - - +
311A ARG* 5.4 5.0 + - - +
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Residues in contact with PHE 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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54A MET* 4.2 8.1 - - + -
55A LEU* 4.8 1.3 - - - -
57A LEU* 3.8 13.7 - - + +
58A GLY* 3.6 37.9 - - - -
109A LEU* 4.9 11.7 - - + -
117A LEU* 3.9 26.2 - - + -
118A LEU 3.3 7.4 + - - +
120A SER* 1.3 79.3 + - - +
122A SER* 1.3 61.0 + - - +
124A ASP* 3.3 5.0 + - - +
125A ILE* 3.0 63.4 + - + +
175A LEU* 5.8 3.8 - - + -
311A ARG* 3.1 22.2 - - + +
312A ILE* 3.9 31.4 - - + +
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Residues in contact with SER 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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117A LEU* 3.8 24.6 + - - +
118A LEU 3.1 11.5 + - - -
119A GLU* 3.1 17.5 + - - -
121A PHE* 1.3 76.6 - - - +
123A ALA* 1.3 62.4 + - - +
125A ILE* 3.4 10.2 - - - +
126A LYS* 3.2 47.4 + - - +
133A VAL* 5.0 0.2 - - - -
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Residues in contact with ALA 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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119A GLU* 3.0 31.2 + - + +
120A SER* 3.9 6.7 - - - +
122A SER* 1.3 78.5 + - - +
124A ASP* 1.3 58.9 + - - +
126A LYS* 4.0 5.8 - - - +
127A HIS* 3.1 31.1 + - - +
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Residues in contact with ASP 124 (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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57A LEU* 3.7 33.5 - - + +
120A SER* 3.0 30.6 + - - +
121A PHE* 3.3 6.2 + - - +
123A ALA* 1.3 77.9 - - - +
125A ILE* 1.3 60.9 + - - +
127A HIS* 4.6 1.0 - - - +
128A TYR* 3.0 57.6 + - + +
311A ARG* 5.7 1.4 + - - -
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Residues in contact with ILE 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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54A MET* 3.9 24.9 - - + +
57A LEU* 4.0 9.0 - - + -
109A LEU* 4.4 8.5 - - + -
117A LEU* 4.3 2.5 - - + -
121A PHE* 3.0 58.8 + - + +
122A SER* 3.4 15.3 - - - +
124A ASP* 1.3 75.3 - - - +
126A LYS* 1.3 60.8 + - + +
129A TYR* 3.2 23.7 + - - +
130A GLU 3.2 0.2 + - - -
131A SER* 3.1 37.0 + - - +
133A VAL* 3.8 26.5 - - + -
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Residues in contact with LYS 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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122A SER* 3.2 28.0 + - - +
123A ALA* 4.1 4.7 - - - +
125A ILE* 1.3 80.1 - - + +
127A HIS* 1.3 62.6 + - - +
130A GLU* 3.3 18.9 - - - +
131A SER 3.4 23.1 - - - +
133A VAL* 3.8 28.9 - - - +
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Residues in contact with HIS 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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88A GLN* 3.8 25.3 + - - +
123A ALA 3.1 19.8 + - - +
124A ASP* 4.0 2.7 - - - +
126A LYS* 1.3 80.5 - - - +
128A TYR* 1.3 93.4 + + + +
130A GLU* 4.3 2.6 + - - +
119B GLU* 3.1 38.4 + - + +
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Residues in contact with TYR 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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57A LEU* 4.9 1.3 - - + -
81A THR* 4.4 19.0 - - + +
84A HIS* 3.5 37.9 - + + +
85A GLN* 3.9 13.3 + - + +
87A PHE 4.3 1.6 - - - +
88A GLN* 3.2 44.5 + - - +
91A HIS* 4.9 2.4 + - - +
124A ASP* 3.0 51.0 + - + +
127A HIS* 1.3 92.3 - + - +
129A TYR* 1.3 74.1 + - + +
130A GLU 3.6 0.2 - - - -
119B GLU* 3.3 37.7 + - - +
123B ALA* 5.3 5.2 - - - +
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Residues in contact with TYR 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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50A MET* 3.5 35.2 - - + -
53A ALA* 3.3 19.2 - - - +
54A MET* 3.6 36.3 - - + -
57A LEU* 3.9 16.4 - - + -
84A HIS* 2.8 34.3 + - - -
87A PHE* 3.6 32.6 - + + +
91A HIS* 3.9 10.6 + - + -
107A ASN* 2.9 32.6 + - - +
124A ASP 4.4 2.0 - - - -
125A ILE* 3.2 13.4 + - - +
128A TYR* 1.3 90.7 - - + +
130A GLU* 1.3 69.1 - - - +
131A SER 3.1 0.9 + - - -
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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