Contacts of the helix formed by residues 119 - 127 (chain A) in PDB entry 1Y1V
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 ASN 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A LEU* 3.9 32.6 - - + +
116A ASP 3.4 8.1 + - - +
117A GLU 3.5 5.8 - - - +
118A HIS* 1.3 76.7 - - - +
120A GLU* 1.3 62.0 + - - +
121A LEU* 3.2 28.1 + - - +
122A MET* 3.0 29.8 + - + +
123A ARG 3.7 1.0 + - - -
145A LYS* 4.6 12.1 - - - +
149A GLU* 5.8 1.0 + - - -
152A VAL* 5.6 6.6 - - + +
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Residues in contact with GLU 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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118A HIS 3.0 7.7 + - - +
119A ASN* 1.3 68.9 + - - +
121A LEU* 1.3 67.3 + - + +
122A MET 2.7 5.9 + - - -
123A ARG* 3.1 48.3 + - + +
124A GLN* 3.7 10.3 + - + +
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Residues in contact with LEU 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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119A ASN* 3.2 14.8 + - - +
120A GLU* 1.3 79.7 - - + +
122A MET* 1.3 63.1 + - - +
124A GLN* 3.7 21.2 - - - +
125A ALA* 3.9 2.3 + - - +
141A LEU* 3.5 31.9 - - + +
122E LYS* 4.8 15.9 - - - +
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Residues in contact with MET 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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113A LEU* 4.7 10.5 - - + -
115A LEU* 2.8 60.6 - - + +
116A ASP 3.5 9.2 - - - +
119A ASN* 3.0 24.4 + - + +
120A GLU 2.7 0.8 + - - -
121A LEU* 1.3 76.8 - - - +
123A ARG* 1.3 55.9 + - - +
125A ALA* 2.4 41.5 + - - +
126A LEU* 3.1 27.5 + - + -
138A ILE* 3.8 28.9 - - + -
141A LEU* 3.9 11.4 - - - +
142A CYS* 4.6 1.3 - - - -
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Residues in contact with ARG 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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117A GLU* 3.2 33.7 + - + +
118A HIS* 4.5 6.5 + - - +
119A ASN 4.2 0.7 - - - +
120A GLU* 3.6 39.5 + - + +
122A MET* 1.3 76.3 - - - +
124A GLN* 1.3 56.2 + - + +
125A ALA 2.6 13.5 + - - -
126A LEU* 2.7 26.2 + - - +
127A ALA* 3.3 11.3 + - - +
155A GLU* 4.1 25.7 + - - +
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Residues in contact with GLN 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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120A GLU* 3.7 12.7 + - + +
121A LEU* 3.7 18.3 - - - +
122A MET 2.9 2.2 + - - -
123A ARG* 1.3 77.8 - - + +
125A ALA* 1.3 55.9 + - - +
127A ALA* 4.4 7.1 - - - +
128A ILE* 3.5 21.3 + - - +
180E ARG* 6.2 0.2 - - - +
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Residues in contact with ALA 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 LEU 3.9 4.9 + - - +
122A MET* 2.4 25.2 + - - +
123A ARG 2.6 0.2 + - - -
124A GLN* 1.3 71.1 - - - +
126A LEU* 1.3 53.8 + - - +
127A ALA 2.5 17.8 + - - -
128A ILE* 2.8 27.5 + - - +
134A ARG* 3.9 10.1 - - - +
137A ALA* 4.4 16.2 - - + -
138A ILE* 4.4 19.1 - - + +
141A LEU* 4.6 11.4 - - + -
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Residues in contact with LEU 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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113A LEU* 5.3 6.1 - - + -
115A LEU 5.0 1.8 - - - +
116A ASP 5.1 0.2 - - - -
117A GLU* 4.9 25.1 - - + +
122A MET* 4.2 33.9 - - + +
123A ARG* 2.7 17.5 + - - +
125A ALA* 1.3 72.1 - - - +
127A ALA* 1.3 56.4 + - - -
128A ILE 5.0 0.2 - - - -
134A ARG* 4.7 12.7 + - + -
138A ILE* 4.1 24.5 - - + -
221A SER* 4.2 19.3 - - - +
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Residues in contact with ALA 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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123A ARG 3.3 10.0 + - - +
124A GLN* 4.6 6.5 - - - +
125A ALA 2.5 7.1 + - - -
126A LEU* 1.3 76.7 - - - +
128A ILE* 1.3 65.1 + - - +
129A LYS* 2.8 20.8 + - - +
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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