Contacts of the helix formed by residues 121 - 131 (chain A) in PDB entry 1WZV
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 ARG 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ILE 4.1 16.8 + - - -
74A TYR* 4.1 16.2 - - - +
75A HIS 3.8 5.2 - - - -
76A PRO* 2.9 12.5 + - + +
78A VAL 3.3 24.5 - - - +
79A ASP* 4.2 11.2 - - + +
80A GLU* 3.5 41.1 + - + +
119A PRO* 4.2 1.3 - - - -
120A LEU* 1.3 81.7 - - - +
122A MET* 1.3 64.6 + - - +
123A ASP* 3.3 13.5 + - - +
124A LEU* 3.2 41.6 + - + +
125A ALA* 3.1 20.3 + - - +
142A PHE* 5.8 4.0 - - - -
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Residues in contact with MET 122 (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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119A PRO* 3.9 34.8 - - + +
120A LEU 3.8 2.8 + - - +
121A ARG* 1.3 72.2 - - - +
123A ASP* 1.3 57.9 + - - +
125A ALA* 3.2 3.1 + - - +
126A ASP* 2.9 38.3 + - - +
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Residues in contact with ASP 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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121A ARG* 3.9 14.3 + - - +
122A MET* 1.3 74.2 + - - +
124A LEU* 1.3 76.5 + - - +
126A ASP* 3.5 10.0 + - - +
127A LEU* 2.9 29.0 + - - +
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Residues in contact with LEU 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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74A TYR* 3.6 41.3 - - + +
75A HIS* 3.6 37.9 - - - +
76A PRO* 4.0 9.2 - - + -
121A ARG* 3.2 42.3 + - + +
123A ASP* 1.3 94.9 + - - +
125A ALA* 1.3 60.6 + - - +
127A LEU* 4.3 4.7 - - + -
128A LEU* 2.8 31.2 + - - +
135A PHE* 3.6 9.1 - - + -
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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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76A PRO* 3.9 8.9 - - + +
116A ILE* 3.8 25.1 - - + +
119A PRO* 3.6 35.7 - - + -
121A ARG 3.1 5.9 + - - -
122A MET 3.5 7.4 - - - +
124A LEU* 1.3 75.9 - - - +
126A ASP* 1.3 66.1 + - - +
128A LEU* 3.4 2.9 + - - +
129A THR* 3.1 27.5 + - - -
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Residues in contact with ASP 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 MET* 2.9 25.8 + - - +
123A ASP* 3.6 8.1 - - - +
125A ALA* 1.3 77.8 - - - +
127A LEU* 1.3 56.7 + - - +
129A THR* 3.3 5.9 + - - -
130A GLN* 2.9 40.6 + - + +
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Residues in contact with LEU 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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74A TYR* 3.6 12.3 - - - +
123A ASP 2.9 19.2 + - - +
124A LEU* 3.7 5.2 - - + +
126A ASP* 1.3 75.1 - - - +
128A LEU* 1.3 61.0 + - - +
130A GLN* 4.5 3.8 - - + +
131A ASN* 2.8 53.4 + - + +
134A LEU* 3.7 26.2 - - + -
135A PHE* 3.9 20.2 - - + -
138A ASN* 3.5 28.7 - - - +
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Residues in contact with LEU 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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76A PRO* 4.3 7.9 - - + -
114A PRO* 3.8 33.9 - - + -
116A ILE* 4.0 16.8 - - + -
124A LEU 2.8 21.6 + - - +
125A ALA 3.7 5.4 - - - +
127A LEU* 1.3 74.1 - - - +
129A THR* 1.3 59.5 + - - +
132A PRO* 3.4 27.4 - - + +
135A PHE* 3.7 39.0 - - + -
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Residues in contact with THR 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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116A ILE* 3.8 22.8 - - + +
125A ALA 3.1 13.9 + - - -
126A ASP* 3.6 8.3 - - - -
128A LEU* 1.3 80.1 - - - +
130A GLN* 1.3 75.5 + - - +
131A ASN 3.7 0.2 + - - -
132A PRO* 4.1 8.1 - - - +
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Residues in contact with GLN 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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126A ASP* 2.9 29.9 + - + +
127A LEU* 4.2 3.6 - - + +
129A THR* 1.3 87.3 - - - +
131A ASN* 1.3 62.7 + - + +
132A PRO* 3.9 2.8 - - - +
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Residues in contact with ASN 131 (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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127A LEU* 2.8 31.3 + - + +
130A GLN* 1.3 77.7 - - + +
132A PRO* 1.4 60.7 - - - +
133A GLU* 3.5 8.0 + - - +
134A LEU* 3.1 35.0 + - + +
135A PHE 3.0 22.5 + - - -
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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