Contacts of the helix formed by residues 133 - 143 (chain A) in PDB entry 4YVF
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 GLY 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ASP* 3.1 16.2 + - - -
131A ASP 3.5 0.8 - - - -
132A GLY* 1.3 78.0 - - - +
134A ASP* 1.3 53.6 + - - +
136A THR* 3.0 8.4 + - - -
137A ASN* 2.7 45.0 + - - -
155A GLU* 3.2 13.7 + - - -
160A GLY* 4.4 6.3 - - - -
163A ASN* 4.7 4.9 - - - -
164A LEU* 6.5 0.4 - - - -
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Residues in contact with ASP 134 (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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53A CYS* 4.4 4.9 - - - -
79A CYS* 4.1 5.7 - - + +
110A TYR* 2.5 39.4 + - - +
114A ILE* 4.0 12.6 - - + -
130A ASP* 3.6 1.2 + - - -
131A ASP 5.8 0.7 - - - +
132A GLY* 3.3 9.2 - - - +
133A GLY* 1.3 75.0 - - - +
135A LEU* 1.3 59.0 + - - +
137A ASN* 3.1 9.8 + - - +
138A LEU* 2.8 32.7 + - - +
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Residues in contact with LEU 135 (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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51A ALA* 3.0 39.3 - - + +
52A GLY 4.1 0.4 - - - -
53A CYS* 3.6 24.5 - - + +
114A ILE* 3.6 27.4 - - + -
117A THR* 4.6 5.2 - - - +
118A LEU* 3.9 23.1 - - + -
125A LEU* 4.8 1.1 - - + -
128A ILE* 3.9 23.8 - - + -
129A LEU 4.1 1.6 - - - +
130A ASP* 3.2 15.4 + - - +
134A ASP* 1.3 78.4 - - - +
136A THR* 1.3 62.8 + - - +
138A LEU* 3.5 1.4 + - + +
139A ILE* 3.2 34.0 + - + +
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Residues in contact with THR 136 (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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128A ILE* 3.8 15.7 - - - +
130A ASP* 2.6 33.9 + - - +
133A GLY* 3.4 8.4 - - - -
135A LEU* 1.3 79.1 - - - +
137A ASN* 1.3 62.0 + - - +
139A ILE* 3.6 1.2 + - - +
140A HIS* 2.9 42.3 + - + +
153A ILE* 3.5 31.4 - - + +
155A GLU* 4.6 1.0 + - - -
163A ASN* 5.4 1.6 - - - +
164A LEU* 3.9 19.4 - - + +
167A MET* 4.5 7.4 - - - -
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Residues in contact with ASN 137 (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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132A GLY 5.1 2.0 + - - -
133A GLY* 2.7 25.8 + - - +
134A ASP* 3.8 8.4 + - - +
136A THR* 1.3 70.5 - - - +
138A LEU* 1.3 59.3 + - - +
140A HIS* 4.6 3.0 - - - +
141A THR* 2.7 46.9 + - - +
163A ASN* 2.9 39.1 + - - +
167A MET* 3.7 12.0 - - - +
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Residues in contact with LEU 138 (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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111A LEU* 4.3 21.8 - - + +
114A ILE* 3.4 32.5 - - + -
115A GLU* 3.8 23.3 - - + +
118A LEU* 4.1 17.3 - - + -
134A ASP 2.8 20.5 + - - +
135A LEU* 3.7 4.9 - - + +
137A ASN* 1.3 73.2 - - - +
139A ILE* 1.3 56.0 + - - +
141A THR* 4.9 1.6 - - - -
142A LYS* 2.7 56.6 + - + +
143A TYR* 3.2 11.9 + - + -
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Residues in contact with ILE 139 (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 LEU* 3.2 43.1 - - + -
125A LEU* 4.6 7.6 - - + -
128A ILE* 4.1 15.9 - - + -
135A LEU* 3.2 22.5 + - + +
136A THR 3.9 3.6 - - - +
137A ASN 3.2 0.4 - - - -
138A LEU* 1.3 78.6 - - + +
140A HIS* 1.3 58.3 + - - +
143A TYR* 2.7 51.8 + - + +
144A PRO* 2.8 3.3 - - - +
146A LEU* 4.4 7.2 - - + -
147A LEU* 3.4 25.8 - - + +
150A ILE* 3.7 15.9 - - + -
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Residues in contact with HIS 140 (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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128A ILE* 5.8 0.7 - - + -
136A THR* 2.9 34.7 + - + +
137A ASN* 4.0 3.8 - - - +
139A ILE* 1.3 80.9 - - + +
141A THR* 1.3 62.5 + - - +
144A PRO* 3.9 13.7 - - - +
147A LEU* 3.3 43.6 - - + +
153A ILE* 4.2 9.0 - - + -
167A MET* 3.3 28.9 - - + +
172A ILE* 3.3 28.7 - - + +
173A LEU* 3.8 12.6 - - + -
174A LYS* 3.1 21.2 + - - +
175A VAL 4.7 1.6 - - - -
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Residues in contact with THR 141 (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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137A ASN* 2.7 31.5 + - - +
138A LEU* 4.4 1.6 - - - -
140A HIS* 1.3 77.5 - - - +
142A LYS* 1.3 62.2 + - + +
144A PRO* 4.0 5.6 - - - +
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Residues in contact with LYS 142 (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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111A LEU* 5.1 10.0 - - + +
115A GLU* 2.6 34.8 + - - +
138A LEU* 2.7 31.2 + - + +
141A THR* 1.3 76.5 - - + +
143A TYR* 1.3 79.9 + - + +
144A PRO* 3.3 9.0 - - - +
145A GLN* 3.9 5.9 + - - +
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Residues in contact with TYR 143 (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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115A GLU* 2.6 35.9 + - + +
118A LEU* 3.4 31.2 - - + -
119A TYR* 4.6 15.9 - + - -
138A LEU* 3.2 20.2 + - + -
139A ILE* 2.7 23.4 + - + +
142A LYS* 1.3 105.2 + - + +
144A PRO* 1.3 61.6 - - - +
145A GLN* 3.0 15.5 - - - -
146A LEU* 2.9 38.3 + - + +
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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