Contacts of the helix formed by residues 120 - 134 (chain A) in PDB entry 2Y4U
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 LYS 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A LEU* 5.1 8.5 - - - +
115A LEU* 2.8 26.0 + - + +
118A GLN* 3.3 31.6 + - + +
119A GLY* 1.3 76.1 - - - +
121A LEU* 1.3 60.5 + - - +
123A GLU* 3.0 40.8 - - - +
124A ALA 3.2 14.6 + - - -
158A ARG* 5.7 0.4 - - - +
189A GLU* 6.1 1.3 - - - +
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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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116A LEU* 3.8 28.0 - - + -
119A GLY* 3.1 25.6 + - - +
120A LYS* 1.3 67.9 - - - +
122A ASP* 1.3 67.7 + - - +
123A GLU* 3.9 0.2 + - - -
124A ALA* 3.1 7.2 + - - +
125A GLU* 2.9 26.3 + - - +
151A SER* 4.4 7.4 - - - +
154A MSE 3.9 19.1 - - + -
155A GLN* 3.3 52.0 - - - +
158A ARG* 4.3 22.0 - - + +
180A ILE* 6.3 1.1 - - + -
184A CYS* 4.3 5.2 - - - -
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Residues in contact with ASP 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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120A LYS 3.6 0.4 - - - -
121A LEU* 1.3 74.2 - - - +
123A GLU* 1.3 74.8 + - - +
125A GLU* 3.4 11.6 + - - +
126A ASP* 2.9 36.7 + - - +
155A GLN* 2.8 35.8 + - - +
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Residues in contact with GLU 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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111A ARG* 5.7 0.2 + - - -
115A LEU* 4.0 21.6 - - + +
120A LYS* 3.0 48.0 - - - +
122A ASP* 1.3 84.3 + - - +
124A ALA* 1.3 60.8 - - - +
126A ASP* 3.7 11.6 + - - +
127A ASP* 3.4 22.5 + - - +
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Residues in contact with ALA 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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112A GLY* 3.9 13.8 - - - +
115A LEU* 3.7 29.8 - - + +
116A LEU* 4.1 7.4 - - + +
120A LYS 3.2 12.5 + - - +
121A LEU* 3.1 12.7 + - - +
123A GLU* 1.3 73.8 - - - +
125A GLU* 1.3 54.3 + - - +
127A ASP* 2.9 5.1 + - - +
128A PHE* 2.8 47.2 + - + -
151A SER* 5.3 0.9 - - - +
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Residues in contact with GLU 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 2.9 13.4 + - - +
122A ASP* 3.6 12.1 - - - +
124A ALA* 1.3 74.3 - - - +
126A ASP* 1.3 56.0 + - - +
127A ASP 2.8 11.3 + - - -
128A PHE* 2.9 19.6 + - + +
129A LYS* 3.0 34.1 + - - +
148A LEU* 4.8 12.1 - - + -
151A SER* 2.7 33.5 + - - +
152A ASP* 3.4 20.6 - - - +
155A GLN* 3.0 25.5 - - - +
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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 ASP* 2.9 26.5 + - - +
123A GLU* 3.8 9.6 - - - +
124A ALA 3.3 0.2 - - - -
125A GLU* 1.3 75.9 - - - +
127A ASP* 1.3 56.8 + - - +
129A LYS* 4.4 10.9 - - - +
130A LYS* 3.3 37.2 + - - +
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Residues in contact with ASP 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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108A ARG* 3.2 44.7 + - + +
111A ARG* 2.7 45.4 + - - +
112A GLY* 4.5 3.4 - - - -
115A LEU* 3.5 12.2 - - + +
123A GLU 3.4 10.3 + - - +
124A ALA 2.9 9.4 + - - +
126A ASP* 1.3 77.6 - - - +
128A PHE* 1.3 66.4 + - - +
129A LYS 3.1 2.7 + - - -
130A LYS* 3.3 7.1 + - - +
131A VAL* 3.3 24.5 + - - +
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Residues in contact with PHE 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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108A ARG 5.8 0.2 - - - -
109A LEU* 4.5 17.7 - - + -
112A GLY* 3.8 34.1 - - - -
113A HIS* 4.0 4.3 - + - -
116A LEU* 4.6 10.8 - - + -
124A ALA* 2.8 28.8 + - + -
125A GLU* 3.4 8.1 - - - +
127A ASP* 1.3 76.8 - - - +
129A LYS* 1.3 59.5 + - - +
131A VAL* 3.5 8.7 - - + +
132A LEU* 3.5 23.0 + - - +
144A ALA* 4.1 24.0 - - + +
147A GLN* 3.4 47.8 - - + -
148A LEU* 3.1 32.0 - - + +
151A SER* 5.2 2.2 - - - -
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Residues in contact with LYS 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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125A GLU* 3.0 33.5 + - - +
126A ASP* 4.8 9.0 - - - +
128A PHE* 1.3 73.8 - - - +
130A LYS* 1.3 52.1 + - + +
131A VAL 2.9 4.5 - - - -
132A LEU* 2.9 13.0 + - + +
133A LYS* 2.7 66.3 + - + +
148A LEU* 3.7 29.4 - - + -
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Residues in contact with LYS 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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105A THR* 5.7 1.7 - - - +
108A ARG* 4.0 33.3 - - - +
111A ARG* 6.1 0.4 - - - +
126A ASP* 3.3 24.8 - - - +
127A ASP* 3.3 13.2 + - - +
129A LYS* 1.3 75.4 - - + +
131A VAL* 1.3 58.1 + - - +
133A LYS* 3.8 12.1 - - + +
134A SER* 3.3 28.6 + - - +
135A ASN 4.6 0.3 + - - -
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Residues in contact with VAL 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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105A THR* 4.1 17.7 - - - +
108A ARG* 3.9 14.6 - - + -
109A LEU* 3.8 39.5 - - + +
127A ASP 3.3 13.6 + - - +
128A PHE* 3.5 10.8 - - - +
129A LYS 2.9 0.8 - - - -
130A LYS* 1.3 76.8 - - - +
132A LEU* 1.3 65.1 + - + +
133A LYS 3.1 4.3 + - - -
135A ASN 3.8 6.6 + - - +
136A PRO* 3.4 22.1 - - + +
140A GLU* 5.1 14.6 - - + +
141A GLU 5.7 0.2 - - - +
144A ALA* 4.1 21.3 - - + -
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Residues in contact with LEU 132 (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 PHE 3.5 13.0 + - - +
129A LYS* 2.9 11.0 + - + +
131A VAL* 1.3 78.5 - - + +
133A LYS* 1.4 62.4 + - + +
136A PRO* 3.0 26.3 - - + +
141A GLU* 3.6 45.8 - - + +
144A ALA* 3.8 9.4 - - + -
145A GLN* 4.4 28.0 - - + +
148A LEU* 4.8 9.2 - - + -
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Residues in contact with LYS 133 (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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129A LYS* 2.7 50.5 + - + +
130A LYS* 4.1 8.3 - - + +
131A VAL 3.1 0.2 - - - -
132A LEU* 1.4 85.2 - - + +
134A SER* 1.3 65.9 + - - +
136A PRO* 3.9 6.5 - - - +
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Residues in contact with SER 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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105A THR* 5.6 4.0 - - - -
130A LYS* 3.3 19.3 + - - +
133A LYS* 1.3 79.6 - - - +
135A ASN* 1.3 61.6 + - - +
136A PRO* 3.4 6.4 - - - +
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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