Contacts of the strand formed by residues 120 - 132 (chain A) in PDB entry 2NQY
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 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ILE 4.1 0.2 - - - +
116A THR* 3.4 8.8 - - - +
117A VAL 3.0 30.9 + - - +
118A ASP 3.2 1.4 - - - -
119A GLY* 1.3 79.3 - - - +
121A THR* 1.3 62.8 + - - -
122A TYR* 4.3 3.3 - - - -
148A ARG* 3.5 19.1 - - - -
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Residues in contact with THR 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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114A THR* 4.0 20.2 - - + +
115A ILE 3.5 6.1 - - - +
116A THR* 3.2 25.4 + - - +
120A GLY* 1.3 73.9 + - - -
122A TYR* 1.3 60.7 + - - +
148A ARG* 3.6 3.1 - - - +
149A ARG* 2.8 69.0 + - - +
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Residues in contact with TYR 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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97A ILE* 4.0 6.3 - - + -
98A VAL 3.7 4.3 - - - -
99A ASP* 2.6 31.2 + - - -
114A THR* 3.1 9.0 - - - -
115A ILE* 2.8 50.7 + - + +
117A VAL* 3.6 25.4 - - + -
118A ASP* 4.6 2.5 + - + +
120A GLY 4.4 1.1 - - - -
121A THR* 1.3 79.9 - - - +
123A ASP* 1.3 61.1 + - - +
146A SER* 3.9 7.2 - - - -
147A THR 3.2 17.3 - - - +
148A ARG* 2.7 58.5 + - + -
152A ARG* 3.6 6.1 + - - -
157A ILE* 4.7 3.5 - - - +
162A HIS* 3.7 25.9 + + - -
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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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105A ARG* 2.9 27.9 + - - +
111A PRO* 4.1 17.8 - - + +
113A GLY 3.6 2.7 - - - -
114A THR* 3.6 7.6 - - - +
122A TYR* 1.3 73.4 - - - +
124A ILE* 1.3 59.9 + - - +
125A TYR* 3.3 32.7 - - + +
146A SER* 3.4 3.1 - - - -
147A THR 2.9 30.4 + - - -
149A ARG* 3.0 38.6 + - - +
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Residues in contact with ILE 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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111A PRO* 3.2 4.9 - - - +
112A LYS* 2.7 33.2 + - + -
113A GLY 2.8 15.3 + - - +
114A THR* 3.7 26.7 - - - +
115A ILE* 3.8 17.7 - - + -
123A ASP* 1.3 74.9 - - - +
125A TYR* 1.3 61.2 + - - +
145A TRP 3.2 4.3 - - - +
146A SER* 3.8 15.0 - - - +
165A ALA* 4.2 12.3 - - + -
166A TRP* 3.6 17.5 - - + -
169A LEU* 3.7 24.5 - - + -
171A MET* 3.5 30.1 - - + -
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Residues in contact with TYR 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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105A ARG* 3.3 20.4 + - - -
106A PRO 4.5 1.7 + - - -
107A PRO* 3.5 42.4 - - + -
109A ALA* 3.2 38.8 - - + -
110A THR 3.8 3.6 - - - +
111A PRO* 3.7 24.8 - - + +
112A LYS* 4.3 4.7 - - - -
123A ASP* 3.3 41.9 - - + +
124A ILE* 1.3 73.9 - - - +
126A GLU* 1.3 60.9 + - - +
144A TYR* 3.6 0.2 - - - -
145A TRP* 2.9 41.3 + - + -
147A THR* 4.0 11.9 - - - -
171A MET* 3.2 11.1 - - - +
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Residues in contact with GLU 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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109A ALA* 4.9 4.7 - - - +
110A THR 5.2 1.3 + - - +
112A LYS* 3.7 32.7 + - + +
125A TYR* 1.3 75.3 - - - +
127A THR* 1.3 74.5 + - - +
142A SER* 4.0 10.3 + - - -
143A GLN 3.3 10.1 - - - +
144A TYR* 3.3 29.4 + - + -
170A GLY 4.9 2.5 - - - +
171A MET* 4.0 15.6 - - + +
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Residues in contact with THR 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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107A PRO* 4.2 14.4 - - + +
108A GLY 5.7 0.2 - - - +
109A ALA* 4.0 23.8 - - + -
125A TYR 4.3 0.2 - - - -
126A GLU* 1.3 82.0 - - - +
128A ASP* 1.3 62.8 + - - +
142A SER* 3.3 8.5 + - - -
143A GLN* 2.7 56.3 + - - +
145A TRP* 3.2 18.4 + - - +
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Residues in contact with ASP 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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127A THR* 1.3 78.5 - - - +
129A ARG* 1.3 75.8 + - - +
130A THR* 3.9 17.1 + - - -
140A THR* 4.1 9.2 - - - +
141A PHE 3.5 12.7 - - - +
142A SER* 4.4 5.5 + - - +
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Residues in contact with ARG 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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128A ASP* 1.3 76.4 - - - +
130A THR* 1.3 61.0 - - - +
132A GLN* 3.2 42.8 + - + +
133A PRO* 4.6 0.8 - - - +
139A ALA 4.0 0.6 - - - +
140A THR* 3.2 8.2 - - - +
141A PHE* 2.9 60.6 + - + +
143A GLN* 3.6 32.8 - - + -
3001A XYP 2.6 34.6 + - - -
1C XYP 3.2 32.3 + - - -
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Residues in contact with THR 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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128A ASP* 3.9 16.2 + - - +
129A ARG* 1.3 71.3 - - - +
131A ASN* 1.3 87.6 + - - +
132A GLN* 3.3 16.2 + - - +
140A THR* 3.5 13.8 - - + +
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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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130A THR* 1.3 86.3 - - + +
132A GLN* 1.3 64.6 + - - +
133A PRO* 4.7 0.9 - - - +
138A VAL* 3.6 27.8 - - + +
139A ALA* 3.1 15.3 + - - -
140A THR* 3.1 14.3 + - - -
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Residues in contact with GLN 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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129A ARG* 3.2 58.0 + - + +
130A THR 3.4 18.5 + - - +
131A ASN* 1.3 78.9 + - - +
133A PRO* 1.3 85.1 - - + +
134A SER 3.5 0.2 + - - -
138A VAL* 3.3 4.9 - - - -
139A ALA* 2.8 30.7 + - - +
141A PHE* 4.1 8.8 - - + -
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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