Contacts of the strand formed by residues 126 - 138 (chain A) in PDB entry 2JQY
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 LEU 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A LYS* 3.7 9.9 - - - +
122A LEU* 4.0 9.8 + - + -
123A THR* 3.3 45.7 + - + +
125A ASP* 1.3 87.0 - - + +
127A ARG* 1.3 61.3 + - - +
157A LEU* 4.0 16.2 - - + -
159A TYR* 3.1 47.1 - - + -
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Residues in contact with ARG 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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81A ASP* 6.0 0.2 + - - -
120A VAL 4.7 2.2 - - - -
121A LYS* 4.0 35.7 - - + +
122A LEU* 5.8 0.9 - - - -
125A ASP 5.4 2.8 + - - +
126A LEU* 1.3 79.1 - - - +
128A PHE* 1.3 61.4 + - - +
129A ASN* 5.2 6.3 - - - +
156A GLY 4.6 0.2 - - - -
157A LEU* 3.2 23.5 - - - +
158A GLN* 3.0 52.4 + - + +
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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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118A TRP 5.7 0.2 - - - -
119A ASP* 3.5 0.7 - - - +
120A VAL* 2.9 63.7 + - + +
122A LEU* 3.9 22.6 - - + +
127A ARG* 1.3 73.7 - - - +
129A ASN* 1.3 87.7 + - - +
130A GLY* 5.5 0.7 - - - -
155A THR* 3.0 34.3 - - + -
156A GLY 3.7 0.7 - - - -
157A LEU* 3.0 26.9 - - + -
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Residues in contact with ASN 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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117A ASP* 5.6 2.0 + - - -
118A TRP* 3.3 5.4 - - - -
119A ASP* 2.9 26.0 + - - +
127A ARG* 5.1 6.0 - - - +
128A PHE* 1.3 98.1 + - - +
130A GLY* 1.3 59.0 + - - +
154A GLU 4.3 0.2 - - - -
155A THR* 3.5 6.2 - - - -
156A GLY* 2.7 43.6 + - - +
168A ARG* 3.5 23.5 - - - +
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Residues in contact with GLY 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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116A PRO 2.7 26.5 - - - +
118A TRP* 2.8 30.9 + - - +
128A PHE* 5.5 1.8 - - - -
129A ASN* 1.3 77.3 - - - +
131A TRP* 1.3 59.6 + - - +
132A LEU* 5.8 2.2 - - - -
154A GLU 3.2 7.9 - - - -
155A THR* 4.7 0.9 - - - -
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Residues in contact with TRP 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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74A HIS* 5.6 6.5 - + - -
88A THR* 3.6 22.2 - - + -
113A LYS* 5.5 13.7 - - - -
115A ALA* 3.4 27.0 + - + +
117A ASP* 2.6 38.9 + - - -
130A GLY* 1.3 80.0 - - - -
132A LEU* 1.3 61.5 + - - +
133A SER* 6.0 3.4 - - - -
154A GLU* 2.8 69.9 + - + +
170A ASN* 5.9 1.1 - - - +
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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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114A ILE 2.7 25.8 - - - +
115A ALA* 3.4 2.2 - - - -
116A PRO* 3.1 34.3 + - + +
130A GLY* 4.2 2.6 + - - -
131A TRP* 1.3 72.4 - - - +
133A SER* 1.3 57.5 + - - +
134A MET* 3.3 28.9 + - + +
151A VAL* 4.0 12.3 - - + -
152A GLU 3.1 9.6 - - - +
153A THR* 3.4 33.7 - - - +
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Residues in contact with SER 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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113A LYS* 4.8 8.4 - - - +
114A ILE 3.8 3.4 - - - -
115A ALA* 5.2 2.7 - - - +
131A TRP* 3.8 3.5 - - - +
132A LEU* 1.3 69.1 - - - +
134A MET* 1.3 61.4 + - - +
135A TYR* 3.1 33.0 + - - -
150A ARG 3.8 1.0 - - - +
151A VAL* 3.5 3.1 + - - -
152A GLU* 2.6 46.8 + - - +
154A GLU* 3.2 22.4 + - - -
172A TYR* 4.4 7.0 + - - -
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Residues in contact with MET 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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112A TRP 3.1 13.3 - - - +
113A LYS* 3.3 15.1 - - - +
114A ILE* 3.1 36.3 + - + +
116A PRO* 5.5 7.6 - - + -
132A LEU* 3.8 34.8 - - + +
133A SER* 1.3 76.5 + - - +
135A TYR* 1.3 62.9 + - - +
136A LYS* 5.2 13.7 - - - +
149A THR* 6.2 2.7 - - + -
150A ARG 3.3 10.8 - - - +
151A VAL* 4.0 15.9 - - + -
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Residues in contact with TYR 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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92A ARG* 3.3 38.9 + - - -
111A ARG* 5.2 12.8 - - + -
112A TRP 3.4 9.6 - - - -
113A LYS* 3.2 33.7 + - + -
133A SER* 3.1 29.6 + - - -
134A MET* 1.3 74.1 - - - +
136A LYS* 1.3 66.1 + - - +
137A PHE* 4.1 17.8 + + + -
148A ASP 4.6 0.7 - - - +
149A THR* 4.3 1.4 - - - -
150A ARG* 3.3 50.1 + - + +
152A GLU* 5.2 7.0 - - - -
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Residues in contact with LYS 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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110A GLN 3.7 0.2 - - - +
111A ARG* 3.2 7.1 - - - +
112A TRP* 3.1 56.1 + - + -
114A ILE* 4.9 16.6 - - - -
134A MET* 5.2 11.8 - - - +
135A TYR* 1.3 75.7 + - - +
137A PHE* 1.3 69.4 + - - +
138A ALA 3.7 0.2 + - - -
148A ASP 4.6 10.5 - - - +
149A THR* 3.4 33.0 + - - +
150A ARG 5.2 1.6 + - - -
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Residues in contact with PHE 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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109A MET* 4.0 14.1 - - + -
110A GLN 3.8 3.4 - - - -
111A ARG* 3.3 52.5 - - - -
112A TRP* 5.2 0.5 - - - -
135A TYR* 4.7 19.1 - + + -
136A LYS* 1.3 80.0 - - - +
138A ALA* 1.3 60.8 + - - +
142A ASN* 5.3 8.5 + - - +
145A GLY 4.8 14.8 - - - +
146A TYR* 6.3 4.5 - + + -
147A ALA* 4.5 15.3 - - + +
148A ASP 5.0 8.5 + - - +
150A ARG* 3.3 44.0 - - + -
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Residues in contact with ALA 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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109A MET* 3.4 8.4 - - - +
110A GLN* 2.6 56.6 + - + +
112A TRP* 3.6 28.7 - - + -
137A PHE* 1.3 77.0 - - - +
139A ASN* 1.3 59.5 + - - +
142A ASN* 5.3 2.9 - - - -
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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