Contacts of the helix formed by residues 126 - 140 (chain A) in PDB entry 2BQY
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 SER 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A ASP 3.6 2.6 + - - -
125A LEU* 1.3 76.3 - - - +
127A LYS* 1.3 64.7 + - - +
128A HIS* 3.6 9.5 + - - +
129A THR* 3.2 33.9 + - - -
130A LEU* 3.4 11.8 + - - +
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Residues in contact with LYS 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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125A LEU 3.7 1.0 + - - -
126A SER* 1.3 72.1 - - - +
128A HIS* 1.3 68.1 + - - +
130A LEU* 3.1 12.7 + - - +
131A ASP* 2.7 55.7 + - - +
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Residues in contact with HIS 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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126A SER* 3.2 9.1 + - - +
127A LYS* 1.3 85.1 + - - +
129A THR* 1.3 69.3 + - - +
131A ASP* 3.3 7.2 + - - +
132A LYS* 3.0 51.7 + - + +
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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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51A PRO 5.8 2.2 - - - +
73A LEU* 4.2 15.7 - - + -
125A LEU* 5.2 7.6 - - + -
126A SER* 3.2 23.5 + - - -
127A LYS 3.3 0.2 - - - -
128A HIS* 1.3 83.5 - - - +
130A LEU* 1.3 64.1 + - + +
132A LYS* 3.3 9.3 + - + +
133A ILE* 3.0 42.9 + - + +
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Residues in contact with LEU 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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122A ILE* 3.8 32.3 - - + +
123A ASP* 5.5 2.5 - - - -
125A LEU* 3.9 28.3 - - + +
126A SER 3.4 15.9 + - - +
127A LYS* 3.1 11.3 + - - +
129A THR* 1.3 76.3 - - - +
131A ASP* 1.3 60.4 + - - +
133A ILE* 3.5 4.6 + - + +
134A LYS* 3.0 32.5 + - - +
154A PHE* 3.5 44.3 - - + -
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Residues in contact with ASP 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 LYS* 2.7 54.0 + - - +
128A HIS* 3.7 5.2 - - - +
130A LEU* 1.3 76.9 - - - +
132A LYS* 1.3 60.7 + - - +
134A LYS* 3.8 19.8 + - - +
135A HIS* 2.8 33.0 + - - +
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Residues in contact with LYS 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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51A PRO* 4.2 23.8 - - + +
128A HIS* 3.0 43.4 + - + +
129A THR* 3.6 8.3 - - + +
131A ASP* 1.3 76.2 - - - +
133A ILE* 1.3 58.8 + - + +
135A HIS* 3.8 5.5 + - - +
136A PHE* 2.9 29.6 + - + +
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Residues in contact with ILE 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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51A PRO* 3.9 29.6 - - + +
52A ALA* 5.3 0.2 - - + -
71A LEU* 4.0 12.1 - - + -
73A LEU* 4.0 26.7 - - + -
92A LEU* 4.0 12.1 - - + -
105A ILE* 5.5 3.4 - - + -
129A THR* 3.0 35.9 + - + +
130A LEU* 3.8 9.6 - - + +
132A LYS* 1.3 76.8 - - + +
134A LYS* 1.3 62.1 + - - +
136A PHE* 3.3 1.9 + - - +
137A PHE* 3.1 52.5 + - + -
154A PHE* 4.2 10.8 - - + -
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Residues in contact with LYS 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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92A LEU* 4.8 7.4 - - - -
130A LEU* 3.0 18.5 + - - +
131A ASP* 3.8 21.7 + - - +
133A ILE* 1.3 78.7 - - - +
135A HIS* 1.3 58.4 + - - +
137A PHE* 3.5 0.7 + - - -
138A GLU* 3.0 29.9 + - + +
151A VAL* 3.4 36.6 - - + +
152A LYS 5.3 1.7 + - - +
153A GLY* 4.8 10.3 - - - -
154A PHE* 4.3 20.9 - - + -
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Residues in contact with HIS 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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48A GLN* 5.5 2.2 + - - -
131A ASP 2.8 19.4 + - - +
132A LYS* 3.8 5.3 + - - +
134A LYS* 1.3 75.2 - - - +
136A PHE* 1.3 66.1 + - - +
138A GLU* 3.4 7.0 + - + -
139A THR* 2.8 56.3 + - + +
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Residues in contact with PHE 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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44A LEU* 3.9 9.6 - - + -
48A GLN* 3.7 15.9 + - + +
49A ASN 3.5 31.9 - - - -
50A TYR* 3.7 43.3 - + - -
51A PRO* 3.5 20.0 - - + -
132A LYS* 2.9 19.0 + - + +
133A ILE 3.4 5.2 - - - +
134A LYS 3.3 0.2 - - - -
135A HIS* 1.3 78.7 - - - +
137A PHE* 1.3 71.4 + + - +
139A THR* 3.2 3.6 + - - -
140A TYR* 2.7 75.0 + + + +
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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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50A TYR* 5.1 4.7 - + - -
51A PRO* 5.1 1.3 - - + -
54A TYR* 4.5 10.5 - + - -
71A LEU* 3.5 35.4 - - + -
92A LEU* 3.8 17.9 - - + -
94A MET* 3.7 25.6 - - + -
103A LYS* 3.7 26.9 - - + -
133A ILE* 3.1 29.4 + - + +
134A LYS 4.0 2.9 - - - +
136A PHE* 1.3 98.9 - + - +
138A GLU* 1.3 61.2 + - - +
139A THR 3.1 0.7 - - - -
140A TYR* 3.2 40.0 + + - -
141A LYS 4.9 0.3 + - - -
149A VAL* 3.2 22.8 - - - +
151A VAL* 4.2 4.0 - - + -
1174A POP 5.7 0.4 - - - -
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Residues in contact with GLU 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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134A LYS* 3.0 20.0 + - + +
135A HIS* 3.8 10.1 - - + +
136A PHE 3.2 0.4 - - - -
137A PHE* 1.3 76.4 - - - +
139A THR* 1.3 67.4 + - + +
142A ASP* 3.5 7.8 - - - +
149A VAL* 3.0 28.2 + - - +
150A LYS* 3.7 8.0 - - - +
151A VAL* 2.9 38.7 + - + +
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Residues in contact with THR 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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48A GLN* 3.1 22.2 + - - +
135A HIS* 2.8 46.1 + - + +
136A PHE 3.2 0.2 + - - -
138A GLU* 1.3 90.9 - - + +
140A TYR* 1.3 58.2 + - - +
141A LYS 2.8 12.4 + - - -
142A ASP* 3.0 37.7 + - - +
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Residues in contact with TYR 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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28A LYS* 5.6 2.5 - - + -
42A ARG* 6.6 0.2 - - - -
44A LEU* 4.0 22.1 - - + +
45A TYR* 5.2 6.1 + - - +
46A GLY 5.5 1.6 + - - -
48A GLN* 3.2 23.4 - - - +
50A TYR* 3.8 16.8 - + - -
94A MET* 5.7 0.9 - - - -
103A LYS* 4.9 0.2 - - - -
136A PHE* 2.7 51.3 + + + +
137A PHE* 3.2 49.8 - + - -
139A THR* 1.3 71.2 + - - +
141A LYS* 1.3 79.0 + - + +
142A ASP 3.6 0.4 - - - -
144A GLU* 3.9 9.8 - - - +
149A VAL* 3.9 9.2 - - + +
1174A POP 3.6 38.0 + - - -
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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