Contacts of the helix formed by residues 127 - 137 (chain A) in PDB entry 2P82
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 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A GLN* 3.7 2.5 - - - +
117A CYS 3.4 2.3 + - - -
118A PHE 4.5 0.7 - - - -
119A LEU 3.0 22.4 - - - -
121A ARG 2.8 30.7 + - - -
124A CYS* 2.8 16.6 + - - -
125A CYS 3.6 0.8 + - - -
126A TYR* 1.3 82.6 - - - +
128A ILE* 1.3 65.7 + - - +
129A HIS* 3.6 5.4 + - - +
130A GLN* 3.1 21.9 + - - +
131A MET* 3.0 21.2 + - - +
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Residues in contact with ILE 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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61A PHE* 3.9 19.5 - - + -
64A ILE* 4.5 4.3 - - + -
72A ASP* 3.9 25.8 - - + +
75A TRP* 4.5 8.5 - - + -
76A GLY 4.5 0.9 - - - +
79A LEU* 3.7 38.8 - - + -
80A ARG* 3.9 29.4 - - - +
83A GLN* 3.5 9.6 - - - +
119A LEU 4.4 1.0 + - - -
120A ASP* 3.8 19.0 + - + +
127A SER* 1.3 72.3 - - - +
129A HIS* 1.3 75.2 + - + +
131A MET* 3.3 3.6 + - - +
132A ALA* 2.9 34.4 + - - +
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Residues in contact with HIS 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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61A PHE* 3.3 27.7 - + + -
62A SER* 2.5 32.2 + - - -
63A PRO 4.5 1.8 - - - -
64A ILE* 3.6 32.1 - - + +
65A GLY 5.1 1.3 - - - -
120A ASP 3.2 32.8 - - - -
121A ARG* 3.8 0.8 + - - -
122A LYS* 3.8 31.5 + - + -
127A SER* 3.1 8.0 - - - +
128A ILE* 1.3 82.1 - - + +
130A GLN* 1.3 58.5 + - + +
132A ALA* 4.1 1.4 - - - +
133A GLN* 3.0 30.7 + - - +
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Residues in contact with GLN 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 LYS* 3.0 37.6 + - - +
124A CYS 3.4 13.9 - - - +
125A CYS* 3.7 20.9 - - - +
127A SER* 3.1 20.7 + - - +
129A HIS* 1.3 76.9 - - - +
131A MET* 1.3 61.0 + - - +
133A GLN* 3.8 7.4 - - - +
134A MET* 2.9 35.7 + - - +
158A LEU* 3.9 17.4 - - + +
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Residues in contact with MET 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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79A LEU* 3.5 37.2 - - + +
83A GLN* 3.5 34.1 - - - +
118A PHE* 6.1 0.2 - - - -
126A TYR* 4.0 9.0 - - - +
127A SER 3.0 16.4 + - - +
128A ILE* 3.8 4.9 - - - +
130A GLN* 1.3 77.4 - - - +
132A ALA* 1.3 57.5 + - - +
134A MET* 3.3 3.5 + - - +
135A GLY* 3.0 24.4 + - - -
146A PHE* 4.6 1.9 - - - -
151A VAL* 3.7 27.6 - - + -
154A VAL* 3.7 13.0 - - + +
155A LEU* 3.9 22.7 - - + -
158A LEU* 3.6 21.8 - - + -
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Residues in contact with ALA 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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64A ILE* 4.3 9.0 - - + -
75A TRP* 4.1 29.8 - - + -
79A LEU* 4.2 8.4 - - + +
128A ILE 2.9 18.1 + - - +
129A HIS 4.1 2.5 - - - +
131A MET* 1.3 75.4 - - - +
133A GLN* 1.3 62.7 + - - +
135A GLY* 3.1 12.2 + - - -
136A VAL* 3.4 13.9 + - - +
140A LYS 4.6 1.7 - - - +
141A SER 5.3 0.2 - - - -
142A ILE* 3.9 20.0 - - + +
146A PHE* 5.3 4.1 - - - -
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Residues in contact with GLN 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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64A ILE* 4.1 11.1 - - - +
65A GLY* 4.3 12.2 + - - -
129A HIS 3.0 18.5 + - - +
130A GLN* 3.8 11.7 - - - +
132A ALA* 1.3 78.0 - - - +
134A MET* 1.3 61.1 + - - +
136A VAL* 3.2 31.3 + - - +
137A GLY 4.0 1.6 + - - -
142A ILE* 3.2 30.7 - - - +
188B VAL* 6.3 0.8 - - - +
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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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130A GLN* 2.9 22.5 + - - +
131A MET 3.7 4.0 - - - +
133A GLN* 1.3 73.0 - - - +
135A GLY* 1.3 64.6 + - - +
137A GLY* 3.1 18.4 + - - +
138A GLU* 3.7 8.2 + - - +
154A VAL* 4.0 26.0 - - + +
157A LYS* 3.6 37.2 - - + -
158A LEU* 3.7 24.0 - - + +
161A PHE* 4.3 20.2 - - + -
160B LEU* 4.1 23.6 - - + -
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Residues in contact with GLY 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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131A MET 3.0 14.3 + - - -
132A ALA 3.1 7.0 + - - -
134A MET* 1.3 75.7 - - - +
136A VAL* 1.3 55.1 + - - +
138A GLU* 2.9 23.5 + - - +
139A GLY 3.3 0.2 + - - -
140A LYS* 3.0 23.1 + - - +
146A PHE* 4.1 15.9 - - - -
154A VAL* 3.9 14.3 - - - +
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Residues in contact with VAL 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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132A ALA 3.4 9.4 + - - +
133A GLN* 3.3 22.2 - - - +
134A MET 3.1 0.6 - - - -
135A GLY* 1.3 77.0 - - - +
137A GLY* 1.3 56.2 + - - +
139A GLY* 2.9 18.7 + - - -
140A LYS 3.1 17.7 + - - +
141A SER* 4.7 1.3 - - - -
142A ILE* 3.7 28.7 - - + +
184B LYS 3.4 23.1 - - - +
185B MET* 3.4 26.1 + - - +
187B ARG 4.8 5.8 - - - +
221B LYS* 5.8 2.2 - - + -
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Residues in contact with GLY 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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133A GLN 4.0 1.6 + - - -
134A MET* 3.1 14.2 + - - +
136A VAL* 1.3 78.2 - - - +
138A GLU* 1.3 60.8 + - - +
139A GLY 3.3 1.6 - - - -
157A LYS* 6.0 1.1 - - - -
156B LYS* 2.8 33.8 + - - -
160B LEU* 6.1 4.9 - - - -
185B MET* 3.4 17.7 - - - +
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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