Contacts of the helix formed by residues 126 - 137 (chain A) in PDB entry 4P22
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 ASN 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A ASP 3.0 28.2 + - - +
104A GLN* 3.8 11.9 + - - +
105A GLY 3.6 14.0 + - - -
106A THR* 4.2 6.7 - - + +
124A GLY 4.2 0.6 + - - -
125A LYS* 1.3 70.8 - - - +
127A ARG* 1.3 68.5 + - - +
128A ALA* 3.2 20.8 + - - +
129A GLU* 3.1 20.7 + - + +
130A VAL* 3.0 24.8 + - - +
148A THR* 3.2 23.2 - - + +
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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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80A LEU* 3.5 24.7 - - + +
81A ARG* 3.7 17.6 - - - +
103A ASP* 2.9 38.0 + - - +
105A GLY* 3.1 22.0 + - - +
106A THR 3.5 12.1 + - - +
107A ALA* 3.7 25.4 - - + +
108A GLN* 4.7 2.8 - - - +
111A ASP* 2.7 43.8 + - - -
118A LEU* 4.2 11.1 - - + +
125A LYS 3.4 1.3 + - - -
126A ASN* 1.3 71.1 - - - +
128A ALA* 1.3 57.1 + - - +
130A VAL* 3.6 4.5 + - - +
131A SER* 2.9 34.8 + - - -
166A ASN* 3.6 19.2 - - - +
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Residues in contact with ALA 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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80A LEU* 3.5 21.3 - - + -
101A LEU* 3.4 27.9 - - + +
103A ASP* 3.8 17.4 - - + +
126A ASN* 3.2 12.6 + - - +
127A ARG* 1.3 75.5 - - - +
129A GLU* 1.3 60.7 + - + +
132A GLN* 3.0 32.9 + - - +
146A ALA* 3.6 6.8 - - + +
147A TYR 4.7 2.5 - - - +
148A THR* 5.1 0.2 - - + -
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Residues in contact with GLU 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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126A ASN* 3.1 18.5 + - + +
128A ALA* 1.3 78.4 - - - +
130A VAL* 1.3 60.1 + - + +
132A GLN* 4.1 3.0 - - - +
133A PRO* 3.0 24.9 - - - +
146A ALA* 4.2 19.5 - - + +
148A THR* 3.6 31.9 + - + +
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Residues in contact with VAL 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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107A ALA* 5.7 0.7 - - + -
117A TYR 3.9 12.1 - - - +
118A LEU* 4.3 8.3 - - + -
122A ASP* 3.3 39.5 - - + +
125A LYS* 3.6 31.2 - - + +
126A ASN 3.0 18.5 + - - +
127A ARG* 3.9 4.5 - - - +
129A GLU* 1.3 75.5 - - + +
131A SER* 1.3 62.8 + - - +
133A PRO* 3.2 12.5 - - - +
134A ARG* 3.3 22.3 + - - +
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 4.2 11.0 - - - +
85A VAL* 4.8 0.4 - - - -
115A GLN* 2.9 30.1 + - - -
117A TYR* 4.4 12.9 - - - +
118A LEU* 3.7 5.4 - - - +
127A ARG 2.9 18.1 + - - -
128A ALA 4.1 1.8 - - - -
130A VAL* 1.3 76.9 - - - +
132A GLN* 1.3 59.8 + - - +
134A ARG* 3.4 4.9 + - - +
135A LEU* 2.9 47.6 + - - +
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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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101A LEU* 3.5 19.9 - - + +
128A ALA 3.0 18.3 + - - +
129A GLU* 4.1 5.4 - - - +
131A SER* 1.3 75.9 - - - +
133A PRO* 1.3 86.0 - - + +
135A LEU* 3.9 1.1 - - - +
136A ALA* 2.8 35.3 + - - +
144A VAL* 2.6 32.6 - - - +
145A THR* 3.9 3.2 - - - -
146A ALA* 3.9 18.2 - - + +
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Residues in contact with PRO 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 GLU 3.0 27.8 - - - +
130A VAL* 3.2 12.6 - - - +
132A GLN* 1.3 101.7 - - + +
134A ARG* 1.3 66.6 + - + +
136A ALA* 3.2 10.5 + - + +
137A GLU* 3.3 23.7 + - - +
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Residues in contact with ARG 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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117A TYR* 3.4 65.7 + - + +
119A ARG* 3.8 24.9 - - - +
121A GLU* 3.9 15.0 + - - -
122A ASP* 3.7 18.9 + - - -
130A VAL* 3.3 23.6 + - - +
131A SER 3.4 1.9 + - - +
132A GLN 3.3 0.4 - - - -
133A PRO* 1.3 79.8 - - + +
135A LEU* 1.3 61.4 + - - +
137A GLU* 3.5 27.6 + - - +
138A LEU* 4.0 5.2 + - - +
134B ARG* 6.0 3.3 - - - +
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Residues in contact with LEU 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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80A LEU* 4.3 2.2 - - + -
85A VAL* 4.1 12.1 - - + +
88A ALA* 4.0 4.3 - - + -
89A LYS* 3.6 37.2 - - + +
92A ILE* 3.7 24.9 - - + +
101A LEU* 3.7 29.6 - - + -
117A TYR* 3.6 18.2 - - + -
131A SER* 2.9 33.8 + - - +
132A GLN 3.9 2.0 - - - +
134A ARG* 1.3 74.5 - - - +
136A ALA* 1.3 64.3 + - - +
138A LEU* 3.2 29.5 + - + +
144A VAL* 3.9 8.0 - - + +
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Residues in contact with ALA 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 GLN* 2.8 33.6 + - - +
133A PRO* 3.2 7.2 + - + +
135A LEU* 1.3 77.0 - - - +
137A GLU* 1.3 58.2 + - + +
138A LEU 3.2 1.6 + - - -
139A ASN* 3.2 23.0 - - - +
142A VAL 4.8 2.6 - - - +
144A VAL* 3.9 20.3 - - + +
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Residues in contact with GLU 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 PRO* 3.3 21.3 + - - +
134A ARG* 3.8 17.4 - - - +
135A LEU 3.2 1.0 - - - -
136A ALA* 1.3 76.9 - - + +
138A LEU* 1.3 64.3 + - - +
139A ASN* 3.3 1.1 - - - -
119B ARG* 3.0 31.0 + - - +
134B ARG* 5.4 5.4 + - - -
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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