Contacts of the helix formed by residues 124 - 139 (chain A) in PDB entry 5M72
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 ARG 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A LEU* 3.5 30.1 - - - +
102A GLU* 4.8 6.7 + - - -
115A TYR* 4.3 8.3 + - - -
119A LEU* 3.0 34.9 + - + +
122A LEU* 4.0 21.7 - - + +
123A GLU* 1.3 75.6 - - - +
125A TYR* 1.3 59.2 - - - +
126A ASP 3.4 2.4 + - - -
127A GLU* 2.8 47.1 + - - +
128A CYS* 2.9 28.2 + - - +
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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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120A TYR* 3.8 36.0 + + - -
123A GLU* 3.3 57.7 + - + +
124A ARG* 1.3 70.6 - - - +
126A ASP* 1.3 62.5 + - - +
128A CYS* 3.9 3.4 - - + -
129A LEU* 2.8 32.1 + - - +
154A VAL* 3.5 9.9 - - + +
157A ALA* 3.6 42.7 - - + +
158A GLN* 3.8 21.4 + - + -
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Residues in contact with ASP 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG 3.4 0.4 - - - -
125A TYR* 1.3 78.7 - - - +
127A GLU* 1.3 64.2 + - + +
129A LEU* 3.3 3.9 + - - +
130A ALA* 3.2 20.3 + - - +
158A GLN* 2.7 31.2 + - - +
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Residues in contact with GLU 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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115A TYR* 4.8 3.6 + - - +
119A LEU* 4.0 14.1 - - + -
124A ARG* 2.8 59.2 + - - +
125A TYR 3.4 0.2 - - - -
126A ASP* 1.3 78.3 - - + +
128A CYS* 1.3 63.3 + - - +
130A ALA* 3.3 8.0 + - - +
131A VAL* 3.1 26.8 + - + +
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Residues in contact with CYS 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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116A GLY 3.4 23.1 - - - -
119A LEU* 3.9 16.5 - - + +
120A TYR* 3.8 16.4 - - - +
124A ARG 2.9 20.6 + - - +
125A TYR* 3.6 9.4 - - - +
126A ASP 3.2 0.2 - - - -
127A GLU* 1.3 76.6 - - - +
129A LEU* 1.3 62.4 + - - +
131A VAL* 3.2 3.6 + - - +
132A TYR* 2.9 35.8 + - - -
154A VAL* 3.5 27.6 - - + -
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Residues in contact with LEU 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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125A TYR 2.8 20.8 + - - +
126A ASP 3.7 4.5 - - - +
127A GLU 3.3 0.2 - - - -
128A CYS* 1.3 74.5 - - - +
130A ALA* 1.3 56.1 + - - +
132A TYR* 3.3 1.9 + - - -
133A ARG* 2.9 73.9 + - + +
151A LEU* 4.3 13.5 - - + +
154A VAL* 3.7 13.9 - - + +
155A VAL* 3.9 25.1 - - + -
158A GLN* 3.2 28.7 - - - +
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Residues in contact with ALA 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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126A ASP 3.2 10.3 + - - +
127A GLU* 3.3 10.1 + - - +
129A LEU* 1.3 78.8 - - - +
131A VAL* 1.3 62.7 + - + +
133A ARG* 3.5 11.8 + - - +
134A ASP* 3.2 22.2 + - - +
137A ARG* 5.4 0.2 + - - -
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Residues in contact with VAL 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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112A LYS* 3.8 29.8 - - + +
115A TYR* 4.0 14.8 - - + -
116A GLY* 3.7 21.3 - - - +
119A LEU* 3.9 16.6 - - + -
127A GLU* 3.1 15.2 + - + +
128A CYS* 3.2 8.0 + - - +
130A ALA* 1.3 78.5 - - + +
132A TYR* 1.3 58.7 + - - +
134A ASP* 3.2 4.7 + - - +
135A LEU* 2.8 46.3 + - + +
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Residues in contact with TYR 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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113A GLU* 4.2 7.0 + - - -
116A GLY* 3.6 31.2 - - - -
117A GLN* 3.2 31.4 + - - +
128A CYS* 2.9 36.4 + - - +
129A LEU* 3.3 4.9 + - - +
131A VAL* 1.3 73.0 - - - +
133A ARG* 1.3 62.1 + - - +
135A LEU* 3.8 18.3 - - + +
136A VAL* 2.8 34.7 + - - +
147A ARG* 4.1 24.7 - - + -
150A ASN* 3.4 24.3 + - + -
151A LEU* 3.9 22.7 - - + -
154A VAL* 4.2 7.2 - - + -
590B PHE* 3.4 17.7 - + - -
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Residues in contact with ARG 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 2.9 54.5 + - + +
130A ALA* 3.8 9.4 - - - +
132A TYR* 1.3 75.4 - - - +
134A ASP* 1.3 62.3 + - - +
136A VAL* 3.9 1.9 - - - +
137A ARG* 3.1 59.2 + - - +
151A LEU* 4.0 17.0 - - + +
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Residues in contact with ASP 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 LYS* 3.1 28.5 + - - +
130A ALA 3.2 10.5 + - - +
131A VAL 3.2 8.6 + - - +
133A ARG* 1.3 77.2 - - - +
135A LEU* 1.3 65.6 + - - +
137A ARG* 3.3 11.1 + - - +
138A ASN* 2.2 59.3 + - - +
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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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109A ASP* 4.6 5.6 - - + +
112A LYS* 3.7 35.0 - - + +
113A GLU* 3.8 31.0 - - + +
131A VAL* 2.8 42.5 + - + +
132A TYR* 3.8 29.8 - - + +
134A ASP* 1.3 72.2 - - - +
136A VAL* 1.3 63.5 + - - +
138A ASN* 5.1 2.0 - - - -
139A SER* 2.6 38.9 + - - +
147A ARG* 3.8 13.2 - - - -
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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
----------------------------------------------------------
132A TYR* 2.8 24.1 + - - +
133A ARG* 3.9 3.1 - - - +
135A LEU* 1.3 74.6 - - - +
137A ARG* 1.3 67.2 + - + +
139A SER* 3.7 11.1 + - - +
144A ASP* 4.1 10.6 - - - +
147A ARG* 3.8 33.9 - - + +
148A LYS* 3.9 35.4 - - + -
151A LEU* 3.9 20.6 - - + -
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Residues in contact with ARG 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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130A ALA 5.4 0.2 + - - -
133A ARG* 3.1 60.4 + - - +
134A ASP* 3.8 10.5 + - - +
136A VAL* 1.3 81.8 - - + +
138A ASN* 1.3 67.2 + - - +
139A SER 3.6 3.6 + - - +
140A GLN* 5.0 2.1 - - - +
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Residues in contact with ASN 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 ASP* 5.4 4.5 - - - +
112A LYS* 5.6 0.6 - - - +
134A ASP* 2.2 46.7 + - - +
135A LEU* 4.6 1.6 - - - +
137A ARG* 1.3 82.2 - - - +
139A SER* 1.3 59.8 + - - +
140A GLN* 2.8 17.5 - - - +
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASP* 6.1 0.4 - - - -
113A GLU* 5.0 0.9 + - - -
135A LEU* 2.6 32.7 + - - +
136A VAL 3.9 9.5 - - - +
137A ARG 3.4 3.0 - - - +
138A ASN* 1.3 80.1 - - - +
140A GLN* 1.3 65.2 + - - +
141A ASP* 4.0 5.6 - - - -
144A ASP* 5.6 1.4 - - - +
147A ARG* 3.5 34.5 + - - -
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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