Contacts of the helix formed by residues 124 - 138 (chain A) in PDB entry 3RR1
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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122A GLY 3.8 0.4 - - - +
123A ASP* 1.3 81.5 - - + +
125A PRO* 1.3 72.6 - - + +
126A ALA* 3.7 22.3 - - + +
127A ASP* 3.1 32.0 + - - +
128A VAL* 3.4 16.7 + - - +
166A ARG* 5.5 1.8 - - - -
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Residues in contact with PRO 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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123A ASP 4.5 2.2 - - - +
124A ARG* 1.3 83.5 - - + +
126A ALA* 1.3 63.0 + - - +
127A ASP 3.3 0.2 - - - -
128A VAL* 3.4 10.1 + - + +
129A ILE* 3.1 31.1 + - - +
166A ARG* 3.8 36.1 - - + +
169A GLU* 3.3 37.7 - - + +
170A ILE* 4.2 4.8 - - + +
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Residues in contact with ALA 126 (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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124A ARG* 3.2 21.2 - - + +
125A PRO* 1.3 79.5 - - - +
127A ASP* 1.3 57.6 + - - +
129A ILE* 3.5 10.7 + - - +
130A ALA* 3.0 30.3 + - - +
169A GLU* 4.2 7.6 + - - +
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Residues in contact with ASP 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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121A GLY 3.8 8.0 - - - +
122A GLY* 3.7 16.2 - - - -
123A ASP* 3.7 11.8 + - - +
124A ARG* 3.1 44.8 + - - +
125A PRO 3.3 0.4 - - - -
126A ALA* 1.3 74.5 - - - +
128A VAL* 1.3 64.1 + - - +
130A ALA* 3.9 5.8 + - - +
131A GLY* 3.2 16.5 + - - -
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Residues in contact with VAL 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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120A VAL* 3.9 9.2 - - + +
121A GLY 3.8 13.2 - - - +
122A GLY 3.9 15.0 - - - +
124A ARG 3.4 15.3 - - - +
125A PRO* 3.4 6.5 + - + +
126A ALA 3.3 0.4 - - - -
127A ASP* 1.3 74.6 - - - +
129A ILE* 1.3 65.8 + - - +
131A GLY* 3.2 2.3 + - - -
132A MET* 2.9 43.6 + - + +
145A LEU* 3.9 17.7 - - + -
166A ARG* 4.0 20.0 - - - +
170A ILE* 3.9 20.2 - - + -
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Residues in contact with ILE 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 PRO 3.1 26.1 + - - +
126A ALA* 3.7 8.1 - - - +
128A VAL* 1.3 74.3 - - - +
130A ALA* 1.3 57.4 + - - +
132A MET* 3.1 5.0 + - - +
133A LYS* 2.9 50.7 + - + +
169A GLU* 3.7 35.4 - - + +
170A ILE* 4.1 13.9 - - + -
173A ALA* 3.7 28.5 - - + -
174A PHE* 4.2 10.8 - - + -
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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 ALA 3.0 17.3 + - - +
127A ASP* 3.9 8.3 - - - +
129A ILE* 1.3 78.0 - - - +
131A GLY* 1.3 60.7 + - - +
133A LYS* 3.5 8.1 + - - +
134A ALA* 3.2 22.9 + - - +
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Residues in contact with GLY 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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120A VAL* 3.9 17.0 - - - -
121A GLY 5.5 0.2 - - - -
127A ASP 3.2 9.6 + - - -
128A VAL 3.2 6.5 + - - -
130A ALA* 1.3 77.6 - - - +
132A MET* 1.3 60.8 + - - +
134A ALA* 3.5 6.6 + - - +
135A LEU* 3.3 27.4 + - - +
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Residues in contact with MET 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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120A VAL* 4.2 20.0 - - + -
128A VAL* 2.9 26.1 + - - +
129A ILE 3.5 7.0 - - - +
131A GLY* 1.3 74.5 - - - +
133A LYS* 1.3 58.0 + - - +
135A LEU 3.3 0.9 + - - -
136A GLN* 2.8 29.8 + - - +
143A PHE* 3.6 43.1 - - + -
145A LEU* 3.9 8.3 - - + -
170A ILE* 3.7 27.6 - - + -
174A PHE* 3.6 28.3 - - + -
178A VAL* 3.7 16.6 - - + -
180A PHE* 4.2 8.7 - - + -
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Residues in contact with LYS 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 ILE* 2.9 33.7 + - + +
130A ALA* 3.9 7.6 - - - +
131A GLY 3.4 0.2 - - - -
132A MET* 1.3 73.2 - - - +
134A ALA* 1.3 63.9 + - - +
136A GLN* 3.3 17.0 + - - +
137A ALA* 3.1 21.5 + - - +
173A ALA* 3.7 19.4 + - - +
174A PHE* 3.6 25.8 - - + -
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Residues in contact with ALA 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 ALA 3.2 16.5 + - - +
131A GLY* 3.8 7.0 - - - +
132A MET 3.4 0.2 - - - -
133A LYS* 1.3 76.9 - - - +
135A LEU* 1.3 63.2 + - + +
137A ALA* 3.5 10.2 + - - +
138A GLY* 3.5 12.6 + - - -
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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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118A SER* 3.9 19.5 - - - +
119A TRP 5.0 1.3 - - - +
120A VAL* 3.8 29.8 - - + -
131A GLY 3.3 12.7 + - - +
132A MET 3.3 0.4 + - - +
134A ALA* 1.3 77.5 - - + +
136A GLN* 1.3 59.4 + - - +
137A ALA 3.2 0.4 - - - -
138A GLY* 3.0 18.2 + - - +
140A PHE* 3.0 42.4 + - + +
143A PHE* 3.7 19.1 - - + -
313A MET 6.2 4.3 - - - -
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Residues in contact with GLN 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 MET 2.8 16.6 + - - +
133A LYS* 3.3 15.7 + - - +
135A LEU* 1.3 75.1 - - - +
137A ALA* 1.3 63.0 + - - +
139A GLY* 3.4 11.1 + - - -
140A PHE 3.3 20.6 + - - +
141A ASP* 5.5 0.9 - - + +
143A PHE* 4.9 0.4 - - + -
174A PHE* 3.3 21.2 - - - -
177A THR* 3.9 18.6 + - - -
178A VAL* 3.5 27.9 - - + +
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Residues in contact with ALA 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 LYS 3.1 11.4 + - - +
134A ALA* 3.5 12.6 - - - +
136A GLN* 1.3 78.3 - - - +
138A GLY* 1.3 55.6 + - - +
139A GLY 3.2 3.0 + - - -
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Residues in contact with GLY 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 ALA 3.5 5.1 + - - -
135A LEU* 3.0 18.2 + - - -
137A ALA* 1.3 77.0 - - - +
139A GLY* 1.3 54.5 + - - -
140A PHE* 3.3 18.7 + - - -
335A LEU 5.0 5.9 - - - +
337A GLY 4.6 6.2 + - - -
338A GLY 4.7 0.9 + - - -
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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