Contacts of the helix formed by residues 125 - 137 (chain A) in PDB entry 7CAL
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 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A LYS* 3.8 4.7 - - - +
51A ILE* 5.4 0.4 - - - +
123A VAL* 3.6 12.9 + - - +
124A ASP* 1.3 76.2 - - - +
126A PRO* 1.3 66.6 - - - +
127A LYS* 3.0 9.3 + - - +
128A LYS* 3.3 33.8 + - - +
129A ILE* 3.0 24.2 + - - +
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Residues in contact with PRO 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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49A LYS* 3.9 27.6 - - + -
50A HIS* 5.2 11.0 - - + +
51A ILE* 4.8 15.5 - - + -
110A PHE 5.1 6.6 - - - +
111A PHE* 6.0 2.7 - - + -
124A ASP 4.6 0.2 - - - -
125A SER* 1.3 81.8 - - - +
127A LYS* 1.3 61.9 + - - +
129A ILE* 4.1 14.6 - - + +
130A ALA* 3.4 19.2 + - - +
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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 SER* 3.0 3.0 + - - +
126A PRO* 1.3 82.0 - - - +
128A LYS* 1.3 62.9 + - + +
130A ALA* 3.0 22.2 + - + +
131A ILE* 3.0 40.1 + - + +
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Residues in contact with LYS 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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114A TYR* 4.0 19.8 + - - +
116A ASP* 5.0 7.3 + - - -
123A VAL* 4.2 15.7 - - + +
125A SER* 3.2 24.0 + - - +
127A LYS* 1.3 77.2 - - + +
129A ILE* 1.3 64.4 + - - +
131A ILE* 4.1 12.6 - - + +
132A ARG* 3.4 23.2 + - - +
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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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51A ILE* 4.1 17.9 - - + -
109A THR 4.4 4.7 - - - +
110A PHE* 3.6 34.5 - - - +
112A VAL* 3.3 33.9 - - + +
114A TYR* 4.1 20.4 - - + -
123A VAL 4.0 13.0 - - - +
125A SER 3.0 29.7 + - - +
126A PRO* 4.1 8.5 - - + +
128A LYS* 1.3 77.3 - - - +
130A ALA* 1.3 62.3 + - - +
132A ARG* 3.5 2.9 + - - +
133A TYR* 3.1 22.7 + - - +
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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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110A PHE* 3.9 27.7 - - + -
126A PRO 3.4 14.0 + - - +
127A LYS* 3.0 17.7 + - + +
129A ILE* 1.3 78.4 - - - +
131A ILE* 1.3 62.1 + - + +
133A TYR* 3.4 0.9 + - - -
134A LEU* 3.0 41.1 + - + +
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Residues in contact with ILE 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* 3.0 42.0 + - + +
128A LYS* 4.3 12.3 - - + +
129A ILE 3.5 0.2 - - - -
130A ALA* 1.3 76.9 - - + +
132A ARG* 1.3 61.5 + - - +
134A LEU* 4.0 6.8 - - + +
135A SER* 2.8 37.8 + - - +
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Residues in contact with ARG 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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112A VAL* 6.4 0.2 - - - +
114A TYR* 3.4 62.7 + - + +
128A LYS 3.4 16.5 + - - +
129A ILE* 3.7 4.0 - - - +
130A ALA 3.2 0.6 - - - -
131A ILE* 1.3 79.9 - - - +
133A TYR* 1.3 64.3 + - - +
135A SER* 3.3 2.8 + - - -
136A THR* 3.3 44.2 + - + +
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Residues in contact with TYR 133 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A ASP 4.5 1.0 + - - -
106A ILE* 3.9 27.1 - - - +
109A THR* 3.1 41.6 + - + +
110A PHE* 3.7 25.4 - + + -
129A ILE 3.1 15.0 + - - +
130A ALA 3.4 2.7 + - - +
132A ARG* 1.3 81.8 - - - +
134A LEU* 1.3 61.7 + - - +
135A SER 3.4 0.7 + - - -
136A THR* 4.2 5.2 - - - -
137A TRP* 3.2 41.6 + + + -
138A PHE* 3.3 35.3 + + - +
141A ASP* 4.2 10.9 - - - +
176A ARG* 4.6 8.1 + - - -
177A ARG* 5.2 3.3 + - - -
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Residues in contact with LEU 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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110A PHE* 4.0 20.6 - - + -
130A ALA* 3.0 28.3 + - + +
131A ILE* 4.2 7.0 - - + +
132A ARG 3.3 0.2 - - - -
133A TYR* 1.3 76.5 - - - +
135A SER* 1.3 58.6 + - - +
138A PHE* 3.6 49.1 + - + +
139A ALA* 5.0 3.6 + - - +
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Residues in contact with SER 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 ILE* 2.8 29.0 + - - +
132A ARG* 4.0 3.4 - - - -
133A TYR 3.2 0.4 - - - -
134A LEU* 1.3 81.1 - - - +
136A THR* 1.3 64.9 + - - +
138A PHE 5.4 0.2 - - - -
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Residues in contact with THR 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 ARG* 3.3 33.5 + - + +
133A TYR* 4.1 5.5 + - - -
135A SER* 1.3 85.9 - - - +
137A TRP* 1.3 105.3 + - - +
138A PHE 3.8 1.7 + - - -
139A ALA 5.5 0.4 + - - -
140A PHE* 4.6 4.7 + - - +
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Residues in contact with TRP 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 TYR* 3.2 29.5 + + + -
136A THR* 1.3 114.5 + - - +
138A PHE* 1.3 58.3 + - - +
140A PHE* 3.6 46.0 - + + -
141A ASP* 3.3 19.9 - - + +
176A ARG* 3.8 48.7 - - + +
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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