Contacts of the helix formed by residues 129 - 140 (chain A) in PDB entry 3JCA
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A THR* 4.7 5.7 + - - -
125A PRO* 3.0 18.3 + - - +
126A ALA* 5.1 0.7 - - - -
127A TYR 3.3 0.6 - - - -
128A VAL* 1.3 80.9 - - - +
130A ARG* 1.3 61.3 + - - +
131A SER* 2.9 25.5 + - - -
132A ILE* 2.9 28.9 + - - +
133A GLN 3.1 7.4 + - - -
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Residues in contact with ARG 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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128A VAL 3.5 1.8 + - - -
129A SER* 1.3 74.4 + - - +
131A SER* 1.3 63.3 + - - +
133A GLN* 3.1 12.1 + - + +
134A GLU* 2.7 71.9 + - + +
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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
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99A THR* 3.4 29.9 + - - +
103A LEU* 5.6 2.1 - - - +
129A SER* 2.9 17.7 + - - -
130A ARG* 1.3 94.1 - - - +
132A ILE* 1.3 59.8 + - - +
134A GLU* 3.5 10.9 - - - +
135A PHE* 3.2 23.7 + - - +
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Residues in contact with ILE 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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99A THR* 4.0 25.1 - - + +
102A VAL* 4.1 20.6 - - + -
103A LEU* 4.9 9.0 - - + -
106A LEU* 5.4 5.2 - - + -
126A ALA 3.3 25.6 - - - +
127A TYR* 3.3 28.9 - - + +
129A SER* 2.9 16.2 + - - +
131A SER* 1.3 78.6 - - - +
133A GLN* 1.3 62.2 + - - +
134A GLU 3.1 0.2 - - - -
135A PHE* 3.1 6.7 + - + +
136A LEU* 2.9 42.9 + - + +
143A HIS* 5.2 1.3 - - + -
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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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127A TYR 3.1 18.6 + - - -
128A VAL* 3.6 11.6 + - - +
129A SER 3.5 11.4 - - - +
130A ARG* 3.1 14.1 + - + +
132A ILE* 1.3 78.0 - - - +
134A GLU* 1.3 55.5 + - - +
136A LEU* 3.4 16.5 + - - +
137A ALA* 2.9 29.2 + - - +
143A HIS* 3.0 34.0 + - - +
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Residues in contact with GLU 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 ARG* 2.7 52.1 + - - +
131A SER* 3.5 9.1 - - - +
132A ILE 3.1 0.2 - - - -
133A GLN* 1.3 69.8 - - - +
135A PHE* 1.3 65.9 + - - +
137A ALA* 3.0 9.7 + - + +
138A ARG* 2.8 61.7 + - + +
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Residues in contact with PHE 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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103A LEU* 3.5 28.9 - - + -
106A LEU* 4.0 20.9 - - + -
107A ALA* 5.6 2.0 - - + -
110A PHE* 3.5 37.5 - + - -
131A SER 3.2 11.4 + - - +
132A ILE* 3.1 13.4 + - + +
134A GLU* 1.3 79.1 - - - +
136A LEU* 1.3 69.3 + - + +
138A ARG* 3.1 11.3 + - - +
139A TRP* 2.9 72.2 + + + +
141A ILE* 5.5 0.7 - - + -
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Residues in contact with LEU 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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106A LEU* 6.5 0.4 - - + -
119A ILE* 4.3 13.2 - - + -
132A ILE* 2.9 28.3 + - + +
133A GLN* 3.5 21.5 - - - +
135A PHE* 1.3 85.0 - - + +
137A ALA* 1.3 53.0 + - - +
139A TRP* 4.9 1.6 - - - -
140A LYS* 2.6 29.9 + - - +
141A ILE* 3.0 50.5 + - + +
143A HIS* 3.6 37.7 - - + +
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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 GLN 2.9 14.0 + - - +
134A GLU* 3.0 13.0 + - + +
136A LEU* 1.3 75.7 - - - +
138A ARG* 1.3 54.1 + - + +
140A LYS* 2.7 39.7 + - - +
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Residues in contact with ARG 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 GLU* 2.8 50.6 + - + +
135A PHE* 3.1 14.8 + - - +
137A ALA* 1.3 77.3 - - + +
139A TRP* 1.3 71.4 + - + +
140A LYS* 3.5 11.7 + - - +
7B GLU* 5.4 0.4 - - - -
11B LEU* 3.2 52.7 - - + +
12B HIS* 5.3 1.0 + - - -
176B LYS* 6.3 0.6 - - - +
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Residues in contact with TRP 139 (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* 6.1 1.8 - - - -
110A PHE* 3.5 42.8 - + + -
115A ILE* 4.1 20.9 - - + +
135A PHE* 2.9 58.7 + + + +
136A LEU* 3.6 1.6 - - - +
138A ARG* 1.3 90.0 - - + +
140A LYS* 1.3 71.9 + - - +
141A ILE* 3.7 20.2 - - + +
11B LEU* 6.1 1.8 - - + +
12B HIS* 3.7 31.8 - + - -
186B HIS* 3.9 30.2 - + + -
189B PHE* 3.5 22.9 - + + -
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Residues in contact with LYS 140 (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 PRO 5.0 1.2 - - - +
117A GLN* 4.0 6.9 - - - +
136A LEU 2.6 13.9 + - - -
137A ALA* 2.7 23.8 + - - +
138A ARG* 3.3 12.9 + - - +
139A TRP* 1.3 79.3 - - - +
141A ILE* 1.3 59.6 + - - +
142A SER 4.3 0.8 + - - -
4B SER* 6.5 0.4 - - - -
7B GLU* 2.9 35.9 + - - -
11B LEU* 4.8 0.8 - - - +
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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