Contacts of the helix formed by residues 128 - 141 (chain A) in PDB entry 1JPL
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 GLU 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A HIS* 3.5 28.6 - - - +
82A ASN* 3.2 32.7 + - - +
85A GLY* 3.6 29.8 - - - +
125A LEU* 3.2 21.8 + - + +
126A PRO 3.1 2.5 - - - -
127A GLU* 1.3 93.7 - - - +
129A ALA* 1.3 65.3 + - - +
130A LYS 3.3 2.5 - - - -
131A ILE* 3.2 32.9 + - + +
132A LYS* 3.9 5.0 - - - +
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Residues in contact with ALA 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 PRO 4.1 3.1 + - - +
127A GLU 3.4 5.7 + - - +
128A GLU* 1.3 73.9 - - - +
130A LYS* 1.3 64.7 + - + +
132A LYS* 3.0 34.4 + - + +
133A ASP* 3.3 13.1 + - - +
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Residues in contact with LYS 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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85A GLY 3.1 28.9 - - - +
86A LYS* 4.0 8.6 - - - +
87A PHE* 3.5 38.6 - - + -
90A LEU* 3.5 8.0 - - + +
128A GLU 3.3 1.0 - - - -
129A ALA* 1.3 78.0 - - + +
131A ILE* 1.3 56.1 + - - +
133A ASP* 3.3 12.3 + - - +
134A ALA 3.0 22.7 + - - -
306E ASP* 2.6 38.0 + - - +
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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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84A VAL* 4.4 6.7 - - + -
85A GLY* 4.0 14.1 - - - -
90A LEU* 3.9 13.5 - - + -
118A LEU* 3.9 37.0 - - + +
121A TRP* 4.0 33.4 - - + -
122A THR* 4.0 7.2 - - + +
125A LEU* 4.3 11.0 - - + +
128A GLU* 3.6 38.6 - - + +
129A ALA 3.1 1.4 + - - -
130A LYS* 1.3 77.1 - - - +
132A LYS* 1.3 58.8 + - - +
134A ALA* 3.3 3.9 + - - +
135A TYR* 2.9 24.8 + - - +
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Residues in contact with LYS 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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122A THR* 3.3 37.0 + - + +
125A LEU 4.1 1.8 + - - -
126A PRO* 3.3 38.1 + - - +
128A GLU 3.9 10.1 - - - +
129A ALA* 3.0 26.2 - - + +
131A ILE* 1.3 77.0 - - + +
133A ASP* 1.3 63.6 + - - +
135A TYR* 4.0 1.8 - - - -
136A HIS* 2.7 60.4 + - + +
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Residues in contact with ASP 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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87A PHE* 4.1 17.5 - - + -
129A ALA* 3.3 18.1 + - - +
130A LYS* 3.4 18.5 - - - +
131A ILE 3.2 0.2 - - - -
132A LYS* 1.3 81.0 - - - +
134A ALA* 1.3 61.2 + - - +
136A HIS* 4.2 4.4 - - - +
137A MSE 3.2 24.6 + - - +
309E LEU* 4.0 9.1 - - + +
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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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87A PHE* 4.6 0.4 - - - -
90A LEU* 4.2 20.6 - - + -
94A ILE* 4.2 21.5 - - + +
118A LEU* 5.2 6.7 - - + -
130A LYS 3.0 16.1 + - - +
131A ILE 3.6 4.7 - - - +
132A LYS 3.1 0.2 - - - -
133A ASP* 1.3 78.8 - - - +
135A TYR* 1.3 61.7 + - - +
137A MSE 3.6 3.9 + - - +
138A LEU* 3.3 27.3 + - - +
309E LEU* 4.2 15.5 - - + -
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Residues in contact with TYR 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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115A ILE* 4.2 9.0 - - + -
118A LEU* 4.1 24.2 - - + +
119A TYR* 3.6 29.7 - + + -
122A THR* 4.0 18.2 - - + -
131A ILE 2.9 17.0 + - - +
132A LYS* 3.1 3.6 + - - +
134A ALA* 1.3 74.7 - - - +
136A HIS* 1.3 78.3 + + - +
138A LEU* 2.9 25.7 + - + +
139A LYS* 3.1 20.3 + - + +
144A VAL* 3.2 38.5 - - + +
147A ASP* 2.9 30.2 + - - -
148A PRO* 3.4 16.8 - - - +
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Residues in contact with HIS 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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122A THR* 5.9 2.0 - - + -
132A LYS* 2.7 47.7 + - + +
133A ASP* 4.4 4.5 - - - +
135A TYR* 1.3 88.8 - + - +
137A MSE 1.3 51.4 + - - +
139A LYS* 3.1 18.4 + - + +
140A ARG* 2.7 35.4 + - - +
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Residues in contact with MSE 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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94A ILE* 4.4 7.0 - - + -
133A ASP 3.2 19.3 + - - +
134A ALA 3.8 4.3 - - - +
135A TYR 3.1 0.8 - - - -
136A HIS* 1.3 75.9 - - - +
138A LEU* 1.3 69.9 + - - +
140A ARG* 3.4 33.5 + - - +
141A GLN* 3.0 31.6 + - - +
309E LEU* 3.4 39.7 - - + -
310E LEU 3.0 31.6 - - - +
311E HIS* 3.6 9.0 - - + +
312E ILE* 3.8 24.0 - - + -
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Residues in contact with LEU 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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94A ILE* 4.2 23.3 - - + -
97A VAL* 4.0 16.2 - - + -
115A ILE* 4.0 20.6 - - + -
118A LEU* 3.7 29.6 - - + -
134A ALA 3.3 13.7 + - - +
135A TYR* 2.9 12.6 + - + +
137A MSE 1.3 85.3 - - - +
139A LYS* 1.3 58.6 + - - +
141A GLN* 3.7 2.3 + - - +
142A GLY 3.5 1.0 + - - -
143A ILE* 3.0 57.3 + - + -
144A VAL* 3.0 18.8 + - + -
312E ILE* 4.9 0.2 - - + -
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Residues in contact with LYS 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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135A TYR* 3.1 26.9 + - + +
136A HIS* 3.3 21.1 - - + +
138A LEU* 1.3 75.7 - - - +
140A ARG* 1.3 55.0 + - - +
141A GLN 2.7 15.4 + - - -
142A GLY* 2.8 15.8 + - - -
144A VAL* 3.4 30.8 - - + +
145A GLN 4.2 12.4 + - - -
146A SER* 4.7 0.6 - - - +
147A ASP* 3.1 42.1 + - - +
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Residues in contact with ARG 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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136A HIS 2.7 20.6 + - - +
137A MSE 3.7 17.5 - - - +
139A LYS* 1.3 72.1 - - - +
141A GLN* 1.3 90.4 + - - +
142A GLY 3.6 0.4 + - - -
311E HIS* 3.7 30.5 + - - +
312E ILE 5.6 0.4 + - - -
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Residues in contact with GLN 141 (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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137A MSE 3.0 21.3 + - - +
138A LEU 3.7 3.6 + - - +
139A LYS 2.7 1.6 + - - -
140A ARG* 1.3 116.2 + - - +
142A GLY* 1.3 58.6 + - - -
143A ILE* 3.1 10.2 + - + +
312E ILE* 3.1 48.1 + - + +
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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