Contacts of the helix formed by residues 128 - 141 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C HIS* 3.7 18.4 - - - +
82C ASN* 3.3 25.0 - - - +
85C GLY* 3.6 20.4 - - - +
125C LEU* 3.0 32.2 + - + +
126C PRO 4.2 2.2 - - - -
127C GLU* 1.3 91.4 - - - +
129C ALA* 1.3 64.1 + - - +
130C LYS 3.4 2.5 - - - -
131C ILE* 3.2 41.9 + - + +
132C LYS* 3.7 8.7 + - - +
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Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C PRO 4.8 2.9 - - - +
127C GLU 3.1 10.7 + - - +
128C GLU* 1.3 71.4 - - - +
130C LYS* 1.3 59.3 + - + +
132C LYS* 2.9 15.9 + - - +
133C ASP* 2.9 34.7 + - - +
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Residues in contact with LYS 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C GLY 3.2 26.4 + - - +
86C LYS* 4.0 10.7 - - - +
87C PHE* 3.6 32.4 - - + -
90C LEU* 3.5 8.3 - - + +
128C GLU 3.4 0.8 - - - -
129C ALA* 1.3 77.5 - - + +
131C ILE* 1.3 57.3 + - - +
133C ASP* 3.6 12.4 - - - +
134C ALA* 2.9 29.8 + - - +
306G ASP* 2.6 42.3 + - - +
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Residues in contact with ILE 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C HIS 5.4 0.4 - - - +
84C VAL* 4.5 6.1 - - + -
85C GLY* 4.1 12.1 - - - +
90C LEU* 3.7 21.8 - - + -
118C LEU* 3.9 26.9 - - + +
121C TRP* 3.8 45.8 - - + +
122C THR* 4.1 7.4 - - + +
125C LEU* 4.5 8.5 - - + -
128C GLU* 3.2 34.7 + - + +
129C ALA 3.1 0.8 - - - -
130C LYS* 1.3 76.3 - - - +
132C LYS* 1.3 58.8 + - + +
134C ALA* 3.4 2.1 + - - +
135C TYR* 3.0 26.7 + - - +
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Residues in contact with LYS 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU* 5.9 2.2 - - - +
40A LEU* 4.9 9.4 - - - +
122C THR* 2.9 54.3 - - + +
123C MSE 6.1 0.7 - - - -
125C LEU 4.5 1.8 - - - -
126C PRO* 3.1 37.3 + - - +
128C GLU 3.8 7.0 - - - +
129C ALA* 2.9 14.2 + - - +
131C ILE* 1.3 75.8 - - - +
133C ASP* 1.3 60.8 + - - +
135C TYR* 3.3 0.9 + - - +
136C HIS* 2.8 54.9 + - + +
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Residues in contact with ASP 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ALA* 5.9 2.4 - - - +
5A GLU* 5.7 0.9 - - - +
87C PHE* 4.0 19.2 - - + -
129C ALA* 2.9 22.5 + - - +
130C LYS* 3.3 16.0 + - - +
132C LYS* 1.3 79.1 - - - +
134C ALA* 1.3 60.0 + - - +
136C HIS* 4.0 8.8 - - - +
137C MSE 3.3 22.9 + - - +
140C ARG* 4.7 2.3 + - - -
309G LEU* 3.7 9.8 - - + +
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Residues in contact with ALA 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C PHE* 4.7 0.2 - - + -
90C LEU* 4.2 21.3 - - + -
94C ILE* 4.7 11.5 - - + +
118C LEU* 5.2 6.5 - - + -
130C LYS 2.9 17.2 + - - +
131C ILE 3.8 4.0 - - - +
133C ASP* 1.3 73.4 - - - +
135C TYR* 1.3 66.8 + - - +
136C HIS 3.4 0.2 + - - -
137C MSE 3.5 4.7 + - - +
138C LEU* 3.2 27.3 + - - +
309G LEU* 3.9 24.6 - - + +
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Residues in contact with TYR 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ILE* 4.3 8.3 - - + -
118C LEU* 4.2 24.6 - - + +
119C TYR* 3.6 30.4 - + + -
122C THR* 4.0 21.5 - - + -
131C ILE 3.0 18.5 + - - +
132C LYS 3.8 2.7 - - - +
134C ALA* 1.3 77.9 - - - +
136C HIS* 1.3 74.5 + + - +
138C LEU* 3.2 10.9 + - + +
139C LYS* 3.2 39.4 + - + +
144C VAL* 3.6 24.9 - - + +
147C ASP* 2.7 31.1 + - - -
148C PRO* 3.3 21.3 - - - +
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Residues in contact with HIS 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU* 5.1 9.1 + - - -
39A GLU* 3.8 22.4 + - - -
122C THR* 6.1 0.7 - - + -
132C LYS* 2.8 42.4 + - + +
133C ASP* 4.0 8.7 - - - +
135C TYR* 1.3 84.8 - + - +
137C MSE 1.3 50.0 + - - +
139C LYS* 2.6 34.5 + - + +
140C ARG* 2.7 26.5 + - + +
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Residues in contact with MSE 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ILE* 5.9 2.7 - - + -
133C ASP 3.3 13.5 + - - +
134C ALA 3.8 3.8 - - - +
135C TYR 3.4 0.2 - - - -
136C HIS* 1.3 77.2 - - - +
138C LEU* 1.3 73.7 + - + +
140C ARG* 2.9 35.4 + - - +
141C GLN* 2.7 58.3 + - + +
309G LEU* 4.1 16.4 - - + -
310G LEU 3.5 24.7 - - - +
311G HIS* 4.6 8.7 - - + -
312G ILE* 3.5 28.7 - - + -
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ILE* 4.4 20.4 - - + +
97C VAL* 4.1 26.0 - - + -
115C ILE* 5.4 3.4 - - + -
118C LEU* 3.8 28.5 - - + -
134C ALA 3.2 13.8 + - - +
135C TYR* 3.5 10.5 - - + +
136C HIS 3.1 0.6 - - - -
137C MSE 1.3 95.6 - - + +
139C LYS* 1.3 59.5 + - - +
141C GLN* 3.9 1.3 - - - +
142C GLY 3.4 0.7 + - - -
143C ILE* 2.9 49.2 + - + -
144C VAL* 3.0 25.5 + - + -
312G ILE* 4.9 4.3 - - + -
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Residues in contact with LYS 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C TYR* 3.2 40.6 - - + +
136C HIS* 2.6 24.8 + - + +
138C LEU* 1.3 70.7 - - - +
140C ARG* 1.3 61.5 + - + +
141C GLN 3.1 1.6 - - - -
142C GLY* 3.1 13.2 + - - -
144C VAL* 3.7 36.5 - - + +
145C GLN 4.3 6.6 + - - -
146C SER* 4.1 3.8 - - - +
147C ASP* 2.8 35.4 + - - +
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Residues in contact with ARG 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ASP 4.7 3.0 + - - -
136C HIS* 2.7 14.4 + - + +
137C MSE 3.2 46.2 - - - +
139C LYS* 1.3 77.7 - - + +
141C GLN* 1.3 71.8 + - - +
142C GLY 3.3 1.0 + - - -
309G LEU* 4.8 5.3 - - - +
311G HIS* 6.0 2.4 + - - -
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Residues in contact with GLN 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C LYS* 5.3 1.2 + - - -
137C MSE 2.7 40.9 + - + +
138C LEU 3.8 0.4 + - - +
140C ARG* 1.3 93.3 + - - +
142C GLY* 1.3 60.2 + - - +
143C ILE* 3.2 25.2 + - + +
312G ILE* 3.0 30.1 + - + +
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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