Contacts of the helix formed by residues 128 - 141 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B ARG* 5.8 0.7 - - - +
81B HIS* 3.5 19.2 - - + +
82B ASN* 3.1 30.1 + - - +
85B GLY* 3.2 25.2 - - - +
125B LEU* 3.4 37.1 + - + +
126B PRO 3.2 3.7 - - - -
127B GLU* 1.3 88.8 - - + +
129B ALA* 1.3 65.1 + - - +
130B LYS* 3.3 2.7 - - - +
131B ILE* 3.3 35.2 + - + +
132B LYS* 4.0 4.9 + - - -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PRO 4.2 3.1 + - - +
127B GLU 3.5 6.2 + - - +
128B GLU* 1.3 73.4 - - - +
130B LYS* 1.3 56.5 + - + +
132B LYS* 2.7 39.4 + - + +
133B ASP* 3.2 18.2 + - - +
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Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B GLY* 3.2 27.5 + - - +
86B LYS* 4.9 6.5 - - - +
87B PHE* 3.5 39.3 - - + +
90B LEU* 3.6 8.1 - - + +
128B GLU 3.3 0.8 - - - -
129B ALA* 1.3 78.0 - - + +
131B ILE* 1.3 61.1 + - - +
133B ASP* 3.3 12.6 + - - +
134B ALA 3.0 18.9 + - - -
306F ASP* 2.8 36.2 + - - +
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B VAL* 4.3 11.4 - - + -
85B GLY* 4.0 13.7 - - - +
90B LEU* 4.0 14.6 - - + -
118B LEU* 3.9 25.7 - - + +
121B TRP* 3.8 45.3 - - + +
122B THR* 4.1 6.5 - - + +
125B LEU* 4.1 12.6 - - + -
128B GLU* 3.3 32.7 + - + +
129B ALA 3.0 1.0 + - - -
130B LYS* 1.3 77.8 - - - +
132B LYS* 1.3 58.3 + - + +
134B ALA* 3.6 2.4 + - - +
135B TYR* 3.0 25.8 + - - +
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Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B THR* 3.6 43.4 + - + +
125B LEU 3.6 21.8 + - - -
126B PRO* 3.7 18.7 + - - +
128B GLU 4.2 5.6 + - - +
129B ALA* 2.7 15.9 + - + +
131B ILE* 1.3 76.4 - - + +
133B ASP* 1.3 58.1 + - - +
135B TYR* 3.1 0.6 + - - +
136B HIS* 2.6 62.1 + - + +
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B PHE* 4.1 18.2 - - + -
129B ALA* 3.2 11.8 + - - +
130B LYS* 3.5 22.4 + - - +
132B LYS* 1.3 79.9 - - - +
134B ALA* 1.3 62.1 + - - +
136B HIS* 3.8 8.6 - - - +
137B MSE 2.9 25.6 + - - +
140B ARG* 4.8 1.6 + - - -
309F LEU* 4.2 8.8 - - + +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LEU* 4.3 19.3 - - + -
94B ILE* 4.2 14.4 - - + +
118B LEU* 5.4 6.1 - - + -
130B LYS 3.0 16.9 + - - +
131B ILE* 3.8 4.5 - - - +
133B ASP* 1.3 75.0 - - - +
135B TYR* 1.3 63.1 + - - +
137B MSE 3.3 5.8 + - - +
138B LEU* 3.1 28.9 + - + +
309F LEU* 4.1 26.2 - - + +
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Residues in contact with TYR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ILE* 4.4 8.1 - - + -
118B LEU* 4.1 12.7 - - + +
119B TYR* 3.6 38.7 - + + -
122B THR* 3.9 20.2 - - + -
131B ILE 3.0 19.8 + - - +
132B LYS 3.5 2.7 - - - +
134B ALA* 1.3 77.2 - - - +
136B HIS* 1.3 74.4 + + - +
138B LEU* 3.1 15.6 + - + +
139B LYS* 3.1 50.1 + - + +
144B VAL* 3.5 23.6 - - + +
147B ASP* 2.6 23.6 + - - -
148B PRO* 3.4 19.2 - - - +
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Residues in contact with HIS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B THR* 6.0 2.0 - - + -
132B LYS* 2.6 47.9 + - + +
133B ASP* 3.9 9.4 - - - +
135B TYR* 1.3 86.4 - + - +
137B MSE 1.3 58.3 + - - +
139B LYS* 3.4 12.4 + - + +
140B ARG* 2.8 37.0 + - - +
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Residues in contact with MSE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ILE* 5.1 4.0 - - - -
133B ASP 2.9 16.6 + - - +
134B ALA 3.5 5.6 - - - +
135B TYR 3.1 0.2 - - - -
136B HIS* 1.3 76.0 - - - +
138B LEU* 1.3 76.1 + - + +
140B ARG* 2.9 35.4 + - - +
141B GLN* 2.9 35.8 + - + +
309F LEU* 4.2 8.5 - - + -
310F LEU 3.6 24.0 - - - +
311F HIS* 3.7 19.5 - - + +
312F ILE* 3.3 38.1 - - + +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ILE* 4.2 18.6 - - + -
97B VAL* 4.1 14.6 - - + -
115B ILE* 4.1 18.2 - - + -
118B LEU* 3.8 29.2 - - + -
134B ALA 3.1 20.0 + - - +
135B TYR* 3.1 11.4 + - + +
137B MSE 1.3 82.3 - - + +
139B LYS* 1.3 60.7 + - - +
141B GLN 3.2 2.3 + - - -
142B GLY 3.1 3.8 + - - -
143B ILE* 2.9 35.5 + - + +
144B VAL* 3.8 15.5 - - + -
312F ILE* 3.6 28.7 - - + -
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Residues in contact with LYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B TYR* 3.1 41.7 + - + +
136B HIS* 3.6 15.5 - - + +
138B LEU* 1.3 71.0 - - - +
140B ARG* 1.3 54.3 + - - +
141B GLN 2.7 5.9 + - - -
142B GLY* 2.7 25.8 + - - -
144B VAL* 3.4 28.2 - - + +
145B GLN 4.4 15.9 - - - -
146B SER* 5.1 1.0 - - - +
147B ASP* 3.0 34.4 + - - +
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Residues in contact with ARG 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ASP 4.8 1.4 + - - -
136B HIS* 2.8 22.2 + - - +
137B MSE 2.9 45.2 + - - +
139B LYS* 1.3 71.9 - - - +
141B GLN* 1.3 69.4 + - - +
142B GLY 3.5 0.4 - - - -
309F LEU* 5.0 1.8 - - - +
311F HIS* 4.0 14.1 - - - -
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Residues in contact with GLN 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LYS* 5.3 3.3 + - - -
137B MSE 2.9 38.3 + - + +
138B LEU 3.8 1.6 - - - +
139B LYS 2.7 1.0 + - - -
140B ARG* 1.3 95.2 + - - +
142B GLY* 1.3 58.9 + - - +
143B ILE* 3.2 14.0 + - + +
312F ILE* 3.6 30.0 - - + +
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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