Contacts of the helix formed by residues 86 - 98 (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 LYS 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B ASN* 2.8 31.6 - - - +
83B GLU* 3.3 39.3 + - - +
84B VAL 2.9 1.6 + - - -
85B GLY* 1.3 81.9 - - - +
87B PHE* 1.3 54.5 + - - +
88B ARG* 2.8 17.2 - - + +
89B PHE* 2.7 25.4 + - - +
90B LEU* 2.9 13.4 + - - +
130B LYS* 4.9 5.8 - - - +
305F SER* 4.8 11.8 + - - +
306F ASP* 3.5 25.1 - - + +
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Residues in contact with PHE 87 (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 4.2 0.6 + - - -
86B LYS* 1.3 71.6 - - - +
88B ARG* 1.3 56.0 + - - +
90B LEU* 3.7 15.2 - - + +
91B ASN* 2.8 46.9 + - - +
130B LYS* 3.5 49.6 - - + -
133B ASP* 4.1 19.1 - - + -
306F ASP* 2.9 17.0 + - - -
307F GLU 3.2 26.0 - - - +
308F ASP* 4.6 0.9 - - - -
309F LEU* 3.6 48.9 - - + +
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Residues in contact with ARG 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 4.5 28.0 + - - +
47B VAL* 6.5 1.1 - - - -
48B ARG* 5.6 7.0 - - + +
83B GLU* 6.1 1.6 - - - -
86B LYS* 4.1 11.6 - - + +
87B PHE* 1.3 78.1 - - - +
89B PHE* 1.3 56.9 + - - +
92B GLU* 3.7 19.6 + - - +
305F SER* 3.6 6.9 + - - +
306F ASP* 2.8 49.8 + - - +
307F GLU* 3.6 34.5 + - + +
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 3.4 49.8 - - + -
50B LEU* 5.0 1.8 - - + -
51B ALA* 3.9 19.5 - - + -
54B ILE* 4.9 0.9 - - + -
69B LEU* 4.2 25.1 - - + -
83B GLU 3.7 13.9 - - - +
84B VAL* 3.4 42.2 - - + -
86B LYS* 2.7 14.0 + - + +
88B ARG* 1.3 74.3 - - + +
90B LEU* 1.3 65.6 + - + +
91B ASN 3.3 1.8 - - - -
92B GLU* 3.0 21.7 + - - +
93B LEU* 3.6 35.3 + - + +
121B TRP* 4.4 2.2 - + - -
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Residues in contact with LEU 90 (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* 3.2 28.9 - - + +
85B GLY 4.2 3.8 - - - -
86B LYS 2.9 21.2 + - - +
87B PHE* 4.1 13.0 - - + -
89B PHE* 1.3 85.1 - - + +
91B ASN* 1.3 56.9 + - - +
93B LEU* 2.9 23.6 + - + +
94B ILE* 3.0 17.0 + - + +
118B LEU* 4.1 22.4 - - + +
121B TRP* 4.7 0.4 - - + -
130B LYS* 3.6 31.9 - - + +
131B ILE* 4.0 19.3 - - + +
134B ALA* 4.3 13.7 - - + -
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Residues in contact with ASN 91 (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* 2.8 29.2 + - - +
88B ARG 4.9 1.1 - - - +
90B LEU* 1.3 72.7 - - - +
92B GLU* 1.3 61.6 + - + +
93B LEU 3.3 0.2 - - - -
94B ILE* 3.6 8.6 - - - +
95B LYS* 3.1 32.5 + - + +
307F GLU* 2.9 27.7 + - - +
308F ASP 3.0 23.6 + - - -
309F LEU* 3.5 14.6 - - - +
310F LEU* 2.7 40.7 + - + +
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Residues in contact with GLU 92 (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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102A LEU* 5.8 1.6 - - - +
105A ARG* 3.7 21.6 + - - -
51B ALA* 3.7 23.6 - - + -
55B GLN* 2.8 41.4 + - - +
88B ARG 3.7 20.5 - - - +
89B PHE* 3.3 10.5 - - - +
90B LEU 3.0 1.0 - - - -
91B ASN* 1.3 81.6 - - - +
93B LEU* 1.3 59.9 + - - +
95B LYS* 3.1 30.0 + - - -
96B VAL* 3.4 10.9 + - - +
307F GLU* 5.2 4.2 - - - +
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Residues in contact with LEU 93 (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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51B ALA* 5.5 2.7 - - - -
54B ILE* 4.0 38.1 - - + -
66B LEU* 5.3 0.9 - - + -
69B LEU* 5.2 2.0 - - + -
89B PHE* 3.9 35.9 - - + +
90B LEU* 2.9 11.0 + - + +
92B GLU* 1.3 77.1 - - - +
94B ILE* 1.3 66.6 + - - +
95B LYS 3.2 0.4 - - - -
96B VAL* 3.0 21.6 + - + +
97B VAL* 3.5 7.8 + - - +
114B VAL* 4.1 24.6 - - + +
117B LEU* 6.2 1.6 - - + -
118B LEU* 4.1 22.7 - - + -
121B TRP* 4.0 21.8 - - + -
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Residues in contact with ILE 94 (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 3.0 15.1 + - - +
91B ASN* 3.6 20.2 - - - +
92B GLU 3.3 0.2 - - - -
93B LEU* 1.3 79.1 - - + +
95B LYS* 1.3 56.8 + - - +
96B VAL 3.2 0.2 + - - -
97B VAL* 3.4 8.4 + - - +
98B SER* 3.0 33.1 + - - -
118B LEU* 5.8 2.5 - - + -
134B ALA* 4.2 17.3 - - + +
137B MSE 5.1 3.6 - - - -
138B LEU* 4.2 16.2 - - + -
309F LEU* 3.6 31.4 - - + -
310F LEU* 4.0 13.5 - - + +
312F ILE* 3.4 39.3 - - + -
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Residues in contact with LYS 95 (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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102A LEU* 5.1 13.1 - - - +
55B GLN* 4.4 5.4 + - - +
91B ASN* 3.1 19.9 + - + +
92B GLU* 3.1 36.7 + - - +
93B LEU 3.2 0.4 - - - -
94B ILE* 1.3 77.1 - - - +
96B VAL* 1.3 60.5 + - - +
97B VAL 3.6 0.2 + - - -
98B SER* 3.6 1.7 - - - +
101B TYR* 3.5 31.4 - - + +
102B LEU* 2.9 46.2 + - + +
103B GLY 3.4 1.9 + - - -
310F LEU* 3.8 19.7 - - + -
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Residues in contact with VAL 96 (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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54B ILE* 4.3 15.7 - - + +
55B GLN* 3.8 24.0 - - + -
92B GLU 3.4 17.3 - - - +
93B LEU* 3.0 16.7 + - + +
95B LYS* 1.3 79.1 - - - +
97B VAL* 1.3 56.2 + - + +
102B LEU* 4.2 5.8 - - + -
103B GLY* 3.3 18.5 + - - -
106B VAL* 3.7 28.6 - - + +
110B VAL* 4.1 6.5 - - + -
111B LYS* 3.6 11.5 - - + +
114B VAL* 4.0 23.6 - - + -
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Residues in contact with VAL 97 (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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93B LEU 4.1 5.2 - - - +
94B ILE* 3.6 9.6 - - - +
96B VAL* 1.3 77.4 - - - +
98B SER* 1.3 63.3 + - - +
99B PRO* 3.1 15.1 - - - +
103B GLY* 4.0 4.5 - - - -
111B LYS* 3.8 44.5 + - + +
114B VAL* 4.0 17.0 - - + -
115B ILE* 4.0 17.7 - - + -
138B LEU* 4.1 17.3 - - + -
143B ILE* 3.6 29.3 - - + +
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Residues in contact with SER 98 (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 3.0 19.2 + - - -
95B LYS 4.4 0.4 - - - -
96B VAL 3.5 0.4 - - - -
97B VAL* 1.3 75.8 - - - +
99B PRO* 1.3 62.9 - - - +
100B LYS* 3.4 12.6 + - - +
101B TYR* 2.9 25.9 + - - -
102B LEU 3.4 1.7 + - - -
103B GLY 2.8 19.2 + - - -
143B ILE* 4.4 0.4 - - - -
312F ILE* 3.3 46.7 + - - +
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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