Contacts of the helix formed by residues 81 - 92 (chain D) in PDB entry 1JPM
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 GLY 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C GLY 3.6 6.5 - - - -
125C GLY 3.9 10.5 - - - -
78D SER* 3.1 12.8 + - - +
79D LEU 3.0 0.4 - - - -
80D ALA* 1.3 78.7 - - - +
82D TYR* 1.3 62.4 + - - -
83D GLU 3.4 2.4 + - - -
84D ALA* 3.6 10.9 + - - +
85D ILE* 3.4 23.4 + - - +
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Residues in contact with TYR 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C GLN 5.3 2.0 - - - +
124C GLY* 3.3 12.7 + - - +
79D LEU* 3.4 36.2 + - + +
80D ALA 3.4 0.8 - - - -
81D GLY* 1.3 73.1 - - - +
83D GLU* 1.3 61.3 + - - +
85D ILE* 3.1 9.6 + - + +
86D LEU* 2.8 57.7 + - + +
107D LEU* 3.2 18.9 - - + +
108D TYR* 3.0 71.9 + + - -
111D TRP* 3.9 37.2 - + + +
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Residues in contact with GLU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C LEU 4.8 1.6 - - - +
124C GLY* 3.1 21.6 + - - +
126C TYR* 3.7 13.7 - - + -
282C ASN* 5.2 0.9 + - - -
286C GLU* 4.4 9.8 - - - +
313C SER 3.6 19.0 - - - +
314C LYS* 3.4 21.9 + - - +
315C ARG* 2.8 36.1 + - + +
316C ASN 4.3 1.4 + - - -
82D TYR* 1.3 75.6 - - - +
84D ALA* 1.3 59.2 + - - +
86D LEU* 3.3 11.5 + - - +
87D HIS* 2.9 29.0 + - + +
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Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C TYR* 3.9 29.7 - - + +
81D GLY* 3.6 11.3 + - - +
82D TYR 3.3 0.6 - - - -
83D GLU* 1.3 77.8 - - - +
85D ILE* 1.3 64.4 + - + +
87D HIS* 3.2 5.5 + - - +
88D ASP* 2.9 32.3 + - - +
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Residues in contact with ILE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ILE* 4.8 2.0 - - + -
74D LEU* 3.5 23.6 - - + -
77D LYS* 3.8 31.0 - - + -
78D SER 3.4 25.1 - - - +
79D LEU* 4.0 22.9 - - + -
81D GLY 3.4 10.9 + - - +
82D TYR* 3.1 11.3 + - + +
84D ALA* 1.3 77.4 - - + +
86D LEU* 1.3 64.2 + - + +
88D ASP* 3.1 10.0 + - - +
89D ILE* 3.0 21.7 + - + +
107D LEU* 3.6 28.0 - - + -
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Residues in contact with LEU 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D TYR* 2.8 53.5 + - + +
83D GLU* 3.7 11.0 - - - +
85D ILE* 1.3 72.9 - - + +
87D HIS* 1.3 63.2 + - - +
89D ILE* 3.4 9.7 + - + +
90D GLN* 3.1 29.8 + - + +
104D GLU* 3.5 37.5 - - + +
107D LEU* 5.1 2.7 - - + -
108D TYR* 3.6 24.0 - - + +
276D SER* 3.9 13.5 - - - +
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Residues in contact with HIS 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C GLU* 5.5 4.5 - - - -
315C ARG* 3.2 61.4 + - + -
83D GLU* 2.9 17.6 + - + +
84D ALA* 3.2 6.7 + - - +
86D LEU* 1.3 76.4 - - - +
88D ASP* 1.3 66.6 + - - +
90D GLN* 4.9 0.4 - - - -
91D HIS* 2.9 79.8 + + + +
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Residues in contact with ASP 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ALA* 4.9 13.8 - - + +
74D LEU* 5.0 5.5 - - + +
77D LYS* 5.1 8.8 - - - +
84D ALA* 2.9 23.0 + - - +
85D ILE* 3.4 10.9 - - - +
87D HIS* 1.3 80.8 + - - +
89D ILE* 1.3 60.6 + - - +
91D HIS* 5.3 0.2 - - - -
92D LEU* 2.9 65.6 + - + +
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Residues in contact with ILE 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D LEU* 3.8 25.3 - - + +
74D LEU* 4.1 15.5 - - + -
85D ILE* 3.0 18.8 + - + +
86D LEU* 3.7 9.2 - - + +
88D ASP* 1.3 77.2 - - - +
90D GLN* 1.3 69.0 + - - +
91D HIS 3.6 0.2 + - - -
93D LEU* 3.9 3.5 - - - +
100D LYS* 3.4 50.5 - - + +
103D VAL* 3.9 11.0 - - + -
104D GLU* 4.3 12.6 - - + -
107D LEU* 3.1 36.3 - - + -
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Residues in contact with GLN 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D LEU* 3.1 17.9 + - + +
87D HIS* 4.9 0.4 - - - -
89D ILE* 1.3 82.7 - - - +
91D HIS* 1.3 79.2 + - + +
93D LEU 3.6 1.6 - - - +
94D THR* 5.5 0.2 - - - -
97D MET* 4.5 6.6 - - - +
100D LYS* 3.2 42.8 + - - +
104D GLU* 3.0 18.9 + - - +
272D ALA 4.0 12.7 + - - +
273D GLY* 2.8 29.3 + - - -
276D SER* 4.3 8.0 + - - +
277D GLY* 5.9 0.7 - - - -
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Residues in contact with HIS 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D HIS* 2.9 65.1 + + + +
88D ASP* 5.3 0.2 - - - -
90D GLN* 1.3 94.4 + - + +
92D LEU* 1.3 63.5 + - - +
93D LEU* 3.1 6.7 + - - +
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Residues in contact with LEU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D VAL* 3.8 29.1 - - + +
70D LEU* 5.1 3.8 - - + -
73D ALA* 3.4 33.2 - - + -
88D ASP* 2.9 49.9 + - + +
89D ILE 4.4 0.4 + - - -
91D HIS* 1.3 73.0 - - - +
93D LEU* 1.3 62.3 + - + +
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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