Contacts of the helix formed by residues 58 - 69 (chain C) 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 SER 58 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C PRO* 3.8 11.4 - - - -
52C LEU* 3.8 21.5 - - - -
56C GLY 3.8 1.5 + - - -
57C ASP* 1.3 74.9 - - - +
59C MET* 1.3 65.4 + - - +
60C ASP* 3.4 8.4 + - - +
61C SER* 2.9 25.9 + - - -
62C ILE* 3.0 25.4 + - - +
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Residues in contact with MET 59 (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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10C ARG* 3.5 32.2 + - - +
30C GLU* 3.3 30.1 - - - +
31C SER 3.8 20.2 - - - +
32C VAL* 3.3 31.3 - - + +
48C ALA 3.7 8.7 - - - +
50C PRO* 3.1 39.9 - - + +
58C SER* 1.3 73.7 - - - +
60C ASP* 1.3 58.8 + - - +
62C ILE* 3.8 4.9 - - + +
63C GLU* 3.0 30.8 + - - +
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Residues in contact with ASP 60 (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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10C ARG* 2.6 36.7 + - - +
58C SER* 3.2 6.5 + - - +
59C MET* 1.3 76.4 - - - +
61C SER* 1.3 60.2 + - - +
63C GLU* 3.4 2.5 + - - +
64C SER* 2.8 33.2 + - - -
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Residues in contact with SER 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLY 5.4 1.8 - - - -
57C ASP* 3.5 13.7 + - - +
58C SER* 2.9 37.7 + - - -
60C ASP* 1.3 77.7 - - - +
62C ILE* 1.3 58.2 + - - +
64C SER* 3.8 4.1 - - - -
65C ALA* 2.9 31.6 + - - +
96C ASN* 4.2 12.4 + - - +
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Residues in contact with ILE 62 (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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32C VAL* 3.9 21.8 - - + -
48C ALA* 3.8 22.7 - - + +
49C PRO 3.6 27.4 - - - +
50C PRO* 4.1 0.2 - - + -
57C ASP* 3.8 18.8 - - + -
58C SER 3.0 26.3 + - - +
59C MET* 3.8 7.0 - - + +
61C SER* 1.3 82.8 + - - +
63C GLU* 1.3 63.0 + - - +
65C ALA* 3.3 2.3 + - - +
66C ILE* 3.1 36.6 + - + +
96C ASN* 5.5 0.7 - - - -
98C SER* 4.0 15.5 - - - -
99C ALA* 4.2 13.7 - - - +
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Residues in contact with GLU 63 (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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39B ASP 5.3 3.2 - - - +
8C THR* 3.5 22.2 + - - +
9C SER* 5.0 0.2 - - - -
10C ARG* 3.0 47.7 + - - +
32C VAL* 4.9 7.4 - - + +
59C MET 3.0 14.5 + - - +
60C ASP* 3.9 2.7 - - - +
62C ILE* 1.3 80.9 - - - +
64C SER* 1.3 58.2 + - - +
66C ILE* 3.3 6.8 + - - +
67C HIS* 2.9 61.1 + - + +
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Residues in contact with SER 64 (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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60C ASP 2.8 19.5 + - - -
61C SER* 3.8 4.9 - - - -
63C GLU* 1.3 77.0 - - - +
65C ALA* 1.3 57.2 + - - +
67C HIS* 4.5 1.8 - - - -
68C HIS* 2.8 54.9 + - - +
69C VAL* 4.9 0.2 - - - +
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Residues in contact with ALA 65 (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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61C SER 2.9 19.8 + - - +
62C ILE 3.6 4.7 - - - +
64C SER* 1.3 76.4 - - - +
66C ILE* 1.3 57.1 + - - +
69C VAL* 3.0 33.7 + - - +
70C LEU* 3.1 12.9 + - + +
93C LEU* 4.0 21.3 - - + -
96C ASN* 4.0 8.1 - - - +
99C ALA* 3.8 17.7 - - + -
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Residues in contact with ILE 66 (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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6C ILE* 4.2 20.6 - - + -
8C THR* 3.9 24.0 - - + -
32C VAL* 4.5 2.7 - - + -
34C VAL* 3.4 29.2 - - + -
62C ILE* 3.1 32.1 + - + +
63C GLU 3.8 3.6 - - - +
65C ALA* 1.3 76.1 - - - +
67C HIS* 1.3 62.9 + - + +
70C LEU* 4.1 8.3 - - + -
71C LYS* 2.8 34.8 + - + +
99C ALA* 4.0 25.4 - - + +
102C ALA* 4.8 1.8 - - + -
103C VAL* 4.3 14.1 - - + -
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Residues in contact with HIS 67 (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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39B ASP 3.6 23.1 - - - -
40B SER* 3.7 26.0 + - - +
41B GLY* 5.2 1.4 - - - -
6C ILE 5.6 2.9 - - - -
7C GLU* 5.6 0.4 - - - -
8C THR* 2.7 40.4 + - + +
63C GLU* 2.9 37.4 + - + +
64C SER* 4.0 2.4 - - - +
66C ILE* 1.3 81.7 - - + +
68C HIS* 1.3 74.7 + - + +
71C LYS* 3.8 20.2 - - + +
72C PRO* 3.4 15.4 - - - +
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Residues in contact with HIS 68 (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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64C SER* 2.8 47.1 + - - +
67C HIS* 1.3 86.6 - - + +
69C VAL* 1.3 66.5 + - + +
72C PRO* 3.4 15.8 - - - +
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Residues in contact with VAL 69 (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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65C ALA* 3.0 16.1 + - - +
67C HIS 3.7 0.8 - - - -
68C HIS* 1.3 90.2 - - + +
70C LEU* 1.3 68.6 + - + +
71C LYS 3.5 0.4 - - - -
72C PRO* 3.6 3.5 - - - +
73C ALA* 3.5 21.0 + - - +
92C LEU* 3.8 36.4 - - + +
93C LEU* 4.2 27.4 - - + -
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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