Contacts of the helix formed by residues 58 - 69 (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 SER 58 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D PRO* 3.7 10.1 - - - -
52D LEU* 3.7 21.8 - - - -
56D GLY 3.7 1.7 + - - -
57D ASP* 1.3 74.6 - - - +
59D MET* 1.3 64.7 + - - +
60D ASP* 3.6 7.8 + - - +
61D SER* 2.8 26.8 + - - -
62D ILE* 2.9 25.8 + - - +
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Residues in contact with MET 59 (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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10D ARG* 3.6 36.2 + - - +
11D ILE 5.5 0.2 - - - +
30D GLU* 3.9 23.1 - - - +
31D SER* 3.4 20.6 - - - +
32D VAL* 3.4 38.3 - - + +
48D ALA 3.6 4.5 - - - +
49D PRO 4.3 0.4 - - - -
50D PRO* 3.3 37.7 - - + +
58D SER* 1.3 73.7 - - - +
60D ASP* 1.3 62.1 + - - +
62D ILE* 3.5 3.4 + - + +
63D GLU* 3.1 26.3 + - - +
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Residues in contact with ASP 60 (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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10D ARG* 2.7 34.9 + - - +
58D SER* 3.2 7.4 + - - +
59D MET* 1.3 74.9 - - - +
61D SER* 1.3 65.8 + - - +
63D GLU* 4.2 0.8 - - - +
64D SER* 3.0 28.0 + - - -
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Residues in contact with SER 61 (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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56D GLY 5.3 1.6 - - - -
57D ASP* 3.4 14.3 + - - +
58D SER* 2.8 36.5 + - - -
60D ASP* 1.3 78.0 - - - +
62D ILE* 1.3 57.3 + - - +
64D SER* 4.0 4.0 - - - -
65D ALA* 3.0 31.9 + - - +
96D ASN* 4.0 12.3 - - - +
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Residues in contact with ILE 62 (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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32D VAL* 4.1 16.2 - - + -
48D ALA* 4.0 18.6 - - + +
49D PRO 3.7 25.6 - - - +
50D PRO* 4.3 0.7 - - + -
57D ASP* 3.9 18.4 - - + +
58D SER 2.9 26.8 + - - +
59D MET* 3.7 7.0 - - + +
61D SER* 1.3 73.2 - - - +
63D GLU* 1.3 67.1 + - - +
65D ALA* 3.2 3.6 + - - +
66D ILE* 3.0 39.1 + - + +
96D ASN* 5.5 0.2 - - - -
98D SER* 3.9 16.2 - - - -
99D ALA* 3.8 26.0 - - + +
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Residues in contact with GLU 63 (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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8D THR* 3.4 31.1 + - - +
9D SER* 4.3 6.1 + - - -
10D ARG* 2.9 49.6 + - - +
32D VAL* 4.0 15.6 - - + +
59D MET 3.1 11.5 + - - +
60D ASP* 4.2 2.0 - - - +
62D ILE* 1.3 80.5 - - - +
64D SER* 1.3 62.2 + - - +
66D ILE* 3.4 5.1 + - - +
67D HIS* 3.0 37.5 + - + -
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Residues in contact with SER 64 (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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60D ASP 3.0 19.9 + - - -
61D SER* 4.0 4.0 - - - -
63D GLU* 1.3 77.3 - - - +
65D ALA* 1.3 59.0 + - - +
67D HIS* 4.8 1.8 - - - -
68D HIS* 2.8 63.9 + - - +
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Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D SER 3.0 19.9 + - - +
62D ILE 3.5 4.0 - - - +
64D SER* 1.3 77.1 - - - +
66D ILE* 1.3 61.5 + - - +
69D VAL* 3.0 30.6 + - - +
70D LEU* 3.2 12.1 + - + +
93D LEU* 4.1 15.3 - - + -
96D ASN* 3.8 14.6 - - - +
99D ALA* 3.8 17.0 - - + -
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Residues in contact with ILE 66 (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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6D ILE* 4.2 20.2 - - + -
8D THR* 3.8 24.7 - - + -
32D VAL* 4.4 4.0 - - + -
34D VAL* 3.5 28.7 - - + -
62D ILE* 3.0 36.0 + - + +
63D GLU* 3.7 4.0 - - - +
65D ALA* 1.3 76.6 - - - +
67D HIS* 1.3 60.2 + - + +
70D LEU* 4.1 8.1 - - + -
71D LYS* 2.7 34.5 + - + +
99D ALA* 4.1 12.8 - - + +
102D ALA* 4.5 2.2 - - + -
103D VAL* 4.0 23.3 - - + -
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Residues in contact with HIS 67 (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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6D ILE 4.8 9.4 - - - -
7D GLU* 5.0 0.4 - - - -
8D THR* 2.5 45.0 + - + -
63D GLU* 3.0 37.9 + - + +
64D SER* 4.1 2.0 - - - +
66D ILE* 1.3 77.7 - - + +
68D HIS* 1.3 71.2 + - + +
71D LYS* 3.7 26.9 + - + +
72D PRO* 3.2 19.8 - - - +
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Residues in contact with HIS 68 (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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64D SER* 2.8 47.6 + - - +
67D HIS* 1.3 84.1 - - + +
69D VAL* 1.3 65.7 + - + +
72D PRO* 3.6 11.4 - - - +
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Residues in contact with VAL 69 (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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65D ALA* 3.0 16.2 + - - +
67D HIS 3.5 0.4 - - - -
68D HIS* 1.3 89.2 - - + +
70D LEU* 1.3 67.6 + - - +
71D LYS 3.5 0.7 - - - -
72D PRO* 3.4 12.9 - - - +
73D ALA* 3.6 12.5 - - - +
92D LEU* 3.8 33.3 - - + +
93D LEU* 4.0 32.8 - - + -
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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