Contacts of the helix formed by residues 58 - 69 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A PRO* 3.7 10.5 - - - -
52A LEU* 3.9 20.6 - - - -
56A GLY 3.7 2.1 + - - -
57A ASP* 1.3 74.6 - - - +
59A MET* 1.3 60.5 + - - +
60A ASP* 3.5 8.3 + - - +
61A SER* 2.8 27.4 + - - -
62A ILE* 2.9 32.8 + - - +
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Residues in contact with MET 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 3.4 55.5 + - + +
11A ILE 4.6 1.6 - - - +
30A GLU* 4.0 27.8 - - + +
31A SER 3.6 38.8 - - - +
32A VAL* 3.7 18.7 - - + +
48A ALA 4.8 0.7 - - - +
50A PRO* 3.8 26.9 - - + +
58A SER* 1.3 74.9 - - - +
60A ASP* 1.3 59.1 + - - +
62A ILE* 3.4 2.8 + - - +
63A GLU* 2.9 31.4 + - - +
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Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 2.7 35.3 + - - +
58A SER* 3.2 7.2 + - - +
59A MET* 1.3 75.8 - - - +
61A SER* 1.3 60.9 + - - +
63A GLU* 4.1 0.4 - - - +
64A SER* 2.9 32.6 + - - -
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLY 5.2 2.2 - - - -
57A ASP* 3.6 12.2 + - - +
58A SER* 2.8 39.3 + - - -
60A ASP* 1.3 76.7 - - - +
62A ILE* 1.3 57.9 + - - +
64A SER* 3.9 4.1 - - - -
65A ALA* 2.9 31.9 + - - +
96A ASN* 4.1 12.4 + - - +
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A VAL* 3.8 27.4 - - + -
48A ALA* 3.9 20.6 - - + +
49A PRO 3.7 26.2 - - - +
50A PRO* 4.4 0.7 - - + -
57A ASP* 4.0 17.3 - - + -
58A SER 2.9 28.6 + - - +
59A MET* 3.6 5.6 - - - +
61A SER* 1.3 80.1 + - - +
63A GLU* 1.3 64.3 + - - +
65A ALA* 3.3 2.1 + - - +
66A ILE* 3.2 33.0 + - + +
96A ASN* 5.6 0.4 - - - -
98A SER* 3.9 18.6 - - - -
99A ALA* 3.8 14.3 - - + +
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A THR* 3.5 24.3 + - - +
9A SER* 4.2 7.3 + - - -
10A ARG* 2.7 53.2 + - - +
32A VAL* 3.8 20.9 - - + -
59A MET 2.9 15.8 + - - +
60A ASP 4.1 2.0 - - - +
62A ILE* 1.3 78.2 - - - +
64A SER* 1.3 62.9 + - - +
66A ILE* 3.3 6.0 + - - +
67A HIS* 3.1 36.5 + - + +
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Residues in contact with SER 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ASP 2.9 20.0 + - - -
61A SER* 3.9 5.2 - - - -
63A GLU* 1.3 76.2 - - - +
65A ALA* 1.3 57.8 + - - +
67A HIS* 5.0 1.6 - - - -
68A HIS* 2.9 61.8 + - - +
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Residues in contact with ALA 65 (chain A).
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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61A SER 2.9 19.2 + - - +
62A ILE 3.7 3.8 - - - +
64A SER* 1.3 76.0 - - - +
66A ILE* 1.3 64.1 + - - +
69A VAL* 3.2 14.8 + - - +
70A LEU* 3.1 23.7 + - + +
93A LEU* 4.0 18.4 - - + -
96A ASN* 3.9 15.0 - - - +
99A ALA* 3.9 16.8 - - + -
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 4.2 18.4 - - + -
8A THR* 3.8 25.8 - - + -
32A VAL* 4.6 2.2 - - + -
34A VAL* 3.5 28.9 - - + -
62A ILE* 3.2 31.2 + - + +
63A GLU* 3.7 5.6 - - - +
65A ALA* 1.3 77.7 - - - +
67A HIS* 1.3 59.1 + - - +
70A LEU* 4.1 6.5 - - + -
71A LYS* 2.7 35.4 + - + +
99A ALA* 4.1 15.7 - - + +
102A ALA* 4.6 2.2 - - + -
103A VAL* 4.2 23.8 - - + -
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Residues in contact with HIS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE 4.7 8.5 - - - -
7A GLU* 5.0 0.9 - - - -
8A THR* 2.6 46.2 + - + +
63A GLU* 3.1 33.5 + - + +
64A SER* 4.2 1.8 - - - +
66A ILE* 1.3 78.8 - - + +
68A HIS* 1.3 70.5 + - + +
71A LYS* 4.0 26.6 + - + +
72A PRO* 3.3 17.3 - - - +
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Residues in contact with HIS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER* 2.9 48.9 + - - +
67A HIS* 1.3 82.8 - - + +
69A VAL* 1.3 67.7 + - + +
72A PRO* 3.4 13.0 - - - +
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA* 3.2 14.9 + - - +
67A HIS 3.6 0.2 - - - -
68A HIS* 1.3 89.6 - - + +
70A LEU* 1.3 69.9 + - + +
71A LYS 3.5 0.7 - - - -
72A PRO* 3.3 12.3 - - - +
73A ALA* 3.6 12.5 + - - +
92A LEU* 3.7 38.6 - - + +
93A LEU* 4.2 26.2 - - + -
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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