Contacts of the helix formed by residues 58 - 69 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B PRO* 3.7 10.1 - - - -
52B LEU* 3.8 20.9 - - - -
56B GLY 3.8 1.5 + - - -
57B ASP* 1.3 73.0 - - - +
59B MET* 1.3 65.2 + - - +
60B ASP* 3.5 7.7 + - - +
61B SER* 2.9 24.0 + - - -
62B ILE* 2.9 24.9 + - - +
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Residues in contact with MET 59 (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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10B ARG* 3.6 51.9 + - + +
11B ILE 4.5 1.6 - - - +
30B GLU* 3.9 24.5 - - + +
31B SER* 3.6 39.7 - - - +
32B VAL* 3.9 13.8 - - + +
48B ALA 4.8 0.4 - - - +
50B PRO* 3.6 35.7 - - + +
58B SER* 1.3 73.2 - - - +
60B ASP* 1.3 63.9 + - - +
62B ILE* 3.4 2.6 + - - +
63B GLU* 3.1 25.6 + - - +
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Residues in contact with ASP 60 (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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10B ARG* 2.6 35.1 + - - +
58B SER* 3.2 7.0 + - - +
59B MET* 1.3 78.6 - - - +
61B SER* 1.3 60.5 + - - +
63B GLU* 4.1 1.3 - - - +
64B SER* 3.0 30.8 + - - -
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Residues in contact with SER 61 (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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56B GLY 5.4 1.6 - - - -
57B ASP* 3.6 13.7 + - - +
58B SER* 2.9 32.8 + - - -
60B ASP* 1.3 75.4 - - - +
62B ILE* 1.3 68.5 + - - +
64B SER* 3.9 4.5 - - - -
65B ALA* 3.0 26.7 + - - +
96B ASN* 4.1 12.3 + - - +
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Residues in contact with ILE 62 (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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32B VAL* 3.8 23.1 - - + -
48B ALA* 3.7 22.2 - - + +
49B PRO 3.5 27.8 - - - +
50B PRO* 4.3 0.7 - - + -
57B ASP* 3.9 19.3 - - + -
58B SER 2.9 18.9 + - - +
59B MET* 3.7 4.0 - - - +
61B SER* 1.3 83.8 + - - +
63B GLU* 1.3 63.8 + - - +
65B ALA* 3.4 2.3 + - - +
66B ILE* 3.1 41.9 + - + +
96B ASN* 5.5 0.2 - - - -
98B SER* 3.9 17.3 - - - -
99B ALA* 3.8 14.3 - - + +
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Residues in contact with GLU 63 (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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8B THR* 2.9 43.2 + - - +
9B SER* 4.2 1.2 + - - -
10B ARG* 2.7 48.9 + - - +
32B VAL* 4.2 8.3 - - + -
59B MET 3.1 11.9 + - - +
60B ASP 4.1 2.2 - - - +
62B ILE* 1.3 81.2 - - - +
64B SER* 1.3 63.8 + - - +
66B ILE* 3.3 6.3 + - - +
67B HIS* 2.9 39.7 + - + -
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Residues in contact with SER 64 (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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60B ASP 3.0 20.5 + - - -
61B SER* 3.9 5.2 - - - -
63B GLU* 1.3 76.2 - - - +
65B ALA* 1.3 54.7 + - - +
67B HIS* 4.7 1.3 - - - -
68B HIS* 2.7 61.2 + - - +
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Residues in contact with ALA 65 (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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61B SER 3.0 19.0 + - - +
62B ILE 3.6 4.9 - - - +
64B SER* 1.3 76.0 - - - +
66B ILE* 1.3 58.9 + - - +
68B HIS* 5.3 0.2 - - - -
69B VAL* 3.0 29.5 + - - +
70B LEU* 3.1 13.2 + - + +
93B LEU* 3.9 24.9 - - + -
96B ASN* 4.0 7.0 - - - +
99B ALA* 3.8 17.3 - - + -
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Residues in contact with ILE 66 (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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6B ILE* 4.1 20.9 - - + -
8B THR* 3.8 24.7 - - + -
32B VAL* 4.5 2.5 - - + -
34B VAL* 3.6 28.0 - - + -
62B ILE* 3.1 31.9 + - + +
63B GLU 3.7 5.6 - - - +
64B SER 3.2 0.2 - - - -
65B ALA* 1.3 78.1 - - - +
67B HIS* 1.3 59.8 + - + +
70B LEU* 4.2 6.7 - - + -
71B LYS* 2.8 36.2 + - + +
99B ALA* 4.1 19.3 - - + +
102B ALA* 4.6 1.3 - - + -
103B VAL* 4.2 18.8 - - + -
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Residues in contact with HIS 67 (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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6B ILE* 4.8 9.4 - - + -
7B GLU* 5.0 0.7 - - - -
8B THR* 2.6 44.6 + - + -
63B GLU* 2.9 37.9 + - + +
64B SER* 4.0 2.0 - - - +
66B ILE* 1.3 78.6 - - + +
68B HIS* 1.3 70.8 + - + +
71B LYS* 4.1 24.6 + - - +
72B PRO* 3.5 14.4 - - - +
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Residues in contact with HIS 68 (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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64B SER* 2.7 50.7 + - - +
67B HIS* 1.3 84.3 + - + +
69B VAL* 1.3 66.7 + - + +
72B PRO* 3.7 12.4 - - - +
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Residues in contact with VAL 69 (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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65B ALA* 3.0 14.4 + - - +
67B HIS 3.7 0.4 - - - -
68B HIS* 1.3 89.4 - - + +
70B LEU* 1.3 69.3 + - + +
71B LYS 3.6 0.7 - - - -
72B PRO* 3.5 11.7 - - - +
73B ALA* 3.5 13.0 - - - +
92B LEU* 3.6 37.4 - - + +
93B LEU* 4.2 29.4 - - + -
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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