Contacts of the helix formed by residues 70 - 78 (chain B) in PDB entry 1JI5
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 THR 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A THR* 4.1 1.8 - - - -
82A GLU* 3.2 15.7 - - - -
83A ALA* 3.3 40.8 - - + +
85A TYR* 3.8 6.1 - - + +
68B VAL 4.0 0.2 - - - -
69B ALA* 1.3 84.1 - - - +
71B MET* 1.3 64.8 + - - +
72B LYS* 3.9 6.8 - - - +
73B GLU* 2.7 45.9 + - - +
74B TYR* 3.1 26.8 + - - -
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Residues in contact with MET 71 (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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17A SER 4.2 1.8 - - - +
18A VAL* 4.2 25.1 - - - -
21A THR* 3.5 12.7 - - + +
71A MET* 3.1 71.2 - - + +
74A TYR* 3.7 18.6 - - + -
75A LEU* 3.9 25.4 - - + -
82A GLU* 2.6 16.3 + - - +
70B THR* 1.3 71.5 - - - +
72B LYS* 1.3 62.0 + - - +
74B TYR* 3.2 4.3 + - - +
75B LEU* 2.9 27.0 + - - +
2001B MPD 3.5 19.7 - - + -
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Residues in contact with LYS 72 (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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75A LEU* 4.0 13.4 - - + +
82A GLU* 3.7 15.5 + - - +
83A ALA* 6.3 2.2 - - + -
70B THR* 3.9 9.4 - - - +
71B MET* 1.3 80.7 - - - +
73B GLU* 1.3 66.4 + - + +
75B LEU* 3.3 5.5 + - - +
76B GLU* 3.2 44.9 + - - +
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Residues in contact with GLU 73 (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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85A TYR* 2.5 41.7 + - - -
68B VAL* 3.9 28.1 - - + +
69B ALA 3.9 0.5 + - - -
70B THR* 2.7 25.9 + - - +
72B LYS* 1.3 77.7 - - + +
74B TYR* 1.3 60.4 + - - +
76B GLU* 2.9 27.3 + - + +
77B ILE* 2.5 32.3 + - + +
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Residues in contact with TYR 74 (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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21A THR* 3.5 26.8 - - + +
28A TRP* 3.7 12.3 - - - -
71A MET* 3.7 19.1 - - + -
13B VAL* 3.6 16.5 - - + +
14B ALA* 3.5 29.4 - - + +
17B SER* 3.5 23.7 + - - -
18B VAL* 5.0 0.7 - - + -
53B ILE* 5.2 0.3 - - - +
68B VAL* 3.0 45.0 + - + -
69B ALA* 3.5 6.9 - - - -
70B THR 3.1 20.0 + - - -
71B MET* 3.3 15.5 - - - +
73B GLU* 1.3 76.4 - - - +
75B LEU* 1.3 56.8 + - - +
78B SER* 2.7 40.1 + - - -
2001B MPD 4.8 1.6 - - + -
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Residues in contact with LEU 75 (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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71A MET* 3.9 34.8 - - + -
72A LYS* 4.0 13.7 - - + +
75A LEU* 3.3 33.2 - - + -
18B VAL* 5.0 5.8 - - + -
71B MET 2.9 10.3 + - - +
72B LYS* 3.5 9.2 - - - +
73B GLU 3.1 0.2 - - - -
74B TYR* 1.3 78.6 - - - +
76B GLU* 1.3 59.7 + - - +
77B ILE 3.3 0.9 + - - -
78B SER* 4.1 10.3 + - - +
82B GLU* 4.2 20.2 - - + +
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Residues in contact with GLU 76 (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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72B LYS* 3.2 42.4 + - - +
73B GLU* 3.1 27.5 - - - +
75B LEU* 1.3 77.8 - - - +
77B ILE* 1.3 59.4 + - + +
78B SER 5.0 0.4 - - - -
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Residues in contact with ILE 77 (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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7B GLU* 4.3 16.2 - - - +
10B ASN* 3.7 13.2 - - + +
11B LYS* 2.9 48.0 + - + +
14B ALA* 3.9 7.6 - - + -
68B VAL* 5.0 9.4 - - + -
73B GLU* 2.5 43.1 - - + +
74B TYR* 3.8 5.6 - - - +
76B GLU* 1.3 81.0 - - + +
78B SER* 1.3 68.1 + - - +
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Residues in contact with SER 78 (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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11B LYS* 3.8 0.7 - - - +
14B ALA* 3.9 11.6 - - - +
15B ASP* 3.1 15.2 + - - -
18B VAL* 3.2 31.5 - - - +
74B TYR 2.7 23.0 + - - -
75B LEU* 4.2 9.3 - - - +
76B GLU 5.0 0.3 - - - -
77B ILE* 1.3 77.9 - - - +
79B SER* 1.3 60.9 + - - +
80B ILE* 3.0 18.2 + - - +
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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