Contacts of the helix formed by residues 61 - 74 (chain B) in PDB entry 1JVM
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 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B VAL* 3.7 5.1 - - - +
60B ILE* 1.3 92.6 + - + +
62B TYR* 1.3 63.5 + - - +
63B PRO* 3.4 17.7 - - - +
64B ARG* 3.2 31.6 + - - +
65B ALA* 3.3 15.9 + - - +
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Residues in contact with TYR 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B SER* 4.9 2.5 - - - -
45B TYR* 5.6 11.9 - - + +
48B VAL* 3.3 24.1 - - + +
60B ILE 4.0 0.2 + - - -
61B THR* 1.3 69.6 - - - +
63B PRO* 1.4 67.6 - - + +
65B ALA* 3.2 2.9 + - - +
66B LEU* 2.9 30.7 + - - +
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Residues in contact with PRO 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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61B THR* 3.3 17.9 - - - +
62B TYR* 1.4 94.2 - - + +
64B ARG* 1.3 65.0 + - + +
66B LEU* 3.3 23.5 - - + +
67B TRP* 3.4 8.1 + - - +
89C ARG* 5.0 1.9 + - - -
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Residues in contact with ARG 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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57B ALA 4.8 0.6 + - - -
58B GLN* 2.5 54.0 + - - +
59B LEU* 5.0 2.0 - - - -
60B ILE* 4.5 12.1 - - - +
61B THR* 3.2 33.9 + - - +
62B TYR 3.2 0.2 - - - -
63B PRO* 1.3 77.3 - - + +
65B ALA* 1.3 67.0 + - - +
67B TRP* 2.9 19.8 + - - +
68B TRP 3.0 10.0 + - - -
81B LEU* 3.7 26.9 - - + +
89C ARG* 5.1 4.9 - - - +
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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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44B SER* 3.8 14.1 - - - +
47B ALA* 5.3 0.4 - - + -
48B VAL* 3.2 39.0 - - + +
59B LEU* 4.1 15.2 - - + +
61B THR 3.3 2.7 + - - +
62B TYR 3.2 2.7 + - - +
64B ARG* 1.3 78.6 - - - +
66B LEU* 1.3 64.0 + - - +
68B TRP* 3.1 16.1 - - + +
69B SER* 2.9 25.5 + - - -
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Residues in contact with LEU 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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40B LEU* 5.6 2.2 - - + +
41B LEU* 4.1 22.9 - - + -
44B SER* 3.1 29.8 + - - +
62B TYR 2.9 13.9 + - - +
63B PRO* 3.3 17.7 - - + +
65B ALA* 1.3 75.3 - - - +
67B TRP* 1.3 65.3 + - - +
69B SER* 3.1 14.4 + - - -
70B VAL* 3.2 15.9 - - + +
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Residues in contact with TRP 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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63B PRO 3.4 5.3 + - - +
64B ARG 2.9 11.2 + - - +
66B LEU* 1.3 75.1 - - - +
68B TRP* 1.3 65.5 + - - +
70B VAL* 2.7 40.6 + - + +
71B GLU* 2.9 37.4 + - + -
78B TYR* 3.9 20.4 - + - -
80B ASP* 3.7 9.2 + - - -
81B LEU* 3.6 19.5 - - + -
82C TYR* 5.1 0.6 - - + -
83C PRO* 3.5 37.6 + - + -
89C ARG* 2.8 72.2 - - + +
92C ALA* 4.0 13.2 - - + -
93C VAL* 4.8 0.4 - - + -
96C MET* 5.3 3.1 - - + -
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Residues in contact with TRP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 2.7 29.6 + + - -
43B GLY 4.5 2.2 - - - -
47B ALA* 3.7 28.7 - - + -
59B LEU* 3.7 28.3 - - + -
64B ARG 3.0 4.7 + - - +
65B ALA* 3.1 21.5 - - + +
67B TRP* 1.3 79.5 - - - +
69B SER* 1.3 64.7 + - - +
71B GLU* 2.9 14.4 + - - +
72B THR* 2.6 55.1 + - + -
81B LEU* 3.3 32.2 + - + -
82B TYR* 3.9 5.1 - - - +
83B PRO* 4.2 11.7 - - + -
88B GLY 4.3 3.1 - - - -
91B VAL* 4.3 7.2 - - + -
92B ALA* 3.8 39.7 - - + -
95B VAL* 4.5 8.5 - - + -
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Residues in contact with SER 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.4 26.2 - - - -
43B GLY* 4.3 0.5 - - - -
44B SER* 3.0 30.5 + - - -
65B ALA 2.9 12.1 + - - -
66B LEU 3.1 9.2 + - - -
68B TRP* 1.3 88.4 - - - +
70B VAL* 1.3 53.6 + - - +
72B THR* 3.5 4.6 - - - -
73B ALA* 2.7 38.8 + - - +
95B VAL* 3.6 7.8 - - - +
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Residues in contact with VAL 70 (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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40B LEU* 4.6 14.4 - - + -
66B LEU* 3.2 16.2 - - + +
67B TRP* 2.7 32.6 + - + +
69B SER* 1.3 72.2 - - - +
71B GLU* 1.3 51.9 + - - +
72B THR 3.0 4.4 + - - -
73B ALA* 3.9 1.8 - - - +
74B THR* 2.6 39.9 + - + +
93C VAL* 3.8 22.9 - - + -
96C MET* 3.4 28.5 - - + -
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Residues in contact with GLU 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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78A TYR* 4.7 3.5 - - + -
67B TRP* 2.9 34.1 + - + +
68B TRP* 3.3 11.9 - - - +
70B VAL* 1.3 80.7 - - - +
72B THR* 1.3 56.0 + - - +
74B THR* 3.5 5.6 + - - -
76B VAL* 3.2 12.3 + - - -
77B GLY* 3.0 31.3 + - - +
78B TYR* 3.4 26.3 + - + +
79B GLY* 3.0 25.3 + - - -
80B ASP* 2.8 31.7 + - - +
81B LEU* 4.1 10.7 - - - +
96C MET* 5.3 2.9 - - - -
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Residues in contact with THR 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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76A VAL* 4.0 7.3 - - + +
78A TYR* 2.6 29.3 + - + +
68B TRP* 2.6 43.2 + - + -
69B SER* 3.5 5.2 - - - -
71B GLU* 1.3 73.0 - - - +
73B ALA* 1.3 57.9 + - - +
74B THR 3.1 5.2 - - - -
75B THR* 2.9 25.3 + - - +
92B ALA* 4.5 1.1 - - - +
95B VAL* 3.9 14.4 - - + -
96B MET* 3.3 30.9 - - + +
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Residues in contact with ALA 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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36B LEU* 4.6 7.9 - - + -
40B LEU* 4.1 12.3 - - + -
69B SER 2.7 21.0 + - - +
70B VAL* 4.1 3.1 - - - +
72B THR* 1.3 73.2 - - - +
74B THR* 1.3 60.0 + - + +
75B THR* 3.3 5.6 - - - +
95B VAL* 3.8 28.0 - - + +
96B MET* 4.5 1.8 - - - +
99B GLY* 3.5 30.2 - - - +
100B ILE* 4.0 2.4 + - - -
103B PHE* 4.0 7.6 - - + -
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Residues in contact with THR 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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129A TBA 4.6 3.5 - - - +
70B VAL* 2.6 26.1 + - + +
71B GLU 3.5 4.7 + - - -
73B ALA* 1.3 78.8 - - + +
75B THR* 1.3 72.5 + - - +
76B VAL* 3.0 28.0 + - - +
103B PHE* 4.5 10.1 - - + -
75C THR* 3.5 15.8 - - - +
96C MET* 3.6 24.9 - - + -
97C VAL* 5.4 2.7 - - + -
100C ILE* 4.0 25.8 - - + +
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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