Contacts of the helix formed by residues 71 - 87 (chain B) in PDB entry 4J00
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 GLU 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LEU* 1.3 75.2 - - - +
72B PRO* 1.3 74.6 - - + +
73B LYS* 3.9 16.9 - - - +
74B ARG* 3.2 35.2 + - + +
75B VAL* 3.4 11.1 + - - +
15D A 4.9 3.5 - - - +
16D C 3.5 28.8 + - + -
17D C 3.7 21.3 + - + -
18D C 3.8 16.2 + - + +
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Residues in contact with PRO 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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61B LEU* 3.8 34.3 - - + +
62B ARG* 3.5 55.2 - - + +
65B GLY* 5.5 0.7 - - - -
66B HIS* 6.0 0.4 - - + -
70B LEU 3.7 3.6 - - - +
71B GLU* 1.3 87.6 - - + +
73B LYS* 1.3 63.2 + - + +
75B VAL* 3.3 25.9 + - + +
76B LYS* 3.4 7.4 + - - +
5C G 6.3 1.3 - - + -
18D C 5.8 2.2 - - - +
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 6.5 0.4 - - + -
71B GLU* 3.2 18.0 - - - +
72B PRO* 1.3 79.0 - - + +
74B ARG* 1.3 65.3 + - - +
76B LYS* 3.0 48.9 + - + +
77B ALA* 3.5 6.4 + - - +
5C G 6.2 0.4 - - - -
6C A 3.7 18.9 + - - -
7C G 2.3 58.4 + - - +
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A HIS* 6.2 0.9 - - + -
47B LYS* 5.2 8.3 - - - +
70B LEU* 4.2 18.2 - - + -
71B GLU* 3.2 29.6 + - + +
73B LYS* 1.3 75.6 - - - +
75B VAL* 1.3 61.5 + - - +
77B ALA* 2.9 42.8 + - - +
78B ILE* 3.2 40.0 + - + +
81B GLU* 5.0 4.8 + - - -
14D A 3.5 44.4 + - - -
15D A 2.9 36.0 + - - +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 4.2 15.7 - - + -
54B TYR* 4.2 15.5 - - + -
61B LEU* 4.2 17.9 - - + +
64B THR* 4.5 7.9 - - + -
65B GLY* 4.7 2.9 - - - +
70B LEU* 3.8 27.4 - - + -
71B GLU 3.4 15.9 - - - +
72B PRO* 3.3 15.7 - - + +
73B LYS 3.2 0.2 - - - -
74B ARG* 1.3 77.4 - - - +
76B LYS* 1.3 50.0 + - - +
78B ILE* 2.9 9.7 + - - +
79B VAL* 2.8 47.0 + - + +
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Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.7 17.4 - - + +
72B PRO 3.4 5.6 + - - +
73B LYS* 3.0 49.1 + - + +
74B ARG 3.2 0.4 - - - -
75B VAL* 1.3 78.9 - - - +
77B ALA* 1.3 60.2 + - - +
79B VAL* 4.1 9.0 - - + +
80B GLU* 3.3 28.7 + - + +
6C A 3.5 27.6 + - - +
7C G 4.1 3.6 + - - -
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LYS 3.5 5.4 + - - +
74B ARG* 2.9 35.3 + - - +
76B LYS* 1.3 78.7 - - - +
78B ILE* 1.3 58.7 + - - +
80B GLU* 4.4 4.1 - - - +
81B GLU* 3.2 30.7 + - - +
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LYS* 3.6 59.2 - - + +
50B ILE* 4.2 19.1 - - + -
51B TYR* 4.6 4.9 - - + +
70B LEU* 5.5 3.4 - - + -
74B ARG* 3.2 46.7 - - + +
75B VAL* 2.9 11.6 + - - +
77B ALA* 1.3 79.1 - - - +
79B VAL* 1.3 70.0 + - + +
80B GLU 3.3 1.6 - - - -
81B GLU* 3.2 16.8 + - - +
82B VAL* 3.2 20.0 + - + +
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 3.9 21.8 - - + -
54B TYR* 3.6 59.7 - - + +
61B LEU* 5.3 1.1 - - + -
75B VAL* 2.8 29.7 + - + +
76B LYS* 3.6 8.5 + - + +
78B ILE* 1.3 75.8 - - + +
80B GLU* 1.3 61.6 + - + +
82B VAL 3.5 0.7 + - - -
83B ARG* 3.3 20.9 + - + +
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Residues in contact with GLU 80 (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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76B LYS* 3.3 17.1 + - + +
77B ALA* 4.6 4.5 - - - +
78B ILE 3.3 0.4 - - - -
79B VAL* 1.3 79.7 - - + +
81B GLU* 1.3 59.2 + - + +
83B ARG* 3.3 28.4 + - - +
84B GLN* 2.6 69.0 + - - +
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LYS* 3.5 28.6 + - - +
74B ARG* 5.0 4.3 + - - -
77B ALA* 3.2 20.6 + - - +
78B ILE* 3.2 16.9 + - - +
80B GLU* 1.3 78.0 - - + +
82B VAL* 1.3 59.8 + - + +
84B GLN* 3.2 7.6 + - - +
85B ALA* 2.8 35.7 + - + +
92B LEU* 4.9 14.0 - - + +
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 6.2 3.8 - - + -
11A LEU* 5.7 8.3 - - + -
47B LYS* 4.6 5.8 - - + +
48B CYS* 5.5 7.0 - - - -
51B TYR* 3.5 59.5 - - + -
78B ILE* 3.2 20.1 + - + +
79B VAL 4.0 0.2 - - - +
81B GLU* 1.3 76.4 - - + +
83B ARG* 1.3 62.9 + - - +
85B ALA* 4.3 4.4 - - - +
86B LEU* 3.5 27.3 + - + +
92B LEU* 5.8 3.4 - - + -
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Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 5.0 6.8 - - - +
79B VAL* 3.3 13.3 + - + +
80B GLU* 3.3 41.3 + - - +
81B GLU 3.1 0.6 - - - -
82B VAL* 1.3 79.5 - - - +
84B GLN* 1.3 76.6 + - - +
87B THR* 2.4 46.2 + - + +
88B GLU* 4.0 12.7 + - - +
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Residues in contact with GLN 84 (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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80B GLU* 2.6 49.7 + - - +
81B GLU* 4.0 6.5 - - - +
83B ARG* 1.3 88.1 - - - +
85B ALA* 1.3 63.6 + - - +
88B GLU* 3.1 50.9 + - + +
89B GLY 3.4 2.4 + - - -
90B LYS* 3.5 15.1 + - + +
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Residues in contact with ALA 85 (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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11A LEU* 6.1 1.8 - - + -
81B GLU 2.8 18.9 + - - +
82B VAL* 4.3 3.4 - - - +
84B GLN* 1.3 77.5 - - - +
86B LEU* 1.3 67.9 + - - +
89B GLY* 3.6 8.8 + - - -
90B LYS* 3.2 27.3 + - - +
91B LEU 5.5 0.2 - - - -
92B LEU* 3.5 35.4 - - + -
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Residues in contact with LEU 86 (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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7A LEU* 6.0 5.8 - - + -
10A ARG* 3.6 44.6 - - + +
11A LEU* 4.2 21.0 - - + +
82B VAL* 3.5 20.5 + - + +
83B ARG 4.5 0.2 - - - +
85B ALA* 1.3 83.8 - - - +
87B THR* 1.3 73.3 + - + +
89B GLY* 4.0 3.8 + - - -
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Residues in contact with THR 87 (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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83B ARG* 2.4 45.5 + - + +
86B LEU* 1.3 89.6 - - + +
88B GLU* 1.3 57.6 + - - +
89B GLY* 3.0 9.8 + - - -
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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