Contacts of the helix formed by residues 62 - 81 (chain A) in PDB entry 4JF7
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 62 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 1.3 84.1 - - - +
63A ASP* 1.3 66.4 + - - +
65A LEU* 3.9 5.7 - - - +
66A ASN* 3.2 27.7 + - - +
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Residues in contact with ASP 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 3.2 2.8 + - - +
62A THR* 1.3 82.2 + - - +
64A LEU* 1.3 70.0 + - + +
65A LEU 3.1 4.6 + - - -
66A ASN* 4.3 1.6 - - - +
67A ASN* 2.8 37.2 + - - +
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 3.1 11.4 + - + +
63A ASP* 1.3 84.1 - - + +
65A LEU* 1.3 70.5 + - + +
67A ASN* 4.3 11.2 - - - +
68A ILE* 4.5 15.2 - - - +
65D LEU* 3.5 42.9 - - + +
66D ASN* 5.6 2.0 - - - -
68D ILE* 5.7 0.7 - - - +
69D LEU* 4.0 35.6 - - + +
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 3.2 46.0 - - + +
62A THR* 3.9 6.1 - - - +
63A ASP 3.1 0.6 - - - -
64A LEU* 1.3 89.9 - - + +
66A ASN* 1.3 65.7 + - - +
67A ASN 3.1 2.0 + - - -
68A ILE* 3.2 16.3 + - - +
69A LEU* 3.3 12.3 + - - +
65B LEU* 3.5 47.3 - - + +
68B ILE* 5.4 2.4 - - - +
65D LEU* 6.3 2.0 - - + -
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Residues in contact with ASN 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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62A THR 3.2 15.5 + - - +
63A ASP 4.5 1.1 - - - +
65A LEU* 1.3 79.2 - - - +
67A ASN* 1.3 62.6 + - - +
69A LEU* 3.7 11.3 + - + +
70A SER* 3.5 22.7 + - - -
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Residues in contact with ASN 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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63A ASP* 2.8 36.4 + - - +
64A LEU* 4.3 8.3 - - - +
65A LEU 3.1 0.6 - - - -
66A ASN* 1.3 76.4 - - - +
68A ILE* 1.3 66.0 + - - +
69A LEU 3.4 0.2 + - - -
70A SER* 3.5 2.7 + - - -
71A VAL* 3.0 30.7 + - + +
69D LEU* 3.8 22.9 - - + +
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Residues in contact with ILE 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 LEU 4.5 11.9 - - - +
65A LEU* 3.2 10.7 + - - +
67A ASN* 1.3 77.9 - - - +
69A LEU* 1.3 57.0 + - - +
71A VAL* 2.9 6.9 + - - -
72A ALA* 2.4 47.7 + - + +
68B ILE* 3.8 35.4 - - + -
68D ILE* 3.7 47.1 - - + +
69D LEU* 4.4 20.6 - - + +
72D ALA* 5.1 8.5 - - + -
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Residues in contact with LEU 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 LEU 3.3 9.3 + - - +
66A ASN* 3.8 13.0 - - + +
67A ASN 3.3 0.2 - - - -
68A ILE* 1.3 80.8 - - - +
70A SER* 1.3 67.0 + - - +
72A ALA* 3.8 2.2 - - - +
73A ASN* 2.9 48.1 + - - +
67B ASN* 4.8 14.1 - - + -
68B ILE* 4.6 17.9 - - + +
71B VAL* 5.4 7.9 - - + +
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Residues in contact with SER 70 (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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66A ASN 3.5 12.9 + - - -
67A ASN* 3.5 4.1 + - - -
68A ILE 3.4 0.2 - - - -
69A LEU* 1.3 87.3 - - - +
71A VAL* 1.3 58.2 + - - +
73A ASN* 3.9 10.3 + - - +
74A GLN* 3.1 36.1 + - - +
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASN* 3.0 24.3 + - + +
68A ILE* 2.9 6.1 + - - +
70A SER* 1.3 78.2 - - - +
72A ALA* 1.3 62.6 + - - +
73A ASN 3.1 4.3 - - - -
74A GLN* 3.1 25.3 + - - +
75A ILE* 3.1 16.9 + - + +
69D LEU* 5.8 6.5 - - + -
72D ALA* 3.6 33.2 - - + +
73D ASN* 4.5 11.2 - - - +
76D ILE* 3.6 12.4 - - + +
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Residues in contact with ALA 72 (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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68A ILE* 2.4 45.4 + - + +
69A LEU* 4.2 2.9 - - - +
71A VAL* 1.3 68.7 - - + +
73A ASN* 1.3 55.0 + - - +
75A ILE* 3.5 17.0 - - + +
76A ILE* 3.1 19.9 + - - +
68B ILE* 5.4 4.5 - - + -
71B VAL* 3.5 34.7 - - + +
75B ILE* 4.2 6.9 - - + +
72D ALA* 6.1 2.5 - - + -
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Residues in contact with ASN 73 (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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69A LEU* 2.9 42.0 + - - +
70A SER* 3.9 10.7 + - - +
72A ALA* 1.3 75.3 - - - +
74A GLN* 1.3 59.7 + - + +
75A ILE 3.1 1.8 - - - -
76A ILE* 3.2 15.0 + - - +
77A TYR* 2.8 27.1 + - - +
71B VAL* 4.1 16.5 - - - +
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Residues in contact with GLN 74 (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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70A SER* 3.1 25.2 + - - +
71A VAL* 3.1 18.4 + - - +
73A ASN* 1.3 78.6 - - + +
75A ILE* 1.3 52.7 + - - +
77A TYR* 3.3 13.5 - - + +
78A ASN* 2.7 41.8 + - - +
76D ILE* 3.8 17.2 - - + +
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Residues in contact with ILE 75 (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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71A VAL* 3.1 15.8 + - + +
72A ALA* 3.5 17.0 - - + +
73A ASN 3.1 0.6 - - - -
74A GLN* 1.3 74.9 - - - +
76A ILE* 1.3 65.8 + - - +
78A ASN* 3.2 7.1 + - - +
79A SER* 2.9 26.8 + - - -
75B ILE* 3.7 32.1 - - + -
72D ALA* 3.8 25.8 - - + +
75D ILE* 3.7 36.3 - - + +
76D ILE* 3.6 16.4 - - + +
79D SER* 4.9 5.1 - - - +
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Residues in contact with ILE 76 (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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72A ALA 3.1 12.5 + - - +
73A ASN* 3.2 17.5 + - - +
75A ILE* 1.3 76.9 - - - +
77A TYR* 1.3 60.3 + - - +
79A SER 3.3 0.2 + - - -
80A ALA* 2.9 36.9 + - + +
70B SER 5.0 0.4 - - - +
71B VAL* 3.6 35.0 - - + +
74B GLN* 3.6 40.2 - - + +
75B ILE* 4.5 5.2 - - + -
78B ASN* 3.6 6.9 + - - +
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Residues in contact with TYR 77 (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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73A ASN 2.8 14.1 + - - +
74A GLN* 3.3 15.7 - - + +
75A ILE 3.1 0.2 - - - -
76A ILE* 1.3 79.5 - - - +
78A ASN* 1.3 75.7 + - - +
80A ALA* 5.1 0.4 - - - -
81A VAL* 3.1 40.7 + - + +
82A ALA* 3.1 37.5 + - + +
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Residues in contact with ASN 78 (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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74A GLN* 2.7 27.5 + - - +
75A ILE* 3.2 5.1 + - - +
77A TYR* 1.3 85.2 - - - +
79A SER* 1.3 56.5 + - - +
82A ALA* 3.6 12.4 - - + +
83A LEU* 2.8 37.2 + - - +
76D ILE* 4.0 16.0 - - - +
79D SER* 2.9 42.2 + - - +
80D ALA* 3.8 19.4 - - - +
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Residues in contact with SER 79 (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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75A ILE* 2.9 20.4 + - - -
76A ILE* 4.8 0.2 - - - -
78A ASN* 1.3 77.6 - - - +
80A ALA* 1.3 60.2 + - - +
83A LEU* 4.7 6.5 - - - +
84A PRO* 3.6 15.3 - - - +
75B ILE* 4.5 2.9 + - - -
78B ASN* 3.3 37.5 + - - +
79B SER* 3.4 18.5 + - - -
82B ALA* 5.4 2.1 - - - +
83B LEU* 3.7 20.6 - - - +
79D SER* 5.8 3.2 - - - -
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Residues in contact with ALA 80 (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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76A ILE* 2.9 23.0 + - + +
77A TYR* 5.0 0.9 - - - -
79A SER* 1.3 78.8 - - - +
81A VAL* 1.3 61.5 + - + +
84A PRO* 3.2 16.4 - - - +
74B GLN* 5.1 3.6 - - - +
78B ASN* 3.5 16.6 - - - +
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Residues in contact with VAL 81 (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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77A TYR* 3.1 41.9 + - + +
80A ALA* 1.3 82.4 - - + +
82A ALA* 1.3 63.1 + - - +
83A LEU 3.6 0.7 - - - -
84A PRO* 3.8 3.5 - - - +
85A LEU* 3.1 37.6 + - + +
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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