Contacts of the helix formed by residues 63 - 82 (chain A) in PDB entry 2CUF
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLU 5.0 1.3 - - - -
37A ARG* 3.3 47.0 + - - -
38A GLU* 3.8 29.6 + - - +
41A ALA* 4.1 8.3 - - - +
62A THR* 1.3 75.4 - - - +
64A LEU* 1.3 63.6 + - - +
66A VAL* 3.5 2.1 + - - +
67A TYR 3.4 6.1 + - - -
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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
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37A ARG* 4.0 12.3 - - - +
62A THR* 3.1 8.8 + - - +
63A SER* 1.3 81.4 + - - +
65A LYS* 1.3 66.0 + - + +
67A TYR* 3.2 11.3 + - + +
68A ASN* 3.1 43.2 + - - +
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Residues in contact with LYS 65 (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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12A PHE* 3.3 41.5 - - + -
14A TRP* 3.5 21.6 - - + -
57A ASP* 3.9 10.1 + - - +
60A ARG* 2.9 33.4 + - - +
61A VAL* 4.1 1.1 - - - -
62A THR* 3.1 42.2 + - - +
64A LEU* 1.3 80.1 - - + +
66A VAL* 1.3 60.9 + - - +
68A ASN* 3.3 12.2 + - - +
69A TRP 3.2 17.0 + - - -
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Residues in contact with VAL 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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22A MET* 4.1 11.7 - - - -
32A PRO* 4.7 0.9 - - + -
37A ARG* 4.3 14.4 - - + +
40A ILE* 3.6 28.7 - - + -
41A ALA* 3.4 37.0 - - + -
61A VAL* 3.6 13.2 - - + -
62A THR 3.2 3.7 + - - +
63A SER 3.7 7.9 - - - +
64A LEU 3.2 0.2 - - - -
65A LYS* 1.3 76.4 - - - +
67A TYR* 1.3 57.1 + - - +
69A TRP* 3.4 1.4 + - - +
70A PHE* 3.0 57.1 + - + -
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Residues in contact with TYR 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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31A TYR* 5.7 2.5 - + + -
32A PRO* 5.8 4.3 - - + -
37A ARG* 3.3 46.9 - - - +
63A SER 3.4 2.2 + - - -
64A LEU* 3.2 16.7 + - + +
66A VAL* 1.3 76.3 - - - +
68A ASN* 1.3 64.3 + - - +
70A PHE* 3.8 4.2 - - + +
71A ALA* 2.8 41.3 + - + +
74A ARG* 3.4 31.0 + - - -
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Residues in contact with ASN 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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14A TRP* 6.3 0.2 - - - +
64A LEU* 3.1 45.4 + - - +
65A LYS* 3.3 13.1 + - - +
67A TYR* 1.3 80.1 - - - +
69A TRP* 1.3 61.2 + - - +
71A ALA* 3.9 5.4 - - - +
72A ASN* 3.2 22.5 + - - +
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Residues in contact with TRP 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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14A TRP* 3.7 30.9 - + + +
19A LEU* 3.4 18.1 - - + +
22A MET* 2.9 50.0 - - + -
23A GLU* 3.8 37.9 - - + -
26A PHE* 4.0 19.1 - + + -
65A LYS 3.2 3.0 + - - -
66A VAL 3.8 1.3 - - - +
68A ASN* 1.3 77.5 - - - +
70A PHE* 1.3 91.1 + + - +
72A ASN* 3.2 16.4 + - + +
73A ARG* 3.2 25.3 + - + +
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Residues in contact with PHE 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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22A MET* 3.0 36.6 - - + -
25A TYR* 3.8 12.1 - - + -
26A PHE* 3.3 34.3 - + + -
29A ASN 3.8 2.7 - - - -
30A GLN 3.3 19.7 - - - -
32A PRO* 3.5 26.2 - - + -
40A ILE* 4.8 0.9 - - + -
66A VAL* 3.0 44.9 + - + +
67A TYR* 3.8 6.7 - - + +
69A TRP* 1.3 96.0 - + - +
71A ALA* 1.3 62.2 + - - +
73A ARG* 3.0 4.9 + - - +
74A ARG* 3.0 38.4 + - - +
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Residues in contact with ALA 71 (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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67A TYR* 2.8 29.5 + - + +
68A ASN* 3.9 6.1 - - - +
70A PHE* 1.3 76.9 - - - +
72A ASN* 1.3 57.4 + - - +
74A ARG* 3.9 20.3 - - - +
75A LYS* 3.0 41.8 + - + +
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Residues in contact with ASN 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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6A SER* 3.6 27.3 + - - -
8A ARG* 4.5 15.6 + - - +
68A ASN 3.2 12.1 + - - +
69A TRP* 3.4 14.1 - - + +
70A PHE 3.2 0.2 - - - -
71A ALA* 1.3 78.8 - - - +
73A ARG* 1.3 57.8 + - - +
75A LYS* 3.3 15.6 - - - +
76A GLU* 2.9 34.4 + - - +
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Residues in contact with ARG 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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26A PHE* 3.3 36.2 - - + -
69A TRP* 3.2 23.6 + - + +
70A PHE 3.0 9.6 + - - +
72A ASN* 1.3 77.4 - - - +
74A ARG* 1.3 55.6 + - - +
76A GLU* 3.5 17.0 + - - +
77A ILE* 2.8 66.7 + - - +
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Residues in contact with ARG 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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26A PHE* 3.5 13.7 - - + -
30A GLN* 2.5 41.4 + - - +
31A TYR* 2.6 60.5 - - - +
32A PRO* 4.3 1.6 - - - +
67A TYR* 3.4 34.8 + - - -
70A PHE* 3.0 34.6 + - - +
71A ALA* 3.9 15.6 - - - +
73A ARG* 1.3 74.3 - - - +
75A LYS* 1.3 56.5 + - - +
77A ILE* 2.9 29.5 - - + +
78A LYS* 2.9 17.9 + - - +
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Residues in contact with LYS 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 ALA* 3.0 25.7 + - + +
72A ASN* 3.3 24.9 - - - +
74A ARG* 1.3 75.3 - - - +
76A GLU* 1.3 65.9 + - - +
78A LYS* 3.2 12.9 - - + +
79A ARG* 2.8 54.4 + - - +
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Residues in contact with GLU 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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5A SER* 4.4 12.5 + - - -
6A SER* 5.2 8.0 - - - -
72A ASN* 2.9 30.5 + - - +
73A ARG* 3.1 19.4 + - - +
75A LYS* 1.3 81.1 - - + +
77A ILE* 1.3 67.0 + - + +
79A ARG* 4.1 5.3 - - - +
80A ARG* 3.4 22.3 + - - +
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Residues in contact with ILE 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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26A PHE* 4.2 6.7 - - + -
30A GLN* 3.6 26.7 - - - +
73A ARG* 2.8 55.6 + - - +
74A ARG* 2.9 34.5 - - + +
76A GLU* 1.3 80.2 - - + +
78A LYS* 1.3 67.5 + - + +
80A ARG* 3.4 6.5 + - - +
81A ALA* 3.2 22.2 + - - +
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Residues in contact with LYS 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 ARG 2.9 24.2 + - - +
75A LYS* 3.2 17.3 - - + +
77A ILE* 1.3 76.8 - - + +
79A ARG* 1.3 89.9 + - + +
81A ALA* 3.1 8.7 + - - +
82A ASN* 3.1 36.6 + - + +
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Residues in contact with ARG 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 LYS* 2.8 45.0 + - - +
76A GLU* 4.1 6.3 - - - +
78A LYS* 1.3 87.2 - - + +
80A ARG* 1.3 55.5 + - - +
82A ASN* 4.8 2.2 - - - -
83A ILE* 2.7 37.4 + - - +
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Residues in contact with ARG 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 GLU 3.4 15.0 + - - +
77A ILE* 3.4 7.5 + - - +
78A LYS 3.2 0.4 - - - -
79A ARG* 1.3 77.6 - - - +
81A ALA* 1.3 59.6 + - - +
82A ASN 3.3 0.2 - - - -
83A ILE* 2.8 33.9 - - + +
94A SER 5.5 0.2 + - - -
95A GLY 4.1 27.2 + - - -
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Residues in contact with ALA 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 ILE 3.2 12.2 + - - +
78A LYS* 3.1 13.1 + - - +
80A ARG* 1.3 77.7 - - - +
82A ASN* 1.3 58.4 + - - +
83A ILE* 4.5 1.2 - - - +
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Residues in contact with ASN 82 (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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78A LYS* 3.1 26.2 + - - +
79A ARG* 4.2 2.9 - - - +
81A ALA* 1.3 79.7 - - - +
83A ILE* 1.3 76.1 + - - +
84A ALA* 3.7 23.0 - - - +
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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