Contacts of the helix formed by residues 66 - 85 (chain A) in PDB entry 2D85
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 ASN 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ASN* 3.2 11.1 - - - +
65A LEU* 1.3 84.0 - - - +
67A ASP* 1.3 55.9 + - - +
68A ASP* 2.6 53.5 + - - +
69A GLU* 2.9 24.1 + - - +
70A LYS* 2.6 35.7 + - - +
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Residues in contact with ASP 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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66A ASN* 1.3 73.2 - - - +
68A ASP* 1.3 66.7 + - - +
70A LYS* 3.9 10.7 - - - +
71A LEU* 3.7 17.5 + - - +
96A VAL* 5.1 9.7 - - - +
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Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN* 2.6 25.7 + - - +
67A ASP* 1.3 77.4 + - - +
69A GLU* 1.3 62.2 + - + +
71A LEU* 3.2 16.3 + - - +
72A ASN* 2.5 26.3 + - - +
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Residues in contact with GLU 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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61A LYS* 3.2 42.5 + - + +
63A GLU 5.8 0.9 - - - +
64A ASN* 6.0 0.2 - - - +
65A LEU* 3.3 22.9 - - + -
66A ASN* 2.9 35.0 + - - +
68A ASP* 1.3 74.1 - - + +
70A LYS* 1.3 68.2 + - - +
71A LEU 2.7 2.1 + - - -
72A ASN* 2.8 24.3 + - - +
73A ASN* 3.1 10.7 + - - +
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Residues in contact with LYS 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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38A SER* 3.5 41.4 + - - +
39A THR* 4.8 4.9 - - - +
40A SER* 4.6 0.3 + - - -
65A LEU* 3.4 20.1 - - + +
66A ASN* 2.6 47.2 + - - +
67A ASP* 3.9 4.0 - - - +
69A GLU* 1.3 73.5 - - - +
71A LEU* 1.3 63.0 + - - +
73A ASN* 3.2 7.1 + - - +
74A ALA* 3.1 14.2 + - - +
96A VAL* 3.4 43.7 + - + +
97A GLU* 6.2 0.2 - - - +
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Residues in contact with LEU 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 ASP 3.7 12.9 + - - +
68A ASP* 3.2 13.1 + - - +
69A GLU 2.7 4.0 + - - -
70A LYS* 1.3 72.2 - - - +
72A ASN* 1.3 62.0 + - - +
73A ASN 2.9 1.1 - - - -
74A ALA* 2.5 27.7 + - - +
75A LYS* 3.0 43.4 + - + +
92A PRO* 4.2 22.2 - - + +
93A GLU* 4.5 14.8 - - + +
96A VAL* 3.5 11.5 - - + +
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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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61A LYS* 5.0 9.6 - - - +
68A ASP* 2.5 36.8 + - - +
69A GLU* 2.8 22.2 + - - +
71A LEU* 1.3 76.8 - - - +
73A ASN* 1.3 61.5 + - - +
75A LYS* 3.5 24.2 + - - +
76A TYR* 3.0 29.1 + - - +
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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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39A THR 3.4 26.2 + - - +
40A SER* 4.0 6.7 + - - +
44A LEU* 4.4 13.2 - - + +
60A LEU* 4.7 9.1 - - - +
61A LYS* 4.1 20.4 + - - +
62A THR* 4.0 10.5 - - - +
65A LEU* 3.2 35.9 - - - +
69A GLU 3.1 5.2 + - - +
70A LYS* 3.3 10.5 - - - +
71A LEU 2.7 4.8 + - - -
72A ASN* 1.3 72.1 - - - +
74A ALA* 1.3 59.0 + - - +
76A TYR* 3.3 5.8 + - - +
77A ALA* 3.0 30.0 + - - +
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Residues in contact with ALA 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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40A SER* 3.9 4.6 + - - +
70A LYS 3.1 10.4 + - - +
71A LEU 2.5 14.5 + - - +
73A ASN* 1.3 73.1 - - - +
75A LYS* 1.3 60.5 + - - +
77A ALA* 3.5 1.8 + - - +
78A ILE* 3.3 29.1 + - - +
92A PRO* 3.2 33.7 - - + +
95A LEU* 3.5 26.4 - - + +
96A VAL* 4.0 4.5 - - + -
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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 LEU* 3.0 32.2 + - + +
72A ASN* 3.8 30.5 + - - +
74A ALA* 1.3 75.5 - - - +
76A TYR* 1.3 63.4 + - - +
78A ILE* 3.7 3.6 + - - +
79A SER* 3.1 22.2 + - - -
92A PRO* 3.5 25.8 - - + -
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Residues in contact with TYR 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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44A LEU* 4.1 8.1 - - + -
54A SER 3.4 18.0 + - - -
55A ILE* 4.2 16.4 - - + -
56A ASN* 4.2 3.8 + - - +
59A LEU* 4.0 27.5 - - + +
60A LEU* 3.5 32.5 - - + -
72A ASN 3.0 18.0 + - - +
73A ASN* 3.6 6.7 - - - +
74A ALA 3.2 0.2 - - - -
75A LYS* 1.3 74.7 - - - +
77A ALA* 1.3 70.1 + - - +
79A SER* 2.9 20.0 + - - -
80A MET* 3.0 45.7 + - + +
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Residues in contact with ALA 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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40A SER* 4.6 6.1 - - - -
43A VAL* 4.7 16.4 - - + -
44A LEU* 3.5 31.8 - - + +
47A ILE* 3.8 11.6 - - + +
73A ASN 3.0 13.8 + - - +
74A ALA* 3.7 7.9 - - - +
76A TYR* 1.3 78.0 - - - +
78A ILE* 1.3 64.7 + - + +
80A MET* 3.1 13.1 + - - +
81A ALA* 3.2 9.2 + - - +
95A LEU* 4.9 4.0 - - + -
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Residues in contact with ILE 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 ALA 3.3 15.5 + - - +
75A LYS* 4.0 4.3 - - - +
77A ALA* 1.3 75.1 - - + +
79A SER* 1.3 65.2 + - - +
81A ALA* 3.1 23.4 + - - +
82A ARG* 3.5 5.5 + - - +
88A VAL* 3.6 28.2 - - + +
90A ALA* 4.2 18.6 - - + +
91A LEU 4.0 5.4 - - - +
92A PRO* 3.6 37.7 - - + -
95A LEU* 4.7 10.8 - - + -
106A VAL* 5.3 9.6 - - + -
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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 LYS 3.1 15.9 + - - -
76A TYR* 2.9 20.2 + - - -
78A ILE* 1.3 77.7 - - - +
80A MET* 1.3 67.7 + - - +
82A ARG* 3.4 6.8 + - - +
83A LYS* 3.3 32.3 + - - +
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Residues in contact with MET 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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47A ILE* 4.3 12.1 - - + -
54A SER* 4.2 24.5 - - - +
55A ILE* 3.7 27.4 - - + -
76A TYR* 3.0 56.9 + - + +
77A ALA 3.1 8.5 + - - +
79A SER* 1.3 76.8 - - - +
81A ALA* 1.3 68.9 - - - +
83A LYS* 2.7 47.6 + - + +
84A ILE* 3.0 10.1 + - + +
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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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47A ILE* 4.6 7.9 - - + +
77A ALA 3.2 6.5 + - - +
78A ILE* 3.1 19.0 + - - +
80A MET* 1.3 75.1 - - - +
82A ARG* 1.3 58.4 + - - +
84A ILE* 2.9 15.7 - - - +
85A GLY 2.9 7.3 + - - -
86A ALA* 2.7 48.3 + - + +
88A VAL* 4.6 8.5 - - + -
110A LEU* 5.5 5.2 - - + -
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Residues in contact with ARG 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 ILE* 3.5 4.0 + - + +
79A SER* 3.4 9.0 + - - +
80A MET 3.3 0.4 - - - -
81A ALA* 1.3 79.0 - - - +
83A LYS* 1.3 71.7 + - - +
85A GLY* 2.8 13.9 + - - -
86A ALA* 3.7 10.0 - - - +
87A ARG* 4.8 17.9 - - + +
88A VAL* 5.7 2.2 - - + +
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Residues in contact with LYS 83 (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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54A SER* 5.5 5.8 - - - +
79A SER* 3.3 19.6 + - - -
80A MET* 2.7 48.9 + - + +
82A ARG* 1.3 82.9 + - - +
84A ILE* 1.3 60.1 + - + +
85A GLY* 4.5 0.3 - - - -
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Residues in contact with ILE 84 (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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47A ILE* 4.0 26.0 - - + +
50A ILE* 5.9 6.5 - - + -
51A GLN* 3.1 48.9 + - + +
54A SER* 4.2 10.3 - - - +
80A MET 3.0 10.2 + - - +
81A ALA* 2.9 23.1 - - - +
83A LYS* 1.3 78.6 - - + +
85A GLY* 1.3 57.9 + - - +
86A ALA* 4.5 7.6 - - + +
110A LEU* 4.8 11.7 - - + -
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Residues in contact with GLY 85 (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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81A ALA 2.9 2.4 + - - -
82A ARG 2.8 14.8 + - - -
84A ILE* 1.3 82.2 - - - +
86A ALA* 1.3 58.5 + - - +
87A ARG 3.6 2.9 + - - -
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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