Contacts of the helix formed by residues 58 - 73 (chain A) in PDB entry 2I5B
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 ASP 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A PRO 4.1 1.4 + - - -
57A ILE* 1.3 74.4 - - - +
59A THR* 1.3 66.3 + - - +
60A ASP* 4.2 8.7 - - + +
61A THR* 2.8 31.2 + - - +
62A ILE* 3.1 9.5 + - - +
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Residues in contact with THR 59 (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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57A ILE 3.3 4.5 + - - -
58A ASP* 1.3 71.3 - - - +
60A ASP* 1.3 57.5 + - - +
62A ILE* 3.3 11.1 + - - +
63A ARG* 2.9 44.3 + - - +
85A THR* 5.7 1.0 - - - +
87A ASP* 4.6 30.5 + - + +
88A ILE* 4.8 8.9 - - + +
91A LEU* 3.9 17.6 - - + +
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Residues in contact with ASP 60 (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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58A ASP* 3.1 6.1 - - + +
59A THR* 1.3 77.3 - - - +
61A THR* 1.3 57.9 + - - +
63A ARG* 2.7 35.6 + - - +
64A ALA* 2.9 27.7 + - - +
55B PHE* 4.9 6.6 - - + -
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Residues in contact with THR 61 (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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57A ILE* 3.6 18.9 - - + +
58A ASP* 2.8 27.3 + - - +
60A ASP* 1.3 70.4 - - - +
62A ILE* 1.3 66.4 + - - +
64A ALA* 3.3 3.5 + - - +
65A GLN* 3.0 36.1 + - - +
41B ILE* 3.9 15.0 - - + -
55B PHE* 3.6 48.3 - - + +
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Residues in contact with ILE 62 (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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9A ILE* 4.8 2.7 - - + -
37A ALA* 4.8 6.3 - - + -
38A LEU 3.6 15.0 - - - +
39A THR* 3.8 30.5 - - + -
57A ILE* 3.6 22.2 - - + +
58A ASP 3.1 9.1 + - - +
59A THR* 3.6 8.7 - - - +
61A THR* 1.3 76.1 - - - +
63A ARG* 1.3 61.3 + - - +
65A GLN* 3.2 10.5 + - - +
66A LEU* 3.0 33.4 + - + +
88A ILE* 3.6 33.9 - - + -
91A LEU* 3.7 16.6 - - + -
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Residues in contact with ARG 63 (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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59A THR* 2.9 24.5 + - - +
60A ASP* 2.7 45.1 + - - +
62A ILE* 1.3 75.3 - - - +
64A ALA* 1.3 52.7 + - - +
66A LEU* 3.3 7.5 + - + +
67A ALA* 2.8 35.9 + - + +
91A LEU* 3.9 34.2 - - + +
94A LYS* 5.4 9.2 - - - +
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Residues in contact with ALA 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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60A ASP 2.9 16.6 + - - +
61A THR 3.6 5.6 - - - +
62A ILE 3.2 0.2 - - - -
63A ARG* 1.3 76.3 - - - +
65A GLN* 1.3 62.0 + - - +
67A ALA* 3.3 9.1 + - - +
68A THR* 2.9 26.7 + - - +
43B ALA* 3.9 7.7 - - + +
53B GLN* 4.2 13.7 - - - +
55B PHE* 3.8 29.2 - - + -
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Residues in contact with GLN 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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36A THR 3.7 6.6 - - - +
37A ALA* 3.5 12.8 - - - -
38A LEU* 2.6 54.4 + - - +
57A ILE* 4.6 0.2 - - - +
61A THR* 3.0 36.5 + - - +
62A ILE* 3.4 6.7 - - - +
64A ALA* 1.3 73.9 - - - +
66A LEU* 1.3 64.6 + - - +
68A THR* 3.3 3.6 + - - +
69A ILE* 3.0 29.4 + - - +
12B SER* 4.9 1.7 + - - -
14B SER* 3.5 24.9 - - - +
41B ILE* 3.6 24.1 - - + +
43B ALA* 4.5 1.8 - - + -
55B PHE* 6.3 0.2 - - + -
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Residues in contact with LEU 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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7A LEU* 4.1 15.0 - - + -
9A ILE* 3.6 39.3 - - + -
37A ALA* 3.8 13.0 - - + -
62A ILE* 3.0 25.1 + - + +
63A ARG* 3.5 9.0 - - + +
65A GLN* 1.3 73.0 - - - +
67A ALA* 1.3 58.0 + - - +
69A ILE* 4.6 2.0 - - - -
70A THR* 2.7 41.4 + - + -
91A LEU* 4.0 24.5 - - + +
92A ALA* 5.4 0.4 - - - -
95A THR* 3.7 34.1 - - + +
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Residues in contact with ALA 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 ARG* 2.8 19.0 + - + +
64A ALA* 3.3 13.6 + - - +
66A LEU* 1.3 71.0 - - - +
68A THR* 1.3 58.2 + - - +
70A THR* 4.4 1.6 - - - -
71A ASP* 2.8 46.4 + - - +
46B PRO* 4.1 20.4 - - + -
53B GLN* 6.0 0.7 - - - +
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Residues in contact with THR 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 ALA 2.9 17.9 - - - +
65A GLN 3.5 8.1 - - - +
67A ALA* 1.3 74.9 - - + +
69A ILE* 1.3 62.4 + - - +
72A GLY* 3.3 16.1 + - - +
73A ILE* 3.4 14.2 + - - +
14B SER* 3.8 23.2 + - - -
15B SER 4.4 1.0 + - - -
43B ALA* 3.5 20.9 - - + -
44B MET* 3.0 33.8 + - - +
46B PRO* 4.3 4.0 - - - +
50B TRP* 4.0 14.5 - - - -
53B GLN* 5.1 0.4 - - - +
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Residues in contact with ILE 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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7A LEU* 4.0 39.9 - - + -
35A MET* 3.9 15.3 - - + -
36A THR 3.3 40.8 - - - +
37A ALA* 4.0 1.3 - - + +
65A GLN* 3.0 25.6 + - + +
66A LEU* 4.0 2.7 - - - +
68A THR* 1.3 76.9 - - - +
70A THR* 1.3 55.1 + - + +
73A ILE* 2.6 36.9 - - - +
74A GLY* 4.1 2.9 - - - -
75A VAL* 4.0 13.0 - - + -
14B SER* 3.4 25.4 - - - +
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Residues in contact with THR 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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7A LEU* 3.8 28.0 - - + -
66A LEU* 2.7 32.1 + - + +
67A ALA* 4.0 0.9 + - - -
69A ILE* 1.3 73.5 - - + +
71A ASP* 1.3 65.5 + - - +
73A ILE 2.9 11.8 - - - +
74A GLY* 4.4 5.2 - - - -
75A VAL* 5.1 4.0 - - + -
95A THR* 4.1 19.5 - - + +
99A LYS* 3.6 34.7 + - - +
101A LEU* 4.2 16.8 - - + +
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Residues in contact with ASP 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 ALA* 2.8 29.9 + - - +
70A THR* 1.3 79.8 + - - +
72A GLY* 1.3 58.9 + - - +
73A ILE 3.9 0.7 - - - +
99A LYS* 2.8 41.7 + - - +
46B PRO* 3.9 19.1 - - + +
47B ASN* 5.3 3.8 - - - +
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Residues in contact with GLY 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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67A ALA 3.5 1.0 + - - -
68A THR 3.3 12.9 + - - -
71A ASP* 1.3 79.1 - - - +
73A ILE* 1.3 61.8 + - - +
46B PRO* 4.1 8.5 - - - +
50B TRP* 3.8 17.3 - - - -
254B ASN* 2.8 31.8 + - - +
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Residues in contact with ILE 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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5A LYS* 3.8 18.8 - - + +
35A MET* 3.6 29.4 - - + -
68A THR* 3.4 16.4 + - - +
69A ILE* 2.6 21.2 - - - +
70A THR 2.9 14.6 - - - +
71A ASP 3.9 0.6 - - - -
72A GLY* 1.3 79.9 + - - +
74A GLY* 1.3 77.6 + - - +
15B SER* 4.0 27.6 - - - +
50B TRP* 4.2 6.1 - - + -
253B LEU* 4.1 31.4 - - + +
254B ASN* 4.2 10.1 - - - +
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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