Contacts of the helix formed by residues 55 - 71 (chain A) in PDB entry 2I59
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 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A GLN* 1.3 79.8 - - - +
56A LYS* 1.3 68.8 + - - +
57A THR* 3.0 27.1 + - - +
58A GLN* 3.9 16.0 - - + +
59A MET* 2.7 35.5 + - - +
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A GLN 4.1 0.2 + - - -
55A ASP* 1.3 81.5 + - - +
57A THR* 1.3 65.7 + - + +
59A MET* 3.3 26.6 - - + +
60A GLN* 3.1 39.6 + - - +
96A HIS* 6.3 2.5 - - - -
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Residues in contact with THR 57 (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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55A ASP* 3.0 15.6 + - - +
56A LYS* 1.3 79.4 - - + +
58A GLN* 1.3 74.5 + - - +
60A GLN* 3.1 18.0 + - - +
61A GLU* 3.0 31.5 + - - +
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Residues in contact with GLN 58 (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 GLN* 3.6 22.9 - - - +
55A ASP* 3.7 22.0 - - + +
56A LYS 3.3 0.2 - - - -
57A THR* 1.3 84.9 + - - +
59A MET* 1.3 53.7 + - - +
61A GLU* 3.1 11.6 + - - +
62A LYS* 2.7 51.6 + - + +
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Residues in contact with MET 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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50A PHE* 3.0 35.8 - - + +
54A GLN* 3.4 24.6 - - + +
55A ASP 2.7 23.5 + - - +
56A LYS* 3.3 34.8 - - + +
58A GLN* 1.3 72.1 - - - +
60A GLN* 1.3 59.1 + - + +
63A ALA* 2.7 32.8 + - + +
95A PRO 4.1 15.9 - - - +
96A HIS* 4.6 2.0 - - - +
97A PRO* 3.2 42.6 - - + -
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Residues in contact with GLN 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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56A LYS* 3.1 28.8 + - - +
57A THR* 3.1 20.5 + - - +
59A MET* 1.3 85.1 - - + +
61A GLU* 1.3 72.0 + - - +
63A ALA* 3.2 12.4 + - - +
64A LYS* 3.3 16.9 + - - +
92A LEU 5.0 1.2 - - - +
93A GLU 4.9 4.3 - - - +
94A GLU* 5.2 0.7 - - - -
95A PRO* 3.7 41.7 - - + +
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Residues in contact with GLU 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 THR* 3.0 18.4 + - - +
58A GLN* 3.6 11.9 - - - +
60A GLN* 1.3 83.8 - - - +
62A LYS* 1.3 60.7 + - + +
64A LYS* 3.2 28.9 + - + +
65A GLU* 3.1 26.2 + - - +
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Residues in contact with LYS 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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50A PHE* 3.6 18.4 - - + -
54A GLN* 3.4 25.8 - - - +
58A GLN* 2.7 37.7 + - - +
59A MET 3.5 5.2 - - - +
61A GLU* 1.3 72.3 - - - +
63A ALA* 1.3 61.6 + - - +
65A GLU* 2.9 40.7 + - - +
66A ILE* 2.9 37.0 + - + +
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Residues in contact with ALA 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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50A PHE* 3.7 7.2 - - + -
59A MET 2.7 15.7 + - - +
60A GLN* 3.2 11.4 + - - +
62A LYS* 1.3 73.3 - - - +
64A LYS* 1.3 61.4 + - - +
66A ILE* 3.2 2.3 - - - +
67A TYR* 3.2 18.7 + - - +
92A LEU* 3.6 4.3 - - + -
95A PRO* 3.6 22.4 - - + -
100A PHE* 3.2 42.0 - - + -
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Residues in contact with LYS 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 GLN 3.3 12.1 + - - +
61A GLU* 3.2 42.6 + - - +
63A ALA* 1.3 77.2 - - - +
65A GLU* 1.3 58.9 + - - +
67A TYR* 3.7 3.4 - - + +
68A MET* 2.8 34.8 + - - +
89A GLU* 5.8 4.6 + - - -
92A LEU* 3.6 36.1 + - + +
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Residues in contact with GLU 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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61A GLU 3.1 21.6 + - - +
62A LYS* 2.9 47.0 + - - +
64A LYS* 1.3 77.2 - - - +
66A ILE* 1.3 60.5 + - - +
68A MET* 3.1 5.2 + - - +
69A THR* 2.7 51.3 + - + +
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Residues in contact with ILE 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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43A PHE* 4.4 9.6 - - + -
46A ALA* 3.7 27.8 - - + +
47A CYS* 4.6 13.9 - - + -
50A PHE* 4.5 16.4 - - + -
62A LYS* 2.9 28.7 + - + +
63A ALA* 3.2 8.5 - - - +
65A GLU* 1.3 81.4 - - - +
67A TYR* 1.3 60.3 + - - +
69A THR* 3.3 7.2 - - - -
70A PHE* 3.0 46.6 + - + +
71A LEU 3.8 0.5 + - - -
100A PHE* 3.6 36.3 - - + -
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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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63A ALA 3.2 15.0 + - - +
64A LYS* 3.7 6.3 - - - +
65A GLU 3.2 0.4 - - - -
66A ILE* 1.3 83.0 - - - +
68A MET* 1.3 56.8 + - + +
71A LEU* 2.9 31.5 + - + -
72A SER* 2.5 55.9 + - - -
73A SER* 4.7 3.8 + - - -
83A GLY 3.9 9.8 + - - -
84A GLN 4.6 2.6 + - - -
86A ARG 2.8 22.4 + - - -
87A LEU* 3.6 28.3 - - + -
88A ASN* 3.2 26.5 + - - -
89A GLU* 4.4 7.6 - - + -
92A LEU* 3.7 21.5 - - + -
100A PHE* 4.5 8.1 - - + -
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Residues in contact with MET 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 LYS 2.8 22.3 + - - +
65A GLU* 3.7 5.2 - - - +
67A TYR* 1.3 79.2 - - + +
69A THR* 1.3 64.6 + - + +
72A SER* 3.3 26.6 + - - +
75A ALA* 3.9 6.8 - - - +
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Residues in contact with THR 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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39A GLU* 4.8 6.6 - - - +
65A GLU* 2.7 35.2 + - + +
66A ILE* 3.2 11.6 + - - -
68A MET* 1.3 84.7 - - + +
70A PHE* 1.3 81.8 + - - +
75A ALA* 3.5 18.1 - - - +
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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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39A GLU* 3.3 35.8 - - + +
42A LEU* 3.5 38.8 - - + -
43A PHE* 3.7 34.3 - + + -
46A ALA* 4.0 12.6 - - + -
66A ILE* 3.0 40.0 + - + +
69A THR* 1.3 94.9 - - - +
71A LEU* 1.3 65.4 + - + +
75A ALA* 4.2 0.9 - - - -
78A GLN* 3.4 24.8 - - - +
79A VAL* 4.0 4.9 + - + +
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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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43A PHE* 3.9 38.6 - - + -
66A ILE 3.8 0.2 + - - -
67A TYR* 2.9 31.8 + - + +
70A PHE* 1.3 83.6 - - + +
72A SER* 1.3 68.2 + - - +
74A LYS 3.9 0.2 - - - -
75A ALA* 3.0 18.8 - - - +
78A GLN* 2.6 37.2 + - + +
79A VAL* 4.2 17.3 - - + -
81A VAL* 4.4 12.8 - - + -
82A GLU 4.7 11.4 - - - +
83A GLY* 4.9 3.1 - - - -
87A LEU* 4.7 10.5 - - + -
100A PHE* 5.8 1.1 - - + -
103A LEU* 5.0 8.1 - - + -
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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