Contacts of the helix formed by residues 69 - 83 (chain A) in PDB entry 2I91
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 LYS 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A MET* 4.5 7.9 - - + -
64A LEU* 2.9 43.1 + - + +
67A ASP* 3.3 14.7 + - + +
68A GLY* 1.3 74.6 - - - +
70A GLY* 1.3 63.9 + - - +
71A CYS 3.4 1.3 - - - -
72A GLU* 2.8 39.5 + - + +
73A VAL* 3.0 26.3 + - + +
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Residues in contact with GLY 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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64A LEU 4.0 2.6 + - - -
65A ILE* 4.1 16.9 - - - +
68A GLY* 2.7 13.7 + - - -
69A LYS* 1.3 75.3 - - - +
71A CYS* 1.3 58.2 + - - -
73A VAL* 3.5 5.0 - - - +
74A VAL* 3.5 14.2 + - - +
104A ASP* 4.7 1.8 - - - -
107A THR* 2.8 40.4 - - - +
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Residues in contact with CYS 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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68A GLY 4.2 2.4 + - - -
69A LYS 3.4 0.2 - - - -
70A GLY* 1.3 71.8 - - - +
72A GLU* 1.3 66.9 + - - +
73A VAL 3.2 1.6 - - - -
74A VAL* 3.9 6.9 - - - +
75A GLN* 3.1 23.7 + - - +
104A ASP* 5.0 0.4 + - - -
106A LYS* 3.9 52.3 - - - -
107A THR* 4.0 2.2 - - - -
110A ALA* 4.2 10.0 - - + +
113A ARG* 5.6 3.1 - - - +
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Residues in contact with GLU 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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30A MET* 2.9 35.7 - - + +
34A ARG* 5.0 3.1 + - - -
69A LYS* 2.8 42.5 + - + +
71A CYS* 1.3 77.7 - - - +
73A VAL* 1.3 58.6 + - - +
75A GLN* 3.3 8.0 + - + +
76A GLU* 2.9 33.1 + - - +
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Residues in contact with VAL 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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30A MET* 4.0 9.4 - - + -
33A LEU* 4.1 14.3 - - + +
61A LEU* 3.9 13.9 - - + -
64A LEU* 3.3 39.3 - - + -
65A ILE* 5.4 1.1 - - + +
69A LYS 3.0 17.8 + - - +
70A GLY* 3.5 10.3 - - - +
72A GLU* 1.3 76.9 - - - +
74A VAL* 1.3 52.7 + - - +
76A GLU* 3.0 4.5 + - - +
77A ILE* 2.7 48.9 + - + +
99A CYS* 3.7 24.7 - - - -
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Residues in contact with VAL 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 GLY 3.5 14.0 + - - +
71A CYS 4.0 6.1 - - - +
73A VAL* 1.3 76.0 - - - +
75A GLN* 1.3 54.2 + - - +
77A ILE* 3.1 11.8 + - + +
78A LYS* 2.6 39.4 + - + +
96A LEU* 5.4 4.9 - - + -
99A CYS* 4.1 22.7 - - + -
107A THR* 4.1 19.5 - - + +
110A ALA* 3.6 32.3 - - + +
111A ALA* 4.2 7.9 - - + +
113A ARG* 5.9 0.4 - - - +
114A ALA* 4.2 15.3 - - + -
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Residues in contact with GLN 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 CYS 3.1 20.0 + - - +
72A GLU* 3.4 9.6 - - + +
74A VAL* 1.3 76.6 - - - +
76A GLU* 1.3 59.2 + - - +
78A LYS* 3.4 20.9 + - - +
79A THR* 2.8 49.5 + - - +
75B GLN* 2.9 41.8 + - + +
78B LYS* 5.8 2.8 - - - +
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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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30A MET* 5.1 3.8 - - + +
33A LEU* 4.1 19.7 - - + -
34A ARG* 3.4 30.2 + - + +
37A LEU* 4.8 2.5 - - + -
72A GLU* 2.9 17.6 + - - +
73A VAL* 3.4 7.6 - - - +
75A GLN* 1.3 74.3 - - - +
77A ILE* 1.3 67.4 + - - +
79A THR* 3.1 9.1 + - - +
80A PHE* 2.9 54.1 + - + +
85A ARG* 4.3 5.2 + - - -
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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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33A LEU* 5.0 2.9 - - + -
37A LEU* 4.5 14.3 - - + +
73A VAL* 2.7 37.7 + - + +
74A VAL* 3.3 12.3 - - - +
76A GLU* 1.3 71.5 - - - +
78A LYS* 1.3 64.2 + - - +
80A PHE* 3.5 0.3 + - - +
81A SER* 3.2 23.6 + - - -
92A THR* 3.8 25.9 - - + +
95A ALA* 3.3 36.1 - - + +
96A LEU* 3.7 38.1 - - + +
99A CYS* 4.5 1.8 - - - -
118A VAL* 4.6 4.3 - - + -
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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 VAL* 2.6 22.7 + - + +
75A GLN* 3.5 23.4 + - - +
77A ILE* 1.3 74.6 - - - +
79A THR* 1.3 56.9 + - - +
81A SER* 4.0 1.0 - - - -
82A GLN* 3.2 47.7 + - - +
96A LEU* 6.4 0.2 - - + -
113A ARG 5.6 0.4 - - - -
114A ALA* 3.6 30.1 - - + +
117A GLU* 2.9 39.4 + - - -
118A VAL* 4.0 15.3 - - + -
75B GLN* 5.8 2.4 - - - +
78B LYS* 5.7 4.8 - - - +
82B GLN* 5.2 2.8 + - - -
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Residues in contact with THR 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 GLN* 2.8 36.7 + - - +
76A GLU* 3.1 10.9 + - - +
78A LYS* 1.3 75.4 - - - +
80A PHE* 1.3 66.6 + - + +
82A GLN* 4.9 2.5 - - - -
83A GLU* 2.5 58.7 + - + +
85A ARG* 4.9 10.1 - - - +
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Residues in contact with PHE 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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34A ARG* 3.8 30.5 - - + -
37A LEU* 3.9 31.6 - - + -
38A CYS* 3.6 25.6 - - - -
76A GLU* 2.9 39.4 + - + +
77A ILE 4.1 2.0 - - - +
79A THR* 1.3 76.7 - - - +
81A SER* 1.3 57.6 + - - +
84A GLY* 2.9 7.3 + - - -
85A ARG* 2.9 71.5 + - + +
86A ALA* 4.2 8.2 + - + -
92A THR* 4.9 4.0 - - + -
520A CYS* 5.9 0.2 - - + -
523A ASP* 3.5 26.5 - - - -
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Residues in contact with SER 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 16.0 + - - -
78A LYS 4.0 2.2 - - - -
80A PHE* 1.3 76.7 - - - +
82A GLN* 1.3 61.7 + - - +
84A GLY* 2.8 21.5 + - - -
86A ALA* 6.2 1.6 - - - -
89A GLN* 4.0 12.5 + - - +
92A THR* 4.4 11.8 - - - +
118A VAL* 3.8 25.8 + - - +
120A ARG* 3.1 37.4 + - - +
318A ARG* 4.0 1.0 - - - -
13D C 4.9 0.5 + - - -
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Residues in contact with GLN 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* 3.2 31.9 + - + +
79A THR* 4.2 3.4 - - - +
81A SER* 1.3 76.6 - - - +
83A GLU* 1.3 61.0 + - + +
84A GLY 3.2 3.5 + - - -
117A GLU* 2.8 62.9 + - - +
118A VAL* 5.5 0.2 - - + -
120A ARG* 4.1 6.3 - - - +
318A ARG* 3.5 27.0 + - - +
78B LYS* 5.2 2.4 + - - -
117B GLU* 3.4 25.0 - - - +
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Residues in contact with GLU 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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79A THR* 2.5 46.6 + - + +
82A GLN* 1.3 77.3 - - + +
84A GLY* 1.3 64.8 + - - +
85A ARG* 3.2 11.1 + - - -
315A LYS* 5.9 2.3 - - - +
318A ARG* 4.8 1.8 - - - -
362A LYS* 2.7 55.2 + - - +
524A SER* 4.6 0.5 + - - -
113B ARG* 4.6 20.0 + - - -
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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