Contacts of the helix formed by residues 64 - 84 (chain A) in PDB entry 1EIA
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 ALA 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLY 2.9 10.0 + - - +
63A GLN* 1.3 75.7 - - - +
65A GLY* 1.3 62.2 + - - +
67A LYS* 3.5 7.1 + - - +
68A GLN* 3.2 26.0 + - - +
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Residues in contact with GLY 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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63A GLN 2.9 1.4 + - - -
64A ALA* 1.3 77.4 - - - +
66A GLN* 1.3 62.1 + - - +
68A GLN* 3.3 7.7 + - - +
69A ILE* 3.2 26.8 + - - +
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Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASN* 3.6 20.3 + - - +
32A LEU* 3.2 18.9 + - + +
33A LEU* 2.7 56.5 + - + +
63A GLN* 2.8 38.0 + - + +
65A GLY* 1.3 69.8 - - - +
67A LYS* 1.3 66.1 + - - +
69A ILE* 3.0 8.5 + - + +
70A LEU* 2.9 18.2 + - - +
144A MET* 3.7 26.5 - - - +
149A LYS* 5.8 1.0 - - - +
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Residues in contact with LYS 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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32A LEU* 3.4 17.8 - - + +
57A LEU* 3.0 35.7 + - + +
58A ASP* 4.0 16.4 + - - +
60A VAL* 4.3 18.9 + - + +
61A PRO 6.1 0.2 - - - +
63A GLN 2.6 23.6 + - - +
64A ALA* 3.8 7.2 - - - +
66A GLN* 1.3 72.9 - - - +
68A GLN* 1.3 57.7 + - + +
70A LEU* 3.1 4.6 + - + +
71A LEU* 2.8 63.6 + - + +
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Residues in contact with GLN 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 3.2 16.2 + - - +
65A GLY* 3.6 9.2 - - - +
66A GLN 3.2 0.2 - - - -
67A LYS* 1.3 74.7 - - + +
69A ILE* 1.3 62.2 + - + +
71A LEU* 3.7 23.1 - - - +
72A ASP* 2.8 60.8 + - - +
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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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33A LEU* 3.8 13.0 - - + -
65A GLY 3.4 16.2 - - - +
66A GLN* 3.0 11.5 + - + +
68A GLN* 1.3 76.8 - - + +
70A LEU* 1.3 65.0 + - - +
72A ASP* 3.9 3.7 - - - +
73A ALA* 3.0 26.3 + - + +
139A GLU 5.3 0.2 - - - -
140A GLY* 3.7 28.5 - - - -
143A VAL* 4.4 28.0 - - + -
144A MET* 4.7 8.5 - - - -
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 6.4 0.4 - - + -
32A LEU* 4.1 24.5 - - + -
33A LEU* 4.5 7.2 - - + +
57A LEU* 3.7 27.8 - - + -
60A VAL* 5.9 0.2 - - + -
66A GLN 2.9 11.4 + - - +
67A LYS* 3.4 11.2 - - + +
68A GLN 3.1 0.2 - - - -
69A ILE* 1.3 77.7 - - - +
71A LEU* 1.3 65.1 + - + +
73A ALA* 3.0 7.5 + - - +
74A ILE* 2.9 36.3 + - + +
133A ILE* 4.1 4.3 - - + +
136A ALA* 3.3 31.0 - - + -
137A MET* 3.6 34.3 - - + +
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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
----------------------------------------------------------
57A LEU* 4.2 29.2 - - + -
67A LYS* 2.8 56.5 + - + +
68A GLN* 3.7 25.8 - - - +
70A LEU* 1.3 73.0 - - + +
72A ASP* 1.3 65.7 + - - +
74A ILE* 3.1 13.8 + - + +
75A ASP* 3.0 29.5 + - - +
108A ARG* 5.4 0.3 + - - -
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Residues in contact with ASP 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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68A GLN* 2.8 47.3 + - - +
69A ILE* 4.0 3.8 - - - +
71A LEU* 1.3 74.9 - - - +
73A ALA* 1.3 62.8 + - - +
75A ASP* 3.1 17.9 + - - +
76A LYS* 3.0 20.4 + - - +
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Residues in contact with ALA 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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69A ILE* 3.0 21.0 + - + +
70A LEU 3.3 4.5 - - - +
72A ASP* 1.3 76.2 - - - +
74A ILE* 1.3 64.1 + - - +
76A LYS* 2.9 33.3 + - - +
77A ILE* 3.1 12.0 + - - +
136A ALA* 3.8 28.0 - - + +
139A GLU* 4.7 7.9 - - + -
140A GLY 5.4 1.1 - - - +
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Residues in contact with ILE 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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57A LEU* 4.1 25.8 - - + -
70A LEU* 2.9 29.5 + - + +
71A LEU* 3.4 13.5 - - + +
73A ALA* 1.3 77.0 - - - +
75A ASP* 1.3 62.8 + - - +
77A ILE* 3.2 8.1 + - - +
78A ALA* 2.9 21.1 + - - +
108A ARG* 4.1 19.7 - - - +
129A TYR* 4.1 23.8 - - + +
132A TRP* 4.9 11.6 - - + -
133A ILE* 4.2 16.6 - - + -
136A ALA* 3.4 17.7 - - + -
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Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 3.0 22.5 + - - +
72A ASP* 3.1 20.5 + - - +
74A ILE* 1.3 74.9 - - - +
76A LYS* 1.3 52.9 + - - +
78A ALA* 3.2 1.0 + - - +
79A ASP* 2.7 48.7 + - - +
108A ARG* 2.7 38.5 + - - +
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Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP 3.0 11.2 + - - +
73A ALA* 2.9 44.3 + - - +
75A ASP* 1.3 76.7 - - - +
77A ILE* 1.3 71.7 + - - +
79A ASP* 3.4 7.5 + - - +
80A ASP* 3.0 28.1 + - + +
139A GLU* 4.8 16.4 - - - +
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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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73A ALA 3.1 13.1 + - - +
74A ILE* 3.8 6.3 - - - +
76A LYS* 1.3 89.9 - - - +
78A ALA* 1.3 57.1 + - - +
80A ASP* 3.3 8.3 + - + +
81A TRP* 2.9 27.0 + - - +
132A TRP* 3.7 39.9 - - + +
135A GLU* 3.5 45.5 - - + +
136A ALA* 3.8 11.0 - - + +
139A GLU* 5.6 2.7 - - + -
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Residues in contact with ALA 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 ILE 2.9 17.3 + - - +
75A ASP 3.5 3.4 - - - +
77A ILE* 1.3 74.7 - - - +
79A ASP* 1.3 67.4 - - - +
81A TRP* 3.2 4.2 + - - +
82A ASP* 3.1 18.9 + - - -
104A ALA* 3.4 18.5 - - + +
108A ARG* 3.6 22.2 - - - +
132A TRP* 3.7 29.3 - - + -
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Residues in contact with ASP 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 ASP* 2.7 33.0 + - - +
76A LYS* 3.9 6.5 + - - +
78A ALA* 1.3 74.9 - - - +
80A ASP* 1.3 63.7 + - - +
82A ASP* 3.1 11.8 + - - +
83A ASN* 3.1 33.7 + - - +
108A ARG* 5.3 1.6 + - - -
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Residues in contact with ASP 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 LYS* 3.0 20.3 + - + +
77A ILE* 3.4 9.4 - - + +
79A ASP* 1.3 76.9 - - - +
81A TRP* 1.3 65.0 + - - +
83A ASN* 3.2 12.0 + - - +
84A ARG* 2.7 60.0 + - - +
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Residues in contact with TRP 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 2.9 9.0 + - - +
78A ALA 3.2 7.6 + - - +
80A ASP* 1.3 79.6 + - - +
82A ASP* 1.3 67.6 + - - +
84A ARG* 3.2 3.3 + - - -
85A HIS* 2.6 81.8 + + + +
102A MET* 3.1 50.4 + - + -
103A THR* 4.2 0.2 - - - +
104A ALA* 3.6 12.5 - - - +
107A ILE* 3.5 18.4 - - + +
128A THR* 4.9 10.1 - - + -
132A TRP* 3.5 30.5 - + + -
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Residues in contact with ASP 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 ALA 3.1 6.1 + - - +
79A ASP* 3.1 13.8 + - - +
81A TRP* 1.3 77.9 - - - +
83A ASN* 1.3 60.9 + - - +
85A HIS 3.1 6.7 - - - +
86A PRO* 2.9 33.2 - - + +
103A THR* 4.0 7.7 - - - +
104A ALA* 3.0 41.4 + - - +
105A ARG 4.9 1.2 + - - -
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Residues in contact with ASN 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 ASP* 3.1 27.8 + - - +
80A ASP* 3.8 8.7 - - - +
82A ASP* 1.3 76.9 - - - +
84A ARG* 1.3 62.9 + - - +
86A PRO* 3.1 15.2 - - - +
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Residues in contact with ARG 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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80A ASP* 2.7 48.5 + - - +
81A TRP* 3.4 2.7 - - - +
83A ASN* 1.3 80.0 - - - +
85A HIS* 1.3 85.6 + - + +
86A PRO* 3.3 6.1 - - - +
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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
------------------------------------------------------------
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