Contacts of the helix formed by residues 68 - 83 (chain A) in PDB entry 2RAE
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 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A THR* 5.6 1.9 + - - +
19A GLN* 3.6 34.5 + - + +
20A ASP* 3.2 24.1 + - - +
66A TRP 3.7 1.5 + - - -
67A GLY* 1.3 68.7 - - - -
69A PHE* 1.3 61.6 + - - +
70A ASP* 3.8 9.0 + - - +
71A ALA* 3.1 37.0 + - + +
72A HIS* 3.3 10.4 + - - +
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Residues in contact with PHE 69 (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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66A TRP* 3.4 50.7 - + + +
67A GLY 3.2 5.2 + - - +
68A ASP* 1.3 71.9 - - - +
70A ASP* 1.3 64.2 + - - +
72A HIS* 3.3 30.6 + + + +
73A LEU* 2.8 60.5 + - + +
131A MET* 3.4 49.6 - - - -
132A TYR* 6.0 0.4 - + - -
135A TRP* 4.0 15.5 - + + -
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Residues in contact with ASP 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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68A ASP* 3.2 9.3 + - - +
69A PHE* 1.3 81.5 - - - +
71A ALA* 1.3 55.3 + - - +
73A LEU* 3.4 14.6 + - - +
74A ALA* 3.0 28.2 + - - +
131A MET* 5.9 4.0 - - - +
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Residues in contact with ALA 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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20A ASP* 6.0 0.7 - - - +
68A ASP* 3.1 32.1 + - + +
70A ASP* 1.3 74.5 - - - +
72A HIS* 1.3 65.1 + - - +
74A ALA* 3.2 8.5 + - - +
75A GLU* 3.1 28.7 + - - +
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Residues in contact with HIS 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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11A ILE* 5.0 16.8 + - + +
68A ASP 3.3 8.2 + - - +
69A PHE* 3.4 36.9 - + + +
71A ALA* 1.3 78.4 - - - +
73A LEU* 1.3 67.1 + - - +
75A GLU* 3.2 15.9 + - - +
76A MET* 3.1 22.4 + - - +
100A PHE* 3.1 52.3 + + + +
101A ASN* 5.7 1.8 - - - -
135A TRP* 5.0 11.9 - - - -
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Residues in contact with LEU 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 PHE* 2.8 45.8 + - + +
70A ASP* 3.7 14.4 - - - +
72A HIS* 1.3 79.8 - - - +
74A ALA* 1.3 56.1 + - - +
76A MET* 3.5 13.9 + - + +
77A ARG* 3.1 28.2 + - - +
134A GLY* 3.8 23.3 - - - +
135A TRP* 3.6 40.6 - - + -
138A VAL* 4.2 13.2 - - + +
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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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70A ASP 3.0 17.8 + - - +
71A ALA* 3.2 8.5 + - - +
73A LEU* 1.3 75.0 - - - +
75A GLU* 1.3 59.9 + - - +
77A ARG* 3.8 9.2 - - - +
78A ALA* 3.0 28.4 + - - +
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Residues in contact with GLU 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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11A ILE* 3.8 17.8 - - - +
14A ARG* 3.4 45.3 + - - +
71A ALA* 3.1 19.7 + - - +
72A HIS* 3.5 10.8 - - - +
74A ALA* 1.3 73.4 - - - +
76A MET* 1.3 65.5 + - - +
78A ALA* 3.3 4.6 + - - +
79A GLN* 2.9 24.8 + - - +
100A PHE* 3.5 25.5 - - + -
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Residues in contact with MET 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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72A HIS* 3.1 14.9 + - - +
73A LEU* 3.8 15.9 - - + +
74A ALA 3.4 0.2 - - - -
75A GLU* 1.3 76.7 - - - +
77A ARG* 1.3 57.0 + - - +
79A GLN* 3.2 2.6 + - - +
80A LEU* 2.9 40.2 + - + +
96A ALA* 4.1 15.7 - - + +
100A PHE* 3.6 40.2 - - + -
135A TRP* 3.5 47.1 - - + +
138A VAL* 3.8 22.9 - - + -
139A ILE* 4.4 9.6 - - + -
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Residues in contact with ARG 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 LEU 3.1 16.4 + - - +
74A ALA* 3.8 9.2 - - - +
76A MET* 1.3 79.6 - - - +
78A ALA* 1.3 56.6 + - - +
80A LEU* 3.4 4.8 + - - +
81A ALA* 2.9 32.2 + - + +
138A VAL* 3.8 23.5 - - + +
141A GLU* 3.0 41.2 + - - +
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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 ALA 3.0 18.9 + - - +
75A GLU* 3.9 4.9 - - - +
77A ARG* 1.3 73.3 - - - +
79A GLN* 1.3 62.5 + - - +
81A ALA* 3.7 5.7 - - - +
82A ALA* 2.8 33.8 + - - +
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Residues in contact with GLN 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 GLU 2.9 14.4 + - - +
76A MET 3.5 7.9 - - - +
78A ALA* 1.3 75.4 - - - +
80A LEU* 1.3 70.5 + - + +
82A ALA* 3.0 6.4 + - - +
83A GLN* 3.0 39.1 + - + +
95A ALA* 3.7 2.8 + - - +
96A ALA* 3.7 28.0 - - + +
99A GLN* 3.1 42.8 + - - +
100A PHE* 3.6 19.7 - - + -
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Residues in contact with LEU 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 MET* 2.9 26.1 + - + +
77A ARG* 3.8 4.3 - - - +
79A GLN* 1.3 78.1 - - + +
81A ALA* 1.3 60.3 + - - +
83A GLN* 3.5 18.7 + - - +
92A GLY* 3.6 28.7 - - - +
93A LEU* 4.6 1.8 - - + +
96A ALA* 3.9 12.6 - - + -
138A VAL* 4.0 17.5 - - + -
139A ILE* 4.0 26.0 - - + -
142A TYR* 3.6 61.3 - - + -
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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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77A ARG* 2.9 20.9 + - + +
78A ALA* 3.8 7.0 - - - +
79A GLN 3.2 0.2 - - - -
80A LEU* 1.3 76.5 - - - +
82A ALA* 1.3 59.6 + - - +
83A GLN 3.4 4.8 - - - +
142A TYR* 5.5 1.3 - - - -
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Residues in contact with ALA 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 2.8 18.3 + - - +
79A GLN* 3.8 5.2 - - - +
81A ALA* 1.3 76.5 - - - +
83A GLN* 1.3 63.7 + - - +
84A PRO* 3.4 7.8 - - - +
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Residues in contact with GLN 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 GLN* 3.0 31.1 + - + +
80A LEU* 3.8 17.0 - - - +
81A ALA 3.4 7.3 - - - +
82A ALA* 1.3 77.4 - - - +
84A PRO* 1.3 75.9 - - + +
85A ASP* 3.5 2.9 + - - +
87A ILE* 4.0 20.9 - - + +
91A ASP 4.4 2.0 + - - -
92A GLY* 3.4 32.8 - - - +
95A ALA* 3.4 25.8 - - - +
142A TYR* 4.9 5.8 + - + +
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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