Contacts of the helix formed by residues 62 - 77 (chain A) in PDB entry 2OEV
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 GLU 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A HIS* 1.3 109.5 + - + +
63A GLY* 1.3 54.5 + - - +
64A ALA 3.3 1.2 - - - +
65A LEU* 3.2 12.4 + - - +
66A GLU* 2.8 38.3 + - + +
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Residues in contact with GLY 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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61A HIS* 3.6 8.4 + - - -
62A GLU* 1.3 78.3 - - - +
64A ALA* 1.3 55.0 + - - +
66A GLU* 3.9 9.2 - - - -
67A THR* 2.7 43.6 + - - -
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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
----------------------------------------------------------
53A ALA* 5.5 1.2 - - - +
58A LEU* 4.4 15.9 - - + +
59A ASP* 3.1 33.4 - - + +
61A HIS* 4.1 10.5 + - + +
62A GLU 4.0 0.8 - - - +
63A GLY* 1.3 75.5 - - - +
65A LEU* 1.3 61.2 + - - +
67A THR* 4.1 4.7 + - - -
68A LEU* 3.6 17.8 + - - +
130A LEU* 4.0 16.5 - - + +
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Residues in contact with LEU 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 HIS 5.2 0.8 - - - +
62A GLU* 3.2 14.5 + - - +
63A GLY 3.1 0.4 - - - -
64A ALA* 1.3 77.2 - - - +
66A GLU* 1.3 66.6 + - + +
68A LEU* 2.8 19.2 + - + +
69A LEU* 2.9 43.2 + - + +
127A CYS* 3.8 27.4 - - - +
130A LEU* 4.0 22.7 - - + +
131A ALA* 4.1 11.2 - - + +
134A ILE* 5.0 7.0 - - + -
151A LYS* 5.6 3.4 - - - +
152A HIS* 3.6 32.3 - - + +
155A PHE* 5.1 3.4 - - + -
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU* 2.8 23.3 + - + +
63A GLY* 3.0 9.8 + - - +
65A LEU* 1.3 73.1 - - + +
67A THR* 1.3 53.0 + - - +
69A LEU* 3.3 25.9 + - + +
70A ARG* 2.7 41.7 + - - +
347A ILE 4.3 1.4 - - - +
348A SER* 3.3 10.7 - - - -
349A GLN* 3.0 43.5 + - - +
350A LYS 4.8 1.0 + - - -
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Residues in contact with THR 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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49A LEU* 3.7 24.5 - - + +
52A ALA* 4.6 9.0 - - + +
53A ALA* 3.8 24.2 - - + +
63A GLY* 2.7 30.2 + - - -
64A ALA* 4.1 5.9 - - - -
66A GLU* 1.3 71.2 - - - +
68A LEU* 1.3 51.5 + - - +
70A ARG* 2.8 11.5 + - - +
71A TYR* 2.7 36.4 + - - +
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Residues in contact with LEU 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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9A LEU* 4.5 2.0 - - + -
53A ALA* 4.4 15.1 - - + +
54A VAL* 5.2 9.4 - - + -
58A LEU* 4.4 14.4 - - + -
64A ALA 3.6 6.9 + - - +
65A LEU* 2.8 13.6 + - + +
67A THR* 1.3 76.6 - - - +
69A LEU* 1.3 56.1 + - - +
71A TYR* 3.6 6.4 + - - +
72A TYR* 3.1 21.5 + - - +
123A VAL* 3.6 29.3 - - + +
126A ASN* 3.8 24.0 - - + +
127A CYS* 3.6 36.8 - - - +
130A LEU* 3.8 28.9 - - + -
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Residues in contact with LEU 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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65A LEU* 2.9 49.6 + - + +
66A GLU* 3.3 33.0 - - + +
68A LEU* 1.3 74.7 - - - +
70A ARG* 1.3 58.4 + - - +
71A TYR 3.1 0.9 - - - -
72A TYR* 3.2 3.5 + - - +
73A ASP* 2.8 34.5 + - - +
127A CYS* 4.1 8.7 - - + -
151A LYS* 6.3 0.7 - - - +
155A PHE* 4.0 19.3 - - + -
347A ILE* 3.6 43.5 - - + +
348A SER* 3.9 5.4 - - - -
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Residues in contact with ARG 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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45A GLU* 5.1 5.1 + - - -
49A LEU* 3.8 27.9 - - + +
66A GLU* 2.7 25.1 + - - +
67A THR* 3.5 6.7 - - - +
69A LEU* 1.3 70.1 - - - +
71A TYR* 1.3 62.7 + - - +
73A ASP* 3.7 4.7 - - - +
74A GLN* 3.3 22.6 + - - +
348A SER* 3.3 25.1 - - - +
350A LYS 3.9 18.6 + - - +
351A PHE* 3.9 14.0 - - + -
352A THR* 3.8 22.8 - - - +
354A LEU* 4.7 17.0 - - - +
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Residues in contact with TYR 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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17A LEU* 4.6 4.0 - - - +
46A LEU* 3.7 22.7 - - + -
49A LEU* 3.7 30.0 - - + +
50A ARG* 2.8 56.9 + - + +
53A ALA* 4.2 16.2 - - + -
54A VAL* 4.6 9.2 - - + -
67A THR 2.7 13.8 + - - +
68A LEU* 3.7 5.4 - - + +
70A ARG* 1.3 74.4 - - - +
72A TYR* 1.3 66.1 + - - +
73A ASP 3.1 0.9 - - - -
74A GLN* 2.8 15.9 + - - +
75A ILE* 2.8 44.1 + - + +
93A PHE* 5.1 0.5 - - - -
119A GLU* 3.0 11.5 + - - -
123A VAL* 3.8 19.3 - - + -
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Residues in contact with TYR 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 LEU 3.1 12.1 + - - +
69A LEU 3.6 6.1 - - - +
71A TYR* 1.3 77.5 - - - +
73A ASP* 1.3 67.2 + - - +
75A ILE* 3.2 12.5 + - - +
76A CYS* 3.2 45.1 + - - -
120A LYS* 3.4 46.7 - - + +
123A VAL* 3.8 9.4 - - + -
124A LEU* 3.8 30.1 - - + +
127A CYS* 4.4 2.7 - - - -
162A HIS* 4.1 18.2 + - - -
343A VAL* 4.2 16.1 - - + +
345A VAL* 4.0 14.6 - - + -
347A ILE* 3.7 22.7 - - + -
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Residues in contact with ASP 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 LEU 2.8 20.7 + - - +
70A ARG 3.7 2.9 - - - +
72A TYR* 1.3 82.4 - - - +
74A GLN* 1.3 60.0 + - - +
75A ILE 2.9 0.3 + - - -
76A CYS* 3.1 3.1 + - - +
77A SER* 2.7 28.8 + - - -
345A VAL* 3.5 15.5 - - - +
346A PRO* 3.0 30.7 - - - +
347A ILE* 3.0 9.9 + - - +
348A SER* 3.0 31.7 + - - -
351A PHE* 3.5 20.6 - - + -
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Residues in contact with GLN 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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46A LEU* 4.3 20.1 - - + +
49A LEU* 4.5 8.5 - - + +
70A ARG* 3.3 11.5 + - - +
71A TYR 2.8 11.5 + - - +
73A ASP* 1.3 76.1 - - - +
75A ILE* 1.3 64.6 + - - +
77A SER* 3.2 5.1 - - - -
78A ILE* 3.1 46.8 + - + +
351A PHE* 3.8 9.1 - - - -
352A THR 3.2 20.3 - - - +
353A ASP* 2.8 29.6 + - - +
354A LEU* 2.9 36.8 + - + +
355A PHE* 3.7 3.7 - - + +
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Residues in contact with ILE 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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46A LEU* 5.7 1.8 - - + +
71A TYR* 2.8 42.8 + - + +
72A TYR* 3.3 15.7 - - - +
73A ASP 2.9 0.8 + - - -
74A GLN* 1.3 71.5 - - - +
76A CYS* 1.3 57.4 + - - +
77A SER 2.9 3.6 - - - -
78A ILE* 2.7 30.7 + - - +
79A GLU 3.4 8.5 + - - -
116A LEU* 4.3 25.8 - - + +
119A GLU* 3.8 8.7 - - + +
120A LYS* 3.7 26.9 - - + +
123A VAL* 3.4 33.2 - - + -
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Residues in contact with CYS 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 TYR* 3.4 51.1 - - - -
73A ASP 3.1 6.3 + - - +
75A ILE* 1.3 82.0 - - - +
77A SER* 1.3 59.6 + - - +
78A ILE 3.1 1.4 + - - -
79A GLU* 3.7 12.9 + - - +
80A PRO* 3.4 18.2 - - - +
120A LYS* 4.1 16.2 - - - +
345A VAL* 4.3 18.6 - - + -
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Residues in contact with SER 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 ASP* 2.7 21.4 + - - +
74A GLN* 3.2 16.5 - - - -
75A ILE 2.9 0.4 + - - -
76A CYS* 1.3 78.1 - - - +
78A ILE* 1.3 62.4 + - - +
80A PRO* 4.1 6.1 - - - +
81A LYS* 4.1 18.2 + - - +
345A VAL* 5.9 3.5 - - - +
351A PHE* 3.8 14.0 - - - -
353A ASP* 3.8 29.0 - - - +
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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