Contacts of the helix formed by residues 63 - 75 (chain A) in PDB entry 4OHN
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 GLY 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A PRO 3.2 13.9 - - - -
52A MET 3.4 5.6 - - - -
54A PHE* 4.0 0.9 - - - -
62A ALA* 1.3 78.9 - - - +
64A PHE* 1.3 66.6 + - - -
65A ASP 3.3 2.2 - - - -
66A ILE* 3.2 2.0 + - - +
67A ASP* 2.9 27.4 + - - -
264A TRP* 3.3 21.7 - - - -
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Residues in contact with PHE 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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51A PRO 2.8 15.9 + - - +
52A MET* 3.7 14.1 - - + -
63A GLY* 1.3 71.4 - - - +
65A ASP* 1.3 68.3 + - - +
67A ASP* 3.4 2.4 + - - +
68A LEU* 2.8 44.8 + - + +
122A TYR* 3.7 23.8 - + - -
123A MET* 4.5 2.2 - - - -
257A PHE* 3.8 29.6 - + - -
260A ILE* 3.5 33.0 - - + +
261A SER* 3.8 21.3 - - - -
264A TRP* 3.5 19.2 - + + +
265A PHE* 3.5 24.9 - + + -
269A VAL* 4.3 6.5 - - + -
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Residues in contact with ASP 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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52A MET* 2.8 27.1 + - - +
53A GLY* 5.2 1.1 - - - -
64A PHE* 1.3 76.1 - - - +
66A ILE* 1.3 61.7 + - + +
68A LEU* 4.3 1.6 - - - +
69A ALA* 2.9 33.8 + - - +
82A TRP* 3.8 3.5 - - + -
103A TRP* 3.0 34.8 + - + +
104A ASN* 3.1 7.2 - - - -
105A GLY 2.8 31.7 + - - -
122A TYR* 2.6 28.1 + - - -
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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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45A PHE* 4.7 4.7 - - + -
53A GLY* 3.9 15.0 - - - -
61A TYR* 4.0 27.8 - - + +
62A ALA* 3.3 31.0 - - - +
63A GLY 3.2 8.9 + - - +
65A ASP* 1.3 77.3 - - + +
67A ASP* 1.3 63.3 + - - +
70A THR* 2.7 37.4 + - - +
82A TRP* 3.6 52.1 - - + +
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Residues in contact with ASP 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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62A ALA* 5.7 0.7 - - - -
63A GLY 2.9 17.6 + - - +
64A PHE 3.7 3.1 - - - +
66A ILE* 1.3 84.7 - - - +
68A LEU* 1.3 62.8 + - - +
70A THR* 3.7 5.3 - - - -
71A ALA* 3.0 25.3 + - - +
260A ILE* 3.8 24.0 - - + +
263A LYS* 2.9 34.8 + - - +
264A TRP* 2.9 15.7 + - - -
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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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64A PHE* 2.8 45.3 + - + +
65A ASP* 4.1 3.8 - - - +
67A ASP* 1.3 73.6 - - - +
69A ALA* 1.3 58.5 + - - +
71A ALA* 3.2 3.5 + - - +
72A VAL* 2.9 31.7 + - - +
103A TRP* 3.9 21.1 - - + +
122A TYR* 4.0 17.5 - - + -
248A PHE* 3.9 16.4 - - + -
251A LEU* 3.9 23.6 - - + -
257A PHE* 3.9 25.1 - - + -
260A ILE* 3.9 16.1 - - + +
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Residues in contact with ALA 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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43A ILE* 4.0 7.6 - - + -
65A ASP 2.9 21.6 + - - +
68A LEU* 1.3 69.9 - - - +
70A THR* 1.3 66.6 + - - +
72A VAL* 3.3 0.3 + - - +
73A PHE* 3.0 29.7 + - - +
80A VAL* 4.4 1.8 - - + -
82A TRP* 3.7 22.2 - - + -
103A TRP* 3.6 36.9 - - + -
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Residues in contact with THR 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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66A ILE* 2.7 28.0 + - - +
67A ASP* 3.7 6.7 - - - -
69A ALA* 1.3 77.4 - - - +
71A ALA* 1.3 57.1 + - - +
73A PHE* 3.8 1.1 - - - +
74A GLU* 2.9 33.1 + - + +
78A ILE 5.1 0.7 - - - +
80A VAL* 4.6 10.0 - - + +
82A TRP* 4.4 12.5 + - - -
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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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67A ASP 3.0 17.4 + - - +
68A LEU 3.6 4.3 - - - +
70A THR* 1.3 74.6 - - - +
72A VAL* 1.3 67.6 + - - +
74A GLU* 3.5 19.0 - - - +
75A LYS* 3.6 13.0 + - - +
251A LEU* 3.9 26.0 - - + +
256A LYS* 4.0 23.6 - - + -
260A ILE* 4.5 2.9 - - + -
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Residues in contact with VAL 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 2.9 20.9 + - - +
69A ALA 3.3 3.6 + - - +
71A ALA* 1.3 75.9 - - - +
73A PHE* 1.3 84.6 + - + +
75A LYS* 3.2 21.0 + - - +
76A TYR* 3.5 8.7 - - + -
103A TRP* 3.9 8.7 - - + -
244A ILE* 4.2 19.3 - - + -
247A ALA* 3.8 21.1 - - + -
248A PHE* 3.8 28.5 - - + -
251A LEU* 3.6 18.2 - - + -
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Residues in contact with PHE 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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32A TRP* 4.4 10.3 - + - -
41A ILE* 3.9 15.3 - - + -
43A ILE* 4.0 7.4 - - + -
69A ALA 3.0 26.4 + - - +
70A THR 4.4 0.7 - - - +
72A VAL* 1.3 81.8 - - + +
74A GLU* 1.3 64.3 + - - +
76A TYR* 3.0 19.4 + + - -
78A ILE* 3.0 62.0 + - + +
80A VAL* 3.9 17.5 - - + -
101A LEU* 3.8 25.4 - - + -
103A TRP* 3.9 21.8 - + - -
240A LEU* 4.0 20.4 - - + -
243A LYS* 6.1 0.4 - - + -
244A ILE* 4.1 10.3 - - + -
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Residues in contact with GLU 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 THR* 2.9 21.9 + - + +
71A ALA* 3.5 11.1 - - - +
72A VAL 3.3 0.2 - - - -
73A PHE* 1.3 76.7 - - - +
75A LYS* 1.3 79.2 + - - +
76A TYR 3.0 1.3 + - - -
77A GLY* 3.2 12.5 + - - +
78A ILE 4.0 4.4 + - - +
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Residues in contact with LYS 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 ALA 3.6 6.7 - - - +
72A VAL 3.2 15.7 + - - +
73A PHE 3.1 1.0 - - - -
74A GLU* 1.3 88.7 + - - +
76A TYR* 1.3 74.3 + - + +
77A GLY 3.6 0.2 - - - -
247A ALA* 4.2 13.9 - - + -
250A SER* 3.6 26.6 + - - +
251A LEU* 3.7 16.6 - - - -
254A ASP* 2.8 29.2 + - - +
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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