Contacts of the helix formed by residues 63 - 77 (chain A) in PDB entry 4OBP
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.3 4.3 - - + -
58A VAL* 3.5 32.9 - - + +
59A THR 3.3 16.8 - - - +
60A GLU* 3.9 17.4 + - - +
61A ASP 3.7 2.6 + - - -
62A GLU* 1.3 73.6 - - - +
64A GLU* 1.4 62.0 + - - +
65A GLU 3.5 0.7 - - - -
66A ILE* 3.4 9.2 - - - +
67A LYS* 3.3 49.6 + - - +
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Residues in contact with GLU 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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60A GLU 5.3 0.4 + - - -
61A ASP 5.4 0.4 + - - -
63A GLU* 1.4 74.3 - - - +
65A GLU* 1.4 61.9 + - + +
66A ILE 3.3 0.2 - - - -
67A LYS* 3.5 24.9 + - - +
68A LEU* 3.2 40.8 + - + +
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Residues in contact with GLU 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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56A MET* 5.1 0.8 - - - +
61A ASP 3.6 16.2 - - - +
62A GLU* 3.3 32.6 - - + +
64A GLU* 1.4 76.9 - - + +
66A ILE* 1.4 64.4 + - + +
68A LEU* 3.5 8.1 + - - +
69A GLU* 3.2 22.7 + - - +
173A GLY 5.8 0.2 - - - +
186A ASN* 2.7 36.4 + - - +
187A THR* 5.9 0.9 - - - +
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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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15A LEU* 3.9 19.1 - - + -
56A MET* 3.7 50.5 - - + +
57A ASP 4.2 9.4 - - - +
58A VAL* 4.8 6.1 - - + -
62A GLU* 3.2 40.6 - - + +
63A GLU* 3.4 14.1 - - - +
64A GLU 3.3 0.2 - - - -
65A GLU* 1.4 77.8 - - + +
67A LYS* 1.4 64.2 + - - +
69A GLU* 3.4 11.1 + - - +
70A ILE* 3.3 20.5 + - - +
101A LEU* 3.6 18.5 - - + +
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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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13A ILE* 4.0 8.4 + - + +
14A ASP* 5.4 2.4 - - - +
15A LEU* 3.7 42.2 - - + +
63A GLU* 3.3 40.0 + - - +
64A GLU* 3.6 26.2 - - - +
65A GLU 3.5 0.2 - - - -
66A ILE* 1.4 76.4 - - - +
68A LEU* 1.3 57.4 + - - +
70A ILE* 3.2 11.7 + - - +
71A ASN* 2.6 44.2 + - - +
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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 GLU* 3.2 30.4 + - + +
65A GLU* 3.7 9.2 - - - +
66A ILE 3.4 0.2 - - - -
67A LYS* 1.3 77.0 - - + +
69A GLU* 1.4 58.5 + - - +
71A ASN* 4.0 9.7 - - + +
72A MET* 3.1 57.6 + - + +
175A SER 5.9 2.7 - - - +
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Residues in contact with GLU 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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54A LYS* 2.7 39.3 + - - +
56A MET* 3.2 26.3 - - + +
65A GLU 3.2 13.1 + - - +
66A ILE 3.8 8.5 - - - +
67A LYS 3.3 0.6 - - - -
68A LEU* 1.4 74.0 - - - +
70A ILE* 1.4 62.3 + - - +
72A MET* 4.2 1.9 - - - +
73A LEU* 3.2 25.6 + - + +
103A LEU* 3.9 10.3 - - + +
171A ASP* 4.0 0.2 - - - +
172A PHE* 4.0 25.0 + - + +
173A GLY* 3.4 21.4 + - - -
403A 2QU 3.6 10.0 - - - -
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Residues in contact with ILE 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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13A ILE* 3.8 30.3 - - + -
15A LEU* 5.0 3.6 - - + -
18A LEU* 5.9 0.2 - - + -
56A MET* 5.0 0.7 - - - -
66A ILE 3.3 15.5 - - - +
67A LYS* 3.2 11.4 + - - +
69A GLU* 1.4 73.8 - - - +
71A ASN* 1.3 54.3 + - - +
73A LEU* 3.8 1.2 - - - +
74A LYS* 2.9 35.9 + - - +
85A TYR* 3.7 24.9 - - + +
88A ALA* 4.0 11.0 - - + -
101A LEU* 3.7 33.7 - - + -
103A LEU* 3.5 36.3 - - + -
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Residues in contact with ASN 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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13A ILE* 2.9 42.0 + - - +
67A LYS* 2.6 33.2 + - - +
68A LEU* 4.0 11.0 - - + +
70A ILE* 1.3 75.2 - - - +
72A MET* 1.3 62.7 + - + +
74A LYS* 3.6 8.4 - - - +
75A LYS* 3.2 24.8 + - - +
76A TYR* 4.9 0.8 - - - -
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Residues in contact with MET 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 40.4 + - + +
69A GLU* 4.2 2.7 - - - +
71A ASN* 1.3 73.2 - - + +
73A LEU* 1.4 60.4 + - - +
74A LYS 3.2 0.5 + - - -
75A LYS 3.2 1.6 + - - -
76A TYR* 2.9 54.0 + - + +
148A HIS 5.7 0.4 - - - +
149A VAL* 4.1 30.3 - - + -
172A PHE* 4.3 16.8 - - + +
175A SER* 4.1 28.0 - - - +
176A ALA 4.3 17.3 - - - -
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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 GLU* 3.2 17.6 + - + +
70A ILE 4.0 1.8 - - - +
72A MET* 1.4 76.6 - - - +
74A LYS* 1.3 55.9 + - - +
77A SER* 2.6 39.5 + - - -
83A ALA* 3.6 24.2 - - + +
84A THR 4.9 0.2 - - - -
85A TYR* 3.7 14.6 - - + +
103A LEU* 3.6 37.0 - - + -
105A MET* 4.0 27.4 - - + -
170A VAL* 6.5 0.7 - - - -
171A ASP 6.2 0.2 - - - +
172A PHE* 3.6 35.1 - - + -
403A 2QU 4.8 3.6 - - - -
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Residues in contact with LYS 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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13A ILE* 3.9 30.7 - - + +
70A ILE 2.9 17.8 + - - +
71A ASN* 3.6 10.1 - - - +
73A LEU* 1.3 77.7 - - - +
75A LYS* 1.3 54.5 + - + +
77A SER* 3.9 0.3 + - - -
78A HIS* 2.7 35.8 + - - +
85A TYR* 3.7 36.7 - - + +
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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 ASN 3.2 13.6 + - - +
72A MET 4.4 0.2 - - - +
74A LYS* 1.3 80.4 - - + +
76A TYR* 1.3 85.2 + - + +
77A SER 3.5 0.4 - - - -
78A HIS* 3.6 17.8 + - + +
143A HIS* 5.1 2.4 + - - -
147A HIS* 4.2 21.8 + - - -
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Residues in contact with TYR 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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71A ASN 4.9 0.7 - - - -
72A MET* 2.9 52.5 + - + +
73A LEU 4.3 0.7 - - - -
75A LYS* 1.3 102.7 - - + +
77A SER* 1.3 57.3 + - - +
78A HIS 3.5 2.7 - - - -
82A ILE* 3.6 14.2 - - - +
143A HIS* 3.4 25.8 - - + +
144A LEU* 3.9 18.0 - - + +
147A HIS* 3.7 44.4 + + + -
149A VAL* 3.7 26.0 - - + +
172A PHE* 4.5 5.2 - + + -
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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 LEU* 2.6 27.3 + - - -
74A LYS 3.9 4.7 + - - -
75A LYS 3.5 1.4 - - - -
76A TYR* 1.3 75.7 - - - +
78A HIS* 1.3 55.2 + - - +
79A HIS 3.0 7.6 + - - +
82A ILE* 3.5 12.8 - - - +
83A ALA 3.5 22.9 - - - -
84A THR* 3.7 6.1 + - - +
85A TYR* 3.0 22.5 + - - +
401A MG 2.6 28.4 - - - -
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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