Contacts of the helix formed by residues 55 - 69 (chain A) in PDB entry 3U9O
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 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ASP* 5.9 0.7 - - - +
20A GLY 5.1 1.4 + - - -
41A ILE* 4.1 19.4 - - - +
42A PRO 5.9 4.5 - - - -
54A TYR* 1.3 78.3 - - - +
56A PRO* 1.3 63.5 - - - +
58A ALA* 3.3 2.8 + - - +
59A ALA* 3.0 26.3 + - - +
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Residues in contact with PRO 56 (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 TYR 4.1 3.1 - - - +
55A GLY* 1.3 90.7 - - - +
57A GLU* 1.3 73.0 + - - +
59A ALA* 3.2 9.7 + - + +
60A ALA* 2.8 30.9 + - - +
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Residues in contact with GLU 57 (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 TYR* 2.8 49.9 + - + +
56A PRO* 1.3 85.7 - - - +
58A ALA* 1.3 64.3 + - - +
60A ALA* 3.3 7.1 + - - +
61A PHE* 3.0 24.9 + - - +
108A LEU* 4.0 21.0 - - + +
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Residues in contact with ALA 58 (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 GLY* 3.6 4.9 - - - -
41A ILE* 3.7 24.2 - - + -
54A TYR 2.7 20.9 + - - +
55A GLY 3.7 4.0 - - - +
57A GLU* 1.3 72.0 - - - +
59A ALA* 1.3 63.5 + - - +
61A PHE* 3.2 2.6 + - - +
62A THR* 3.0 27.2 + - - -
103A LEU* 3.8 13.0 - - + +
108A LEU* 3.4 27.1 - - - +
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Residues in contact with ALA 59 (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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18A ILE 5.0 2.0 - - - +
19A ASP* 3.9 15.0 - - + -
20A GLY* 3.6 20.5 - - - +
55A GLY 3.0 13.2 + - - +
56A PRO* 3.2 13.4 + - + +
58A ALA* 1.3 75.0 - - - +
60A ALA* 1.3 58.2 + - - +
62A THR* 4.0 1.4 - - - -
63A LYS* 2.9 32.9 + - - +
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Residues in contact with ALA 60 (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 PRO 2.8 16.6 + - - +
57A GLU* 3.3 7.8 + - - +
59A ALA* 1.3 75.4 - - - +
61A PHE* 1.3 63.6 + - - +
63A LYS* 3.4 9.3 + - - +
64A LYS* 3.0 24.9 + - - +
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Residues in contact with PHE 61 (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 GLU 3.0 16.3 + - - +
58A ALA 3.5 4.0 - - - +
60A ALA* 1.3 75.5 - - - +
62A THR* 1.3 68.0 + - - +
64A LYS* 3.3 5.6 + - - +
65A MET* 3.0 36.4 + - + +
99A VAL 4.7 1.1 - - - -
102A ALA* 3.7 39.9 - - + -
103A LEU* 3.4 24.0 - - + -
106A GLN* 3.8 24.7 - - + -
108A LEU* 3.7 23.1 - - + -
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Residues in contact with THR 62 (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 ALA* 5.5 1.3 - - + -
19A ASP 3.7 15.5 - - - +
20A GLY 2.8 29.0 + - - +
22A THR 5.4 0.2 - - - +
23A VAL* 4.0 23.6 - - + -
36A LEU* 5.3 0.9 - - + -
58A ALA 3.0 14.6 + - - -
59A ALA 4.0 0.9 - - - -
61A PHE* 1.3 79.2 - - - +
63A LYS* 1.3 64.9 + - - +
65A MET* 3.2 4.9 + - - +
66A VAL* 3.1 24.8 + - + +
99A VAL* 3.9 21.7 - - + +
103A LEU* 3.6 11.3 - - - +
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Residues in contact with LYS 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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17A ALA* 3.8 25.0 - - + +
59A ALA 2.9 20.9 + - - +
60A ALA* 3.6 9.2 - - - +
62A THR* 1.3 75.5 - - - +
64A LYS* 1.3 58.8 + - - +
66A VAL* 3.5 0.7 - - - +
67A GLU* 2.5 80.4 + - - +
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Residues in contact with LYS 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 ALA 3.0 16.5 + - - +
61A PHE* 3.8 5.2 - - - +
62A THR 3.3 0.2 - - - -
63A LYS* 1.3 77.5 - - - +
65A MET* 1.3 64.5 + - - +
67A GLU* 4.6 4.5 - - - -
68A ASN* 3.0 55.3 + - - +
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Residues in contact with MET 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 PHE* 3.0 30.9 + - + +
62A THR* 3.2 5.8 + - - +
64A LYS* 1.3 80.2 - - - +
66A VAL* 1.3 60.8 + - + +
68A ASN* 4.2 2.1 - - - +
69A ALA* 3.4 21.0 + - - +
94A ALA* 3.8 14.2 - - + +
97A LYS* 3.5 38.4 - - + +
98A MET 3.7 6.3 - - - +
99A VAL* 3.7 26.9 - - + -
102A ALA* 3.8 22.9 - - + -
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Residues in contact with VAL 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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14A LEU* 3.9 33.4 - - + +
17A ALA* 4.0 17.3 - - + -
23A VAL* 4.6 12.8 - - + -
25A LEU* 6.1 0.9 - - + -
62A THR* 3.1 29.7 + - + +
63A LYS 3.5 4.3 - - - +
65A MET* 1.3 74.0 - - - +
67A GLU* 1.3 67.9 + - - +
68A ASN 3.4 0.3 + - - -
69A ALA* 3.5 14.7 + - - +
72A ILE* 3.9 26.5 - - + +
92A ILE* 4.8 6.3 - - + -
99A VAL* 4.0 26.2 - - + -
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Residues in contact with GLU 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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14A LEU* 3.8 21.6 - - + +
17A ALA* 4.5 8.0 + - + +
63A LYS* 2.5 64.4 + - + +
64A LYS* 4.1 4.1 - - - +
66A VAL* 1.3 78.7 - - + +
68A ASN* 1.3 67.1 + - - +
69A ALA 3.7 3.5 + - - +
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Residues in contact with ASN 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 LYS* 3.0 52.2 + - - +
65A MET* 4.2 3.1 - - - +
67A GLU* 1.3 81.4 - - - +
69A ALA* 1.3 66.4 + - - +
70A LYS* 3.7 1.4 + - - +
95A ASP* 4.2 1.9 - - - +
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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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65A MET 3.4 17.2 + - - +
66A VAL 3.8 11.0 - - - +
67A GLU 3.4 4.3 - - - +
68A ASN* 1.3 81.0 - - - +
70A LYS* 1.3 60.5 + - - +
71A LYS 3.4 19.7 - - - +
72A ILE* 3.8 7.5 - - + +
94A ALA* 3.7 15.5 - - + -
95A ASP* 3.2 13.2 - - - +
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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