Contacts of the helix formed by residues 53 - 68 (chain A) in PDB entry 1X0O
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 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A CYS* 3.4 8.9 - - - -
50A HIS* 2.5 47.1 + - + +
52A GLU* 1.3 79.6 - - - +
54A GLN* 1.3 65.7 + - - +
55A GLN 3.2 2.5 - - - -
56A LEU* 3.0 25.9 + - + +
57A LEU* 3.0 20.6 + - - +
75A MET 4.5 1.7 - - - +
76A PHE* 3.9 28.6 - - + -
77A ARG* 4.1 6.8 + - - +
87A TRP* 5.0 8.4 - - - -
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Residues in contact with GLN 54 (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 VAL* 3.0 44.2 + - + +
47A GLU* 4.4 5.9 + - - +
49A CYS* 2.7 30.2 + - - +
50A HIS 3.1 14.1 - - - +
51A PRO* 3.5 23.8 - - + +
52A GLU 3.6 1.0 - - - -
53A ASP* 1.3 79.1 - - - +
55A GLN* 1.3 61.5 + - - +
57A LEU* 3.5 4.9 + - - +
58A ARG* 3.2 17.3 + - - +
85A TRP* 5.6 0.4 - - - -
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Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PRO 5.4 0.4 + - - -
52A GLU 5.2 2.2 - - - +
53A ASP 3.2 0.4 - - - -
54A GLN* 1.3 76.9 - - - +
56A LEU* 1.3 60.2 + - - +
58A ARG* 3.1 41.0 + - - +
59A ASP* 2.8 43.6 + - + +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU 5.1 2.2 + - - +
53A ASP* 3.0 34.6 + - + +
55A GLN* 1.3 78.6 - - - +
57A LEU* 1.3 60.1 + - - +
59A ASP* 3.6 8.0 + - + +
60A SER* 3.1 36.7 + - - +
74A VAL* 4.0 10.5 - - + -
75A MET 3.2 27.8 - - - +
76A PHE* 4.9 0.2 - - + -
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Residues in contact with LEU 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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45A ILE* 4.2 21.5 - - + +
46A VAL* 4.9 4.3 - - + -
49A CYS* 3.3 36.1 - - + -
53A ASP 3.0 7.0 + - - +
54A GLN 3.6 7.9 - - - +
56A LEU* 1.3 74.3 - - - +
58A ARG* 1.3 59.5 + - - +
60A SER 3.3 0.9 + - - -
61A PHE* 2.8 53.5 + - + -
74A VAL* 3.6 27.4 - - + -
76A PHE* 3.5 44.9 - - + -
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Residues in contact with ARG 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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46A VAL* 5.9 2.9 - - + +
54A GLN 3.2 10.3 + - - +
55A GLN* 3.1 38.6 + - - +
57A LEU* 1.3 80.0 - - - +
59A ASP* 1.3 64.0 + - - +
61A PHE* 3.1 6.7 + - - +
62A GLN* 2.9 44.7 + - + +
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Residues in contact with ASP 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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55A GLN* 2.8 32.0 + - + +
56A LEU* 3.9 8.9 - - + +
58A ARG* 1.3 72.7 - - - +
60A SER* 1.3 62.8 + - - +
62A GLN* 3.3 10.9 + - - +
63A GLN* 2.8 47.0 + - - +
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Residues in contact with SER 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 LEU* 3.1 24.5 + - - +
57A LEU 3.8 1.8 - - - -
59A ASP* 1.3 76.3 + - - +
61A PHE* 1.3 61.6 + - - +
63A GLN* 3.1 15.7 + - - +
64A VAL* 3.0 24.8 + - - +
72A LEU* 3.2 18.3 - - - +
73A SER 5.3 0.7 + - - -
74A VAL* 3.5 33.1 - - - +
92A SER* 4.9 1.0 + - - -
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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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16A HIS* 3.6 23.6 - + - -
18A ILE 5.0 10.8 - - - +
19A GLU 6.0 0.2 - - - -
20A GLY* 5.3 2.7 - - - -
45A ILE* 3.6 39.3 - - + -
57A LEU* 2.8 55.1 + - + +
58A ARG* 3.6 6.7 - - - +
60A SER* 1.3 75.6 - - - +
62A GLN* 1.3 67.7 + - + +
64A VAL* 3.0 25.5 - - + +
65A VAL* 3.1 13.7 - - - +
74A VAL* 3.8 13.2 - - + -
90A THR* 4.5 9.6 - - + -
92A SER* 4.1 14.8 - - - -
106A ILE* 5.0 9.6 - - + +
108A CYS* 4.6 1.6 - - - -
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Residues in contact with GLN 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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18A ILE 5.5 2.3 - - - +
58A ARG* 2.9 41.4 + - + +
59A ASP* 3.4 12.1 - - - +
61A PHE* 1.3 81.4 - - - +
63A GLN* 1.3 57.0 + - + +
65A VAL* 3.3 13.8 + - - +
66A LYS* 3.0 34.1 + - + +
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Residues in contact with GLN 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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59A ASP* 2.8 49.7 + - - +
60A SER* 3.1 16.4 + - - +
62A GLN* 1.3 76.5 - - + +
64A VAL* 1.3 54.8 + - - +
65A VAL 3.1 0.4 - - - -
66A LYS* 3.0 22.9 + - + +
67A LEU* 2.7 39.5 + - + +
72A LEU* 3.5 15.0 - - + +
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Residues in contact with VAL 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 SER 3.0 8.5 + - - +
61A PHE* 3.0 27.8 - - + +
63A GLN* 1.3 76.3 - - - +
65A VAL* 1.3 58.5 + - + +
67A LEU* 4.3 4.0 - - - +
68A LYS* 2.8 27.0 + - - -
69A GLY 5.4 0.2 - - - +
70A GLN 3.6 13.7 - - - +
72A LEU* 3.5 8.2 - - + +
92A SER* 3.5 51.8 - - - +
93A PHE* 3.9 2.5 - - - +
94A THR* 3.5 22.9 - - + +
106A ILE* 4.7 9.6 - - + -
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Residues in contact with VAL 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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18A ILE* 5.1 11.2 - - + +
61A PHE 3.1 15.7 - - - +
62A GLN* 3.3 15.2 + - - +
63A GLN 3.1 0.2 - - - -
64A VAL* 1.3 78.1 - - + +
66A LYS* 1.3 59.4 + - - +
68A LYS* 3.1 29.8 - - - +
94A THR* 4.1 16.8 - - + -
103A ILE* 4.5 13.7 - - + -
106A ILE* 4.5 12.8 - - + -
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Residues in contact with LYS 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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62A GLN* 3.0 26.4 + - + +
63A GLN* 3.0 26.2 + - + +
65A VAL* 1.3 78.8 - - - +
67A LEU* 1.3 67.6 + - + +
68A LYS* 4.3 5.2 - - - +
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Residues in contact with LEU 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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63A GLN* 2.7 23.8 + - + +
64A VAL* 4.0 4.0 - - - +
66A LYS* 1.3 76.8 - - + +
68A LYS* 1.3 74.9 + - - +
70A GLN* 3.8 36.1 - - + +
72A LEU* 3.5 37.0 - - + -
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Residues in contact with LYS 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 VAL 2.8 15.2 + - - +
65A VAL* 3.1 34.1 - - - +
66A LYS 4.3 3.8 - - - +
67A LEU* 1.3 82.9 - - - +
69A GLY* 1.3 58.5 + - - +
70A GLN* 3.3 1.8 + - - +
94A THR* 3.3 12.1 - - - +
96A GLN* 3.1 38.7 - - - +
101A ASP* 4.8 6.8 + - - +
103A ILE* 4.3 15.0 - - + -
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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