Contacts of the helix formed by residues 57 - 69 (chain A) in PDB entry 1X1O
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 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ALA* 1.3 75.1 - - - +
58A LEU* 1.3 66.3 + - - +
59A TRP* 3.2 4.5 - - - -
60A VAL* 2.9 21.9 + - - +
61A ALA* 2.9 20.6 + - - +
80A GLU* 2.8 12.5 + - - -
111A LEU* 3.6 12.2 + - - +
114A LEU* 4.1 13.2 - - - -
151A TYR* 4.3 2.7 - - - -
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Residues in contact with LEU 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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55A LEU* 4.2 21.5 - - + -
56A ALA 3.5 0.6 - - - -
57A GLY* 1.3 77.2 - - - +
59A TRP* 1.3 57.9 + - + +
61A ALA* 3.4 2.2 + - - +
62A GLU* 3.0 21.1 + - - +
74A PHE* 3.4 28.6 - - + -
76A PRO* 4.7 12.6 - - + -
78A VAL* 3.6 32.5 - - + +
79A ALA 4.0 4.3 - - - +
80A GLU* 3.1 31.8 + - + +
90A VAL* 4.2 19.1 - - + +
91A ALA* 4.7 0.2 - - + -
111A LEU* 3.7 21.7 - - + +
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Residues in contact with TRP 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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10A TRP* 3.5 46.2 - + + -
14A LEU* 3.6 29.2 - - + -
58A LEU* 1.3 77.0 - - - +
60A VAL* 1.3 80.4 + - + +
62A GLU* 3.5 16.0 + - - +
63A ARG* 3.2 23.2 + - + +
76A PRO* 6.4 0.2 - - - -
80A GLU* 3.4 21.9 + - + -
151A TYR* 2.9 33.2 + + - -
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Residues in contact with VAL 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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14A LEU* 4.7 2.0 - - + -
18A LEU* 4.0 17.5 - - + -
57A GLY* 2.9 20.5 + - - +
59A TRP* 1.3 112.6 - - + +
61A ALA* 1.3 66.1 + - - +
63A ARG* 3.1 7.2 + - - +
64A VAL* 3.0 21.7 + - - +
110A LEU* 3.8 32.5 - - + -
114A LEU* 4.5 4.5 - - + -
148A LEU* 4.1 22.0 - - + -
151A TYR* 5.5 0.4 - - + -
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Residues in contact with ALA 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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47A ILE* 5.2 0.4 - - + -
57A GLY 2.9 11.9 + - - +
58A LEU 3.7 8.1 - - - +
60A VAL* 1.3 74.6 - - - +
62A GLU* 1.3 64.8 + - - +
64A VAL* 2.7 28.3 - - - +
65A PHE* 3.1 14.3 + - + -
74A PHE* 4.2 15.5 - - + -
107A ALA* 4.1 25.8 - - + +
110A LEU* 5.9 0.8 - - - +
111A LEU* 4.5 14.6 - - + -
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Residues in contact with GLU 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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58A LEU 3.0 9.5 + - - +
59A TRP* 3.5 17.4 - - - +
61A ALA* 1.3 78.5 - - - +
63A ARG* 1.3 63.4 + - - +
65A PHE* 3.4 3.6 + - - +
66A ALA* 3.1 22.0 + - + +
74A PHE* 3.4 50.7 - - + +
76A PRO* 4.3 10.0 - - - +
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Residues in contact with ARG 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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15A GLU* 2.9 41.6 + - - +
18A LEU* 3.7 24.2 - - + -
19A ARG* 3.7 9.3 - - - +
59A TRP* 3.2 12.3 + - + +
60A VAL* 3.1 9.9 + - - +
62A GLU* 1.3 79.2 - - - +
64A VAL* 1.3 64.8 + - - +
66A ALA* 3.2 19.6 + - - +
67A LEU* 2.9 42.1 + - + +
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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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18A LEU* 4.0 26.0 - - + -
22A LEU* 4.3 5.4 - - + +
60A VAL 3.0 12.0 + - - +
61A ALA* 2.7 28.7 - - - +
63A ARG* 1.3 76.0 - - - +
65A PHE* 1.3 67.4 + - - +
67A LEU* 3.1 11.5 + - - +
68A ALA* 3.1 21.0 + - - +
103A GLY* 4.4 5.8 - - - +
106A LEU* 4.2 17.3 - - + -
107A ALA* 3.1 35.0 - - + +
110A LEU* 4.0 15.3 - - + -
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Residues in contact with PHE 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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47A ILE* 4.5 7.4 - - + -
61A ALA 3.1 18.9 + - - -
62A GLU* 3.7 6.1 - - - +
64A VAL* 1.3 81.8 - - + +
66A ALA* 1.3 62.6 + - - +
68A ALA* 3.2 6.1 + - - +
69A ASP 3.0 24.3 + - - +
72A THR* 4.2 16.8 + - + +
74A PHE* 3.6 33.7 - + + -
93A VAL* 4.3 14.1 - - + -
99A GLY 4.3 2.2 - - - +
100A ILE* 3.5 41.3 - - + -
103A GLY* 3.8 7.9 - - - -
104A GLU* 3.6 15.5 - - - -
107A ALA* 3.5 22.9 - - + -
108A LEU* 4.5 7.4 - - + -
281A LEU* 4.7 12.1 - - + -
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Residues in contact with ALA 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 GLU* 3.1 15.7 + - + +
63A ARG* 3.2 31.1 + - - +
65A PHE* 1.3 77.7 - - - +
67A LEU* 1.3 59.0 + - - +
69A ASP 3.8 7.0 - - - -
70A PRO* 3.1 35.2 - - + +
72A THR 5.3 5.4 - - - +
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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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15A GLU* 3.3 25.8 - - - +
18A LEU* 3.6 33.9 - - + +
19A ARG* 3.3 40.7 + - + +
22A LEU* 3.8 16.1 - - + +
63A ARG* 2.9 38.2 + - + +
64A VAL* 3.5 9.4 - - + +
66A ALA* 1.3 75.5 - - - +
68A ALA* 1.3 64.9 + - - +
69A ASP* 4.6 0.2 - - - -
70A PRO* 5.2 1.4 - - - +
11C GLN* 4.2 12.3 - - - +
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Residues in contact with ALA 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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22A LEU* 3.7 10.0 - - + +
64A VAL 3.1 12.1 + - - +
65A PHE 3.2 7.2 + - - +
67A LEU* 1.3 78.0 - - - +
69A ASP* 1.3 62.8 + - - +
70A PRO* 4.7 0.2 - - - -
99A GLY* 3.5 24.4 - - - +
102A ALA* 4.1 8.7 - - + -
103A GLY* 3.8 17.9 - - - +
11C GLN* 2.9 28.2 + - - +
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Residues in contact with ASP 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 PHE 3.0 14.3 + - - +
66A ALA* 3.3 4.6 - - - +
67A LEU 3.3 0.8 - - - -
68A ALA* 1.3 81.0 - - - +
70A PRO* 1.3 68.6 - - - +
71A ARG* 2.7 74.6 + - - +
72A THR* 3.1 16.5 + - - +
96A PRO* 3.7 12.9 - - - +
98A ARG* 5.9 0.5 - - - +
99A GLY* 3.7 21.2 + - - -
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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