Contacts of the helix formed by residues 66 - 78 (chain A) in PDB entry 1DXO
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 GLN 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ASP* 5.7 0.7 - - - +
64A ASN* 2.8 31.7 + - - +
65A PHE* 1.3 77.4 - - - +
67A TYR* 1.3 66.7 + - - +
68A PRO* 3.3 10.6 - - + -
69A ALA* 3.5 10.8 + - + +
70A GLU* 3.2 27.5 + - + +
193C GLY* 5.8 4.4 - - - -
301C FAD 2.8 44.5 + - - +
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Residues in contact with TYR 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 3.7 27.8 - - + +
51A SER* 3.4 23.8 - - - -
54A ASP* 2.7 30.6 + - + +
55A ILE* 4.8 2.0 - - + -
65A PHE* 3.7 33.5 + + + -
66A GLN* 1.3 70.2 - - - +
68A PRO* 1.3 72.0 - - + +
71A SER* 2.9 50.1 + - - -
84A ILE* 4.5 0.7 - - - +
117A GLU 4.1 9.4 - - - -
118A ARG* 4.2 5.4 + - - -
121A ILE* 3.8 21.1 - - + +
301C FAD 3.4 28.0 - - + -
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Residues in contact with PRO 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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66A GLN* 3.3 10.8 - - + -
67A TYR* 1.3 95.2 - - + +
69A ALA* 1.3 61.0 + - + +
71A SER* 2.7 22.9 + - - +
72A VAL* 3.1 18.4 + - + +
126A TYR* 5.4 1.6 - - - +
301C FAD 3.9 42.0 - - + +
302C DQN 4.2 22.9 - - + +
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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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66A GLN* 3.5 14.1 + - + +
68A PRO* 1.3 78.7 - - - +
70A GLU* 1.3 65.8 + - + +
72A VAL* 3.4 7.7 + - - +
73A LEU* 3.1 24.5 + - - +
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Residues in contact with GLU 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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55A ILE* 3.8 11.2 - - + +
58A LYS 5.0 0.5 - - - +
59A LEU* 3.3 20.0 - - + +
60A LYS* 3.0 26.1 + - - +
61A ASP* 2.9 36.6 + - - +
65A PHE* 3.7 27.8 - - + -
66A GLN* 3.2 21.1 + - + +
67A TYR 4.0 0.4 - - - +
69A ALA* 1.3 77.4 - - + +
71A SER* 1.3 56.6 + - - +
73A LEU* 3.4 10.9 - - - +
74A ALA* 2.9 29.1 + - - +
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Residues in contact with SER 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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54A ASP* 6.2 0.2 - - - -
55A ILE* 4.2 12.3 - - - +
67A TYR* 2.9 40.6 + - - -
68A PRO* 2.7 22.7 + - - +
70A GLU* 1.3 75.5 - - - +
72A VAL* 1.3 59.2 + - - +
74A ALA* 3.5 1.1 + - - -
75A TYR* 3.0 22.9 + - - +
80A LEU* 3.7 7.6 - - - +
121A ILE* 3.3 32.0 - - - +
122A GLY 4.9 0.7 + - - -
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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 PRO* 3.1 21.2 + - + +
69A ALA* 3.7 7.2 - - - +
71A SER* 1.3 80.0 + - - +
73A LEU* 1.3 59.4 + - - +
75A TYR* 3.3 3.6 + - - +
76A LYS* 3.0 63.0 + - - +
121A ILE* 4.0 5.4 - - - -
122A GLY* 3.8 27.1 - - - +
123A GLU* 4.0 16.8 - - + +
126A TYR* 5.0 4.0 - - - +
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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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58A LYS 6.0 2.0 - - - +
60A LYS* 3.5 55.2 - - + +
69A ALA 3.1 16.9 + - - +
70A GLU* 3.4 13.7 - - - +
72A VAL* 1.3 74.8 - - - +
74A ALA* 1.3 54.7 + - - +
76A LYS* 3.0 16.1 + - + +
77A GLU* 2.7 67.9 + - + +
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Residues in contact with ALA 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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55A ILE* 3.6 24.5 - - + -
70A GLU 2.9 18.3 + - - +
71A SER 3.8 4.0 - - - +
73A LEU* 1.3 76.4 - - - +
75A TYR* 1.3 57.1 + - - +
77A GLU* 4.5 1.3 - - - +
78A GLY 2.9 7.1 + - - -
79A HIS* 2.5 59.7 + - + +
80A LEU* 3.4 8.1 + - + -
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Residues in contact with TYR 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 SER 3.0 17.3 + - - +
72A VAL* 3.4 4.0 - - - +
74A ALA* 1.3 76.7 - - - +
76A LYS* 1.3 72.6 + - + +
78A GLY* 3.3 11.3 + - - -
80A LEU* 3.7 18.8 - - + +
88A GLN* 3.6 23.8 - - - -
92A GLU* 4.2 9.3 + - - -
121A ILE* 4.3 6.3 - - + -
122A GLY 4.2 0.9 - - - -
123A GLU* 4.2 23.9 + - + -
124A PHE* 3.3 49.2 - + + +
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Residues in contact with LYS 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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72A VAL* 3.0 47.0 + - + +
73A LEU* 3.0 16.7 + - + +
75A TYR* 1.3 92.2 - - + +
77A GLU* 1.3 63.3 + - + +
78A GLY 3.5 0.2 + - - -
123A GLU* 3.7 23.4 + - + -
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Residues in contact with GLU 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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58A LYS 5.7 0.7 - - - +
60A LYS* 5.6 0.7 - - - -
73A LEU* 2.7 53.0 + - + +
74A ALA* 5.0 0.3 + - - -
76A LYS* 1.3 74.4 - - + +
78A GLY* 1.3 61.7 + - - +
79A HIS* 3.4 39.2 + - + +
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Residues in contact with GLY 78 (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 THR* 5.1 0.2 + - - -
74A ALA 2.9 6.3 + - - -
75A TYR* 3.3 7.0 + - - -
76A LYS 3.2 4.4 + - - -
77A GLU* 1.3 80.1 - - - +
79A HIS* 1.3 65.3 + - - +
80A LEU* 3.5 5.1 + - - +
85A VAL* 6.3 0.7 - - - -
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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