Contacts of the helix formed by residues 72 - 81 (chain A) in PDB entry 1XD7
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 SER 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ASP 4.0 1.0 - - - -
71A ILE* 1.3 73.4 - - - +
73A LEU* 1.3 66.3 + - - +
74A LEU* 4.0 3.9 - - - +
75A GLU* 2.8 52.0 + - - +
76A VAL* 3.1 15.1 + - - +
122A LEU 3.9 7.4 - - - -
123A ALA* 4.2 15.2 - - - +
125A LYS 3.5 15.0 - - - -
126A SER* 4.3 0.4 - - - +
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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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8A LEU* 4.4 10.8 - - + +
12A ILE* 3.6 28.3 - - + -
72A SER* 1.3 71.0 - - - +
74A LEU* 1.3 56.4 + - - +
76A VAL* 2.8 10.7 + - + +
77A TYR* 2.7 35.1 + - - +
122A LEU* 3.1 31.8 + - + +
125A LYS* 3.5 29.0 + - + -
126A SER 4.0 18.2 - - - +
127A LEU* 4.3 7.0 - - - +
130A VAL* 4.2 18.2 - - + -
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Residues in contact with LEU 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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72A SER* 4.2 2.9 - - - +
73A LEU* 1.3 73.1 - - - +
75A GLU* 1.3 67.9 - - - +
77A TYR* 3.0 27.6 + - + +
78A ARG* 3.1 24.8 + - + +
119A GLU* 3.7 48.2 - - + +
122A LEU* 2.6 37.0 + - + +
123A ALA* 3.5 13.2 - - + +
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Residues in contact with GLU 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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50A ALA* 5.5 0.7 - - - +
52A ILE* 3.9 25.4 - - + +
66A LYS* 4.4 16.0 + - - +
70A ASP 3.6 12.2 - - - +
71A ILE* 4.6 7.0 - - + -
72A SER* 2.8 41.5 + - - +
74A LEU* 1.3 84.2 - - + +
76A VAL* 1.3 59.8 + - - +
78A ARG* 3.9 4.3 + - - +
79A ALA* 3.6 12.8 + - - +
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Residues in contact with VAL 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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8A LEU* 3.9 15.3 - - + -
11A ALA* 3.7 29.4 - - + -
12A ILE* 4.1 10.1 - - + -
15A LEU* 4.0 24.7 - - + -
47A LEU* 4.3 5.4 - - + -
52A ILE* 4.1 8.5 - - + -
71A ILE* 4.1 13.9 - - + -
72A SER 3.3 14.4 - - - +
73A LEU* 2.8 14.9 + - + +
75A GLU* 1.3 74.0 - - - +
77A TYR* 1.3 69.2 + - - +
79A ALA* 3.2 12.6 + - - +
80A VAL* 3.3 11.1 + - + +
127A LEU* 6.1 1.3 - - + -
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Residues in contact with TYR 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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8A LEU* 4.4 22.2 - - + +
73A LEU 2.7 15.0 + - - +
74A LEU* 3.2 27.4 - - + +
76A VAL* 1.3 72.2 - - - +
78A ARG* 1.3 60.3 + - + +
80A VAL* 2.9 12.7 + - + +
81A GLN* 2.6 79.5 + - + +
115A GLN* 4.6 11.8 + - - -
118A MET* 4.0 29.5 - - + +
119A GLU* 4.9 6.3 - - + -
122A LEU* 4.1 15.3 - - + -
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Residues in contact with ARG 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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74A LEU* 3.1 21.3 + - + +
75A GLU* 4.3 4.9 - - - +
76A VAL 3.4 0.2 - - - -
77A TYR* 1.3 84.5 - - + +
79A ALA* 1.3 66.9 + - - +
81A GLN* 3.0 29.9 + - + +
119A GLU* 5.5 6.3 - - - +
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Residues in contact with ALA 79 (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 LEU* 3.6 26.2 - - - +
47A LEU* 4.4 10.5 - - + -
50A ALA* 3.3 33.4 - - + -
52A ILE* 4.1 9.2 - - + -
75A GLU 3.6 10.0 + - - +
76A VAL 3.2 10.5 + - - +
77A TYR 3.2 0.4 - - - -
78A ARG* 1.3 82.6 - - - +
80A VAL* 1.3 58.3 + - - +
81A GLN 5.2 0.2 - - - +
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Residues in contact with VAL 80 (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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7A ARG* 3.5 49.5 + - + +
8A LEU* 4.4 6.7 - - + +
11A ALA* 4.0 16.2 - - + -
43A MET* 3.9 22.9 - - - -
46A LEU* 4.5 16.4 - - + -
47A LEU* 4.5 13.0 - - + -
76A VAL 3.3 12.8 - - - +
77A TYR* 2.9 16.6 + - + +
79A ALA* 1.3 80.0 - - - +
81A GLN* 1.3 64.2 + - - +
82A LYS 3.5 2.4 + - - -
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Residues in contact with GLN 81 (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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77A TYR* 2.6 61.7 + - + +
78A ARG* 3.0 30.1 + - + +
79A ALA 5.2 0.3 - - - +
80A VAL* 1.3 74.3 - - - +
82A LYS* 1.3 94.4 + - - +
115A GLN* 5.1 4.4 - - - +
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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