Contacts of the helix formed by residues 71 - 77 (chain A) in PDB entry 1XYY
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 PHE 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A VAL* 4.4 6.3 - - + -
9A GLY* 4.1 7.4 - - - -
38A ALA* 4.1 9.6 - - + -
55A LEU* 3.9 34.5 - - + -
56A GLY 3.4 26.2 - - - -
57A CYS* 3.5 26.2 - - + -
67A LEU* 4.3 3.1 - - + -
68A GLN* 2.8 18.7 + - - +
70A ASP* 1.3 80.2 - - - +
72A ILE* 1.3 65.2 + - - +
74A LEU* 3.1 24.9 + - + +
75A PHE* 3.0 38.5 + - + -
78A LEU* 5.3 1.3 - - + -
108A ILE* 3.9 20.9 - - + -
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Residues in contact with ILE 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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66A GLU* 4.5 13.7 - - + +
67A LEU* 3.4 27.4 - - + +
68A GLN 3.2 11.0 + - - +
69A ASP* 3.4 28.9 + - - +
71A PHE* 1.3 74.6 - - - +
73A PRO* 1.3 66.6 - - + +
75A PHE* 3.2 8.6 + - + +
76A ASP* 2.8 49.1 + - - +
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Residues in contact with PRO 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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41A VAL 6.1 0.4 - - - +
43A ALA* 4.9 0.6 - - - +
69A ASP 3.3 13.5 - - - +
70A ASP* 4.0 8.1 - - - +
71A PHE 3.7 2.0 - - - -
72A ILE* 1.3 97.0 - - + +
74A LEU* 1.3 63.7 + - - +
76A ASP* 3.3 9.0 + - + +
77A SER* 3.2 25.6 + - - -
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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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7A VAL* 3.6 32.8 - - + -
38A ALA* 4.8 1.3 - - + -
41A VAL* 4.1 11.2 - - + -
43A ALA* 3.5 15.3 - - + +
46A LEU* 3.4 30.5 - - + -
47A PHE* 5.0 0.9 - - + -
55A LEU* 4.8 5.2 - - + -
70A ASP 4.8 2.4 + - - +
71A PHE* 3.1 30.2 + - + +
73A PRO* 1.3 75.9 - - - +
75A PHE* 1.4 61.5 + - - +
77A SER 3.2 3.1 + - - -
78A LEU* 3.0 34.5 + - + +
81A THR* 3.5 22.0 - - + -
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Residues in contact with PHE 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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67A LEU* 3.5 31.4 - - + -
71A PHE* 3.0 19.9 + + + +
72A ILE* 3.5 7.9 - - + +
74A LEU* 1.4 77.6 - - - +
76A ASP* 1.3 71.7 + - - +
77A SER 3.2 0.9 + - - -
78A LEU* 3.3 13.4 + - + +
107A ALA* 3.4 41.5 - - + -
108A ILE* 3.8 19.3 - - + -
111A LYS* 2.9 58.8 + - + +
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Residues in contact with ASP 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 ILE* 2.8 40.6 + - - +
73A PRO* 3.3 7.9 + - + +
75A PHE* 1.3 84.2 - - - +
77A SER* 1.3 62.4 + - - +
78A LEU 3.6 0.2 - - - -
79A GLU* 3.3 12.6 - - - +
111A LYS* 4.1 9.8 + - - +
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Residues in contact with SER 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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43A ALA* 3.6 24.4 - - - +
73A PRO 3.2 12.6 + - - -
74A LEU 3.4 3.1 - - - -
75A PHE 3.1 0.8 - - - -
76A ASP* 1.3 84.5 + - - +
78A LEU* 1.3 57.2 + - - +
79A GLU* 3.0 10.0 + - - -
80A GLU* 2.7 44.1 + - - +
81A THR 3.8 0.3 + - - -
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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