Contacts of the helix formed by residues 71 - 79 (chain B) in PDB entry 2XGZ
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 VAL 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LYS* 6.2 0.2 - - + -
67B ASN* 3.1 28.2 + - - +
70B ASP* 1.3 86.2 - - + +
72B ILE* 1.3 70.3 + - - +
73B ALA 3.4 1.1 - - - -
74B PRO* 3.6 8.3 - - - +
75B ALA* 3.7 15.9 + - - +
96B LEU* 4.1 16.9 - - + +
104B LYS* 6.1 2.2 - - - +
105B LEU* 3.9 23.8 - - + -
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL* 5.1 1.3 - - + -
67B ASN 2.9 16.3 + - - +
68B VAL* 3.9 15.9 - - + +
71B VAL* 1.3 74.9 - - - +
73B ALA* 1.3 56.0 + - - +
75B ALA* 3.7 0.9 - - - +
76B PHE* 2.7 46.0 + - + +
92B PHE* 4.6 0.9 - - + -
93B LEU* 3.5 27.4 - - + -
96B LEU* 3.6 11.7 - - + -
105B LEU* 3.9 29.4 - - + -
109B ALA* 4.0 39.5 - - + +
110B ILE* 4.4 6.3 - - + +
113B VAL* 4.0 14.1 - - + -
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL* 3.4 43.5 - - + +
68B VAL 2.8 23.5 + - - +
69B ASN 3.7 7.6 - - - +
72B ILE* 1.3 74.2 - - - +
74B PRO* 1.4 71.0 - - + +
76B PHE* 4.4 0.4 - - - -
77B VAL* 3.0 30.1 + - + +
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Residues in contact with PRO 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ASN 3.6 13.7 - - - +
70B ASP 3.4 21.5 - - - +
71B VAL 3.6 7.9 - - - +
73B ALA* 1.4 93.4 - - + +
75B ALA* 1.3 57.5 + - - +
77B VAL* 4.2 3.1 - - + +
78B LYS* 3.0 31.9 + - - +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B VAL 3.7 13.9 - - - +
72B ILE 3.4 1.7 + - - +
73B ALA 3.3 0.2 - - - -
74B PRO* 1.3 78.2 - - - +
76B PHE* 1.3 61.8 + - - +
78B LYS* 3.4 6.1 + - - +
79B ALA* 2.9 30.8 + - - +
92B PHE* 3.4 18.2 - - + -
96B LEU* 4.4 15.3 - - + -
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B VAL* 3.9 31.9 - - + +
5B VAL* 3.9 18.8 - - + -
23B LEU* 4.1 11.2 - - + -
72B ILE* 2.7 26.6 + - + +
73B ALA 3.7 2.7 - - - +
75B ALA* 1.3 69.7 - - - +
77B VAL* 1.3 67.1 + - - +
79B ALA* 3.2 12.4 + - - +
80B ASN* 3.5 7.1 + - - -
81B ILE* 3.8 27.0 + - + +
83B VAL* 5.0 1.3 - - + -
89B VAL* 4.0 31.2 - - + -
92B PHE* 3.6 27.9 - + + -
93B LEU* 4.2 6.3 - - + -
113B VAL* 3.8 26.5 - - + -
117B ALA* 4.8 1.3 - - + -
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B VAL* 3.7 24.8 - - + +
3B SER* 3.8 24.0 - - - +
4B LYS* 4.1 2.9 - - - +
5B VAL* 4.0 27.8 - - + +
73B ALA* 3.0 20.9 + - + +
74B PRO* 4.2 3.8 - - + +
76B PHE* 1.3 75.1 - - - +
78B LYS* 1.3 63.9 + - - +
80B ASN* 3.2 15.1 + - - +
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Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B PRO 3.0 20.6 + - - +
75B ALA* 3.6 7.2 - - - +
76B PHE 3.2 0.2 - - - -
77B VAL* 1.3 79.1 - - - +
79B ALA* 1.3 59.5 + - - +
80B ASN* 3.3 5.2 + - - +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ALA 2.9 18.0 + - - +
76B PHE 3.7 5.2 - - - +
77B VAL 3.2 0.8 - - - -
78B LYS* 1.3 74.4 - - - +
80B ASN* 1.3 69.5 + - - +
81B ILE* 3.3 14.5 + - + +
92B PHE* 3.7 23.1 - - + -
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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