Contacts of the helix formed by residues 72 - 81 (chain B) in PDB entry 2XSX
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 THR 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASN* 3.1 14.2 + - - -
70B ASN 3.7 0.6 - - - -
71B SER* 1.3 85.2 + - - +
73B LEU* 1.3 68.7 + - - +
74B GLY 3.4 1.6 - - - -
75B PRO* 3.6 3.3 - - - +
76B ALA* 3.1 26.9 + - + +
97B LEU* 5.2 4.0 - - + -
105B LYS* 6.1 1.1 - - - -
106B PHE* 3.9 27.8 - - + -
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Residues in contact with LEU 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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68B ASN 2.8 19.4 + - - +
69B ILE* 4.2 7.0 - - + -
72B THR* 1.3 76.1 - - - +
74B GLY* 1.3 56.2 + - - +
76B ALA* 3.4 3.4 + - - +
77B LEU* 3.0 29.1 + - + +
93B PHE* 4.9 2.5 - - + -
94B MET* 3.8 33.7 - - + -
97B LEU* 4.2 18.4 - - + -
106B PHE* 4.2 20.9 - - + -
110B ALA* 4.2 12.6 - - + +
111B ILE* 4.1 23.8 - - + -
114B VAL* 4.1 24.5 - - + -
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Residues in contact with GLY 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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6B ILE* 4.1 27.8 - - - +
69B ILE* 2.9 21.6 + - - +
73B LEU* 1.3 74.5 - - - +
75B PRO* 1.3 66.8 - - - +
77B LEU* 3.3 4.0 + - - +
78B LEU* 3.0 31.8 + - - +
114B VAL* 5.8 1.1 - - - -
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Residues in contact with PRO 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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6B ILE 6.0 1.1 - - - +
69B ILE 3.4 11.0 - - - +
70B ASN 3.5 19.5 - - - +
71B SER 3.6 12.8 - - - +
72B THR 3.6 10.5 - - - +
74B GLY* 1.3 88.5 - - - +
76B ALA* 1.3 61.7 + - - +
78B LEU* 3.4 9.8 + - + +
79B GLN* 3.1 27.8 + - - +
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Residues in contact with ALA 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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72B THR* 3.1 20.9 + - + +
73B LEU 3.7 0.7 - - - +
74B GLY 3.3 0.2 - - - -
75B PRO* 1.3 76.7 - - - +
77B LEU* 1.3 63.0 + - - +
79B GLN* 3.5 11.8 + - - +
80B LYS* 3.3 16.3 + - - +
93B PHE* 3.7 14.3 - - + -
97B LEU* 3.7 29.8 - - + -
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Residues in contact with LEU 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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3B MET* 4.0 22.1 - - + +
6B ILE* 3.9 14.6 - - + -
73B LEU* 3.0 19.4 + - + +
74B GLY* 3.3 4.5 + - - +
76B ALA* 1.3 74.6 - - - +
78B LEU* 1.3 66.5 + - - +
80B LYS* 3.0 17.2 + - - +
81B LYS 3.6 4.0 + - - -
82B LEU* 3.9 21.6 + - + -
90B VAL* 3.9 24.5 - - + -
93B PHE* 3.8 28.6 - - + -
94B MET* 4.4 4.9 - - + -
114B VAL* 3.7 29.4 - - + -
118B VAL* 4.4 2.5 - - + -
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Residues in contact with LEU 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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3B MET* 3.4 48.1 - - + +
4B GLN 4.2 5.8 - - - +
5B LYS* 4.2 9.6 - - - +
6B ILE* 3.8 39.7 - - + +
74B GLY 3.0 22.5 + - - +
75B PRO* 3.9 8.3 - - + +
77B LEU* 1.3 75.9 - - - +
79B GLN* 1.3 61.1 + - - +
81B LYS* 3.4 20.1 + - - +
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Residues in contact with GLN 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 PRO 3.1 18.1 + - - +
76B ALA* 3.6 11.0 - - - +
77B LEU 3.2 0.2 - - - -
78B LEU* 1.3 78.3 - - - +
80B LYS* 1.3 58.7 + - - +
81B LYS* 3.3 12.7 + - - +
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Residues in contact with LYS 80 (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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76B ALA 3.3 10.2 + - - +
77B LEU 3.0 12.1 + - - +
79B GLN* 1.3 75.6 - - - +
81B LYS* 1.3 73.3 + - - +
82B LEU* 3.4 33.9 + - + +
93B PHE* 3.8 30.3 - - + -
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Residues in contact with LYS 81 (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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0B SER 3.0 40.9 + - - +
1B MET* 3.9 32.7 - - + -
77B LEU 3.6 2.2 + - - -
78B LEU 3.4 18.7 + - - +
79B GLN* 3.3 10.1 - - - +
80B LYS* 1.3 80.6 - - - +
82B LEU* 1.3 59.2 + - - +
83B SER 4.1 0.2 + - - -
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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