Contacts of the helix formed by residues 72 - 82 (chain B) in PDB entry 2F5Y
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 LYS 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ASP* 3.3 36.2 + - + +
36B SER* 4.8 5.6 - - - +
38B VAL* 3.7 4.2 - - - +
70B HIS 5.2 1.3 - - - +
71B TRP* 1.3 76.3 - - - +
73B CYS* 1.3 66.6 + - - +
74B VAL* 4.2 7.9 - - + +
75B GLU* 3.1 33.4 + - + +
76B LEU* 3.1 18.2 + - - +
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Residues in contact with CYS 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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32B ILE* 3.6 45.6 - - - +
33B CYS* 3.9 8.3 - - - -
34B CYS 3.3 17.8 + - - +
35B ASP* 2.7 14.3 + - - +
38B VAL* 3.5 11.0 - - - +
72B LYS* 1.3 71.1 - - - +
74B VAL* 1.3 61.7 + - + +
76B LEU* 3.2 5.4 + - - +
77B ALA* 2.9 29.4 + - - +
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Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LYS* 3.2 5.9 - - + +
73B CYS* 1.3 83.6 - - + +
75B GLU* 1.3 62.7 + - + +
77B ALA* 3.8 8.6 - - + +
78B HIS* 3.2 25.6 + - - +
81B ARG* 5.2 1.0 + - - -
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B HIS 4.8 0.9 - - - +
71B TRP* 3.7 30.6 - - + +
72B LYS* 3.1 43.2 + - + +
74B VAL* 1.3 80.5 - - + +
76B LEU* 1.3 64.0 + - - +
78B HIS* 3.4 6.9 + - - +
79B GLU* 3.2 17.5 + - - +
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Residues in contact with LEU 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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30B PHE* 6.2 0.2 - - + -
32B ILE* 4.3 6.3 - - + -
38B VAL* 3.7 34.8 - - + -
60B VAL* 4.1 22.0 - - + -
63B LEU* 4.1 17.5 - - + -
68B VAL* 3.9 37.5 - - + -
71B TRP* 3.8 9.9 - - + -
72B LYS 3.1 11.4 + - - +
73B CYS 3.5 7.6 - - - +
75B GLU* 1.3 76.1 - - - +
77B ALA* 1.3 58.4 + - - +
79B GLU* 3.3 2.8 + - - +
80B ILE* 2.9 50.6 + - + +
89B LEU* 5.9 0.2 - - + -
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Residues in contact with ALA 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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32B ILE* 4.0 16.5 - - + +
73B CYS* 2.9 16.5 + - - +
74B VAL* 3.8 10.8 - - + +
76B LEU* 1.3 77.3 - - - +
78B HIS* 1.3 61.0 + - - +
80B ILE* 3.9 6.4 - - - +
81B ARG* 3.1 52.0 + - - +
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Residues in contact with HIS 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 VAL 3.2 15.3 + - - +
75B GLU* 3.7 7.6 - - - +
76B LEU 3.3 0.4 - - - -
77B ALA* 1.3 78.4 - - - +
79B GLU* 1.3 67.1 + - - +
81B ARG* 3.4 24.9 + - - +
82B SER* 3.5 14.2 + - - -
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Residues in contact with GLU 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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63B LEU* 3.6 22.2 - - + -
64B ASN* 5.6 1.4 + - - +
66B ARG* 5.5 8.7 + - - -
71B TRP* 3.8 24.8 - - + -
75B GLU 3.2 10.6 + - - +
76B LEU 3.6 7.2 - - - +
78B HIS* 1.3 81.4 - - - +
80B ILE* 1.3 65.5 + - - +
82B SER* 2.7 28.5 + - - -
83B CYS* 3.5 16.2 - - - -
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Residues in contact with ILE 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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23B ARG* 3.6 7.7 + - - +
28B PHE* 3.6 33.1 - - + -
30B PHE* 4.1 26.5 - - + -
32B ILE* 4.9 4.3 - - + -
63B LEU* 4.0 24.7 - - + -
76B LEU* 2.9 44.8 + - + +
77B ALA* 3.9 8.1 - - - +
78B HIS 3.4 0.2 - - - -
79B GLU* 1.3 77.4 - - - +
81B ARG* 1.3 64.4 + - + +
83B CYS* 3.2 18.2 + - - +
87B ILE* 4.3 9.4 - - + -
89B LEU* 5.0 2.7 - - + -
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Residues in contact with ARG 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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23B ARG* 3.2 25.9 + - - +
74B VAL 5.2 1.0 + - - -
77B ALA* 3.1 49.3 + - - +
78B HIS* 3.7 19.0 + - - +
79B GLU 3.2 0.4 - - - -
80B ILE* 1.3 79.6 - - + +
82B SER* 1.3 58.3 + - - +
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Residues in contact with SER 82 (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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23B ARG* 4.9 0.4 - - - -
78B HIS* 3.5 9.5 + - - -
79B GLU* 2.7 33.8 + - - -
81B ARG* 1.3 79.0 - - - +
83B CYS* 1.3 61.7 + - - +
84B PRO* 3.3 10.4 - - - +
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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