Contacts of the helix formed by residues 72 - 81 (chain F) in PDB entry 2GZJ
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 ASN 72 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E ILE 2.9 19.4 - - - +
54E TYR* 3.4 33.0 + - - +
56E PRO* 4.0 6.7 - - + +
62E ASP* 2.9 21.9 - - - +
71F LEU* 1.3 75.3 - - - +
73F PRO* 1.3 75.2 - - + +
74F SER* 3.3 5.9 + - - +
75F ASN* 3.1 26.7 - - - +
76F LYS* 2.9 21.9 + - - +
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Residues in contact with PRO 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E CYS 4.7 0.7 - - - -
62E ASP* 3.5 25.4 - - - +
72F ASN* 1.3 92.5 - - + +
74F SER* 1.3 57.2 + - - +
76F LYS* 3.3 14.2 + - + +
77F SER* 3.0 29.5 + - - -
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Residues in contact with SER 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ILE 5.0 1.4 - - - +
23E CYS* 3.6 42.9 - - - +
25E ALA* 5.1 0.9 - - - +
53E ILE* 3.4 25.4 + - - -
54E TYR* 3.5 27.0 + - - -
62E ASP 4.6 5.2 + - - -
72F ASN* 3.2 3.9 + - - +
73F PRO* 1.3 78.8 - - - +
75F ASN* 1.3 61.6 + - - +
77F SER* 3.4 4.7 + - - -
78F SER* 3.2 17.8 + - - -
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Residues in contact with ASN 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E TYR* 3.4 28.7 + - - +
55E TYR* 3.7 11.5 + - - -
71F LEU* 4.0 23.5 - - + +
72F ASN* 3.1 18.2 - - - +
74F SER* 1.3 73.0 - - - +
76F LYS* 1.3 65.2 + - - +
78F SER* 3.3 5.2 + - - -
79F VAL* 3.1 28.2 + - - +
85F PRO* 3.3 13.7 - - + +
86F PHE* 2.8 48.0 + - - -
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Residues in contact with LYS 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F SER* 4.5 1.2 + - - -
68F SER* 3.1 35.3 + - - +
69F LYS* 4.2 8.3 + - - +
71F LEU* 2.7 36.1 + - + +
72F ASN 2.9 15.0 + - - +
73F PRO* 3.3 15.4 + - + +
75F ASN* 1.3 75.8 - - - +
77F SER* 1.3 61.4 + - - +
79F VAL* 3.4 10.2 - - + +
80F SER* 3.0 24.8 + - - -
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Residues in contact with SER 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E CYS 2.9 28.7 + - - -
24E ASN* 3.7 22.8 + - - -
25E ALA* 3.6 3.3 - - - +
73F PRO 3.0 11.1 + - - -
74F SER 3.4 4.9 - - - -
75F ASN 3.3 0.2 - - - -
76F LYS* 1.3 74.1 - - - +
78F SER* 1.3 63.1 + - - +
80F SER* 2.6 25.7 + - - -
81F LYS* 3.4 11.8 - - - +
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Residues in contact with SER 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ALA* 3.7 13.4 - - - +
33E LEU* 4.2 11.6 - - - +
54E TYR* 5.4 0.7 - - - -
74F SER 3.2 10.2 + - - -
75F ASN* 3.3 19.0 + - - -
77F SER* 1.3 79.4 - - - +
79F VAL* 1.3 63.7 + - - +
81F LYS* 3.1 9.2 + - - +
83F TYR* 3.0 33.8 + - - +
84F SER 3.1 24.7 + - - -
85F PRO* 4.6 1.1 - - - -
86F PHE* 4.6 5.2 - - - -
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Residues in contact with VAL 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F TRP* 3.4 35.9 - - + +
59F GLU* 3.8 2.3 - - - -
61F VAL* 4.5 1.6 - - + -
62F SER* 3.6 24.0 - - - +
68F SER* 5.6 0.9 - - - -
71F LEU* 3.9 16.2 - - + -
75F ASN 3.1 11.4 + - - +
76F LYS* 3.4 19.7 - - + +
78F SER* 1.3 75.7 - - - +
80F SER* 1.3 58.2 + - - +
82F GLY* 2.9 16.8 + - - -
83F TYR 3.3 16.6 - - - +
85F PRO* 3.7 30.3 - - + -
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Residues in contact with SER 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F GLU* 4.6 7.4 - - - +
62F SER* 3.3 18.2 - - - -
76F LYS 3.0 15.2 + - - -
77F SER* 2.6 23.5 + - - -
79F VAL* 1.3 78.6 - - - +
81F LYS* 1.3 70.0 + - - +
82F GLY 3.3 1.0 + - - -
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Residues in contact with LYS 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E ASN 3.1 18.4 + - - -
25E ALA* 2.8 35.6 + - + +
26E ASP* 4.0 7.7 + - - +
27E THR 5.2 2.3 + - - +
55F LYS* 3.5 20.1 + - - -
59F GLU* 4.6 2.7 - - - -
77F SER* 3.4 11.0 - - - +
78F SER 3.1 7.6 + - - +
79F VAL 3.1 0.8 - - - -
80F SER* 1.3 89.1 - - - +
82F GLY* 1.3 59.8 + - - +
83F TYR* 3.6 32.1 + - + +
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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