Contacts of the strand formed by residues 73 - 79 (chain F) in PDB entry 3A13
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 73 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F TYR* 3.5 51.0 + - - +
12F TYR* 3.5 6.3 - - - +
14F ASP* 4.1 30.2 + - + +
17F TYR* 4.5 27.8 - - + -
68F ALA 5.3 3.0 + - - -
71F SER* 4.0 11.0 + - - +
72F ALA* 1.3 84.2 - - - +
74F ALA* 1.3 61.4 + - - +
75F TYR* 3.4 6.4 + - - -
89F ILE* 3.3 3.7 - - - -
90F ALA 2.8 37.9 + - - +
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Residues in contact with ALA 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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12F TYR 2.9 16.1 + - - +
13F VAL* 3.7 4.2 - - - -
14F ASP 2.9 28.3 + - - -
43F ALA* 4.1 16.6 - - + +
47F ALA* 4.4 1.7 - - + +
73F LYS* 1.3 69.2 - - - +
75F TYR* 1.3 58.8 + - - +
76F ASP 3.9 0.4 - - - -
77F PHE* 3.9 25.1 - - + -
87F VAL* 4.1 7.0 - - + -
88F ARG 3.4 6.7 - - - -
89F ILE* 4.0 19.5 - - + +
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Residues in contact with TYR 75 (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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14F ASP 3.2 18.8 - - - +
15F LYS* 3.5 24.4 - - - +
17F TYR* 3.5 33.4 - + + +
19F PRO* 3.6 31.7 - - + +
26F ILE* 3.5 21.9 - - + +
73F LYS 3.5 12.8 - - - +
74F ALA* 1.3 73.9 - - - +
76F ASP* 1.3 74.5 + - + +
77F PHE* 4.2 2.9 - - - -
88F ARG* 3.0 46.3 + - + -
89F ILE 4.0 1.3 - - - -
90F ALA* 3.9 22.9 - - + -
352F LEU* 5.2 0.7 - - - +
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Residues in contact with ASP 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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75F TYR* 1.3 101.8 - - + +
77F PHE* 1.3 75.3 + - - +
78F HIS* 4.3 6.9 + - - +
86F ILE* 3.3 2.9 - - - +
87F VAL* 3.2 6.2 - - - -
88F ARG* 2.8 64.1 + - - +
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Residues in contact with PHE 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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13F VAL* 4.0 19.3 - - + -
15F LYS* 3.9 34.1 - - + +
39F ILE* 3.9 25.1 - - + -
40F GLU* 4.2 12.3 - - + -
43F ALA* 3.5 32.8 - - + -
74F ALA* 3.9 24.2 - - + -
76F ASP* 1.3 90.1 + - - +
78F HIS* 1.3 61.1 + - - +
79F ASP 4.2 1.1 + - - -
85F TRP* 4.5 9.4 - - + +
86F ILE 3.5 3.6 - - - -
87F VAL* 3.9 14.6 - - + -
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Residues in contact with HIS 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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76F ASP* 4.2 8.0 - - - +
77F PHE* 1.3 71.7 - - - +
79F ASP* 1.3 79.0 + - - +
80F MET* 3.4 19.4 + - - -
85F TRP* 3.4 5.7 - - - -
86F ILE* 2.9 47.5 + - + +
88F ARG* 6.3 0.9 - - - +
349F VAL* 3.4 35.0 - - + +
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Residues in contact with ASP 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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77F PHE 4.2 1.0 + - - -
78F HIS* 1.3 90.0 + - - +
80F MET* 1.3 61.9 + - - +
81F GLY* 2.6 34.4 + - - -
82F ASP 4.4 0.7 + - - -
83F GLY 5.1 1.6 + - - -
84F SER 3.8 4.5 - - - +
85F TRP* 3.3 35.6 - - - +
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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