Contacts of the strand formed by residues 67 - 76 (chain F) in PDB entry 4N3E
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 TYR 67 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56F LYS* 4.4 20.2 - - + +
57F ILE 3.1 16.8 - - - +
58F THR* 4.2 7.2 - - - +
59F PHE* 3.2 15.1 - - - -
66F THR* 1.3 90.4 - - + +
68F MET* 1.3 81.3 + - - +
69F LEU* 3.9 18.6 - - + -
88F GLU* 2.7 37.1 + - - +
89F GLY* 3.9 17.8 + - - -
90F ASP* 2.6 41.4 + - - +
91F VAL 4.0 5.0 + - - -
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Residues in contact with MET 68 (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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31F LEU* 4.6 8.3 - - + -
39F PHE* 4.3 17.5 - - + -
56F LYS* 4.0 0.3 - - - -
57F ILE* 2.9 61.8 + - + +
59F PHE* 4.3 5.4 - - + -
67F TYR* 1.3 83.2 - - - +
69F LEU* 1.3 56.6 + - - +
70F HIS* 3.9 24.2 + - + -
86F LEU* 3.6 10.3 - - + -
88F GLU 3.4 9.0 - - - -
89F GLY* 4.0 1.6 - - - -
91F VAL* 3.6 39.9 - - + -
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Residues in contact with LEU 69 (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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45F ILE* 3.5 26.2 - - + -
54F VAL* 4.3 0.4 - - + -
55F THR 3.3 21.1 - - - +
56F LYS* 3.8 23.8 - - + -
67F TYR* 3.9 13.0 - - + -
68F MET* 1.3 71.0 - - - +
70F HIS* 1.3 61.5 + - - +
86F LEU* 3.3 6.2 - - - +
87F PHE* 3.1 58.5 + - + -
88F GLU* 2.8 37.0 + - - +
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Residues in contact with HIS 70 (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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27F ARG* 6.1 2.2 + - - -
53F THR 3.8 0.2 - - - +
54F VAL* 3.0 6.9 - - - +
55F THR* 2.8 48.6 + - - +
57F ILE* 5.0 6.7 + - + +
68F MET* 3.9 40.1 + - + -
69F LEU* 1.3 74.6 - - - +
71F LYS* 1.3 58.4 + - - +
72F PHE* 4.1 13.5 - + + -
84F TYR* 3.7 32.5 - + + -
85F THR 3.2 3.8 - - - +
86F LEU* 3.9 34.2 - - + +
87F PHE* 3.7 4.3 - - - -
101F TYR* 4.5 6.2 + + - -
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Residues in contact with LYS 71 (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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46F GLU* 4.9 5.2 - - - -
52F GLY* 5.4 6.7 - - - +
53F THR 3.4 7.6 - - - +
54F VAL* 3.0 25.8 - - + -
70F HIS* 1.3 72.1 - - - +
72F PHE* 1.3 55.7 + - - +
73F ASP* 4.1 15.9 - - - +
84F TYR* 2.7 31.4 - - - +
85F THR* 2.7 24.3 + - - +
87F PHE* 3.2 31.5 - - + -
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Residues in contact with PHE 72 (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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24F VAL* 4.5 20.0 - - + -
25F LEU* 6.3 0.2 - - - -
27F ARG* 6.2 3.1 - - + -
49F GLY 5.2 2.5 - - - +
50F GLY 4.9 0.2 - - - +
51F VAL* 3.1 10.4 - - - +
52F GLY* 2.9 29.1 + - - -
53F THR* 2.9 33.5 + - - +
55F THR* 3.7 36.6 - - + -
70F HIS* 4.1 19.5 - + + -
71F LYS* 1.3 71.0 - - - +
73F ASP* 1.3 61.6 + - - +
74F GLU 3.6 1.3 - - - -
75F ILE* 3.9 23.6 - - + -
82F CYS* 4.0 12.8 - - - -
83F LYS 3.9 2.5 - - - +
84F TYR* 3.5 34.5 - + + -
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Residues in contact with ASP 73 (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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51F VAL* 3.3 16.5 - - - +
71F LYS* 4.1 15.6 - - - +
72F PHE* 1.3 76.4 - - - +
74F GLU* 1.3 67.6 + - + +
83F LYS* 2.7 34.0 + - + +
84F TYR* 3.6 6.9 - - - -
85F THR* 2.9 25.5 + - - -
100F VAL* 5.1 1.0 - - - +
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Residues in contact with GLU 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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51F VAL* 2.9 7.0 - - - -
73F ASP* 1.3 85.8 - - - +
75F ILE* 1.3 58.7 + - - +
76F ASP 4.2 0.4 - - - -
81F TYR* 2.4 45.4 + - + -
82F CYS* 2.9 27.8 - - - -
83F LYS* 3.1 37.2 + - + +
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Residues in contact with ILE 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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20F PHE* 4.1 10.8 - - + -
24F VAL* 5.2 0.2 - - + -
25F LEU* 3.9 32.5 - - + -
49F GLY 4.3 11.7 - - - +
50F GLY* 4.5 3.8 - - - -
51F VAL* 2.8 32.0 - - + +
72F PHE* 3.9 21.3 - - + -
74F GLU* 1.3 77.8 - - - +
76F ASP* 1.3 58.6 + - - +
77F ALA* 3.5 19.3 + - + +
81F TYR 3.6 3.4 - - - -
82F CYS* 3.5 17.9 - - - -
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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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74F GLU* 4.2 1.0 - - - +
75F ILE* 1.3 72.2 - - - +
77F ALA* 1.3 64.3 + - - +
78F ALA* 3.2 13.2 + - - +
79F ASN* 3.2 39.4 + - - +
81F TYR* 3.0 46.8 + - + +
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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