Contacts of the helix formed by residues 75 - 87 (chain F) in PDB entry 5B6N
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 SER 75 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74F ASP* 1.3 77.7 + - - +
76F VAL* 1.3 61.5 + - - +
77F GLU* 3.6 29.0 + - - +
78F ASP* 3.5 15.2 + - - +
79F HIS* 3.0 31.3 + - - -
106F ARG* 3.5 25.8 + - - +
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Residues in contact with VAL 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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17F ASN* 4.7 8.7 - - + +
18F THR 3.2 33.4 - - - +
19F THR* 4.0 10.1 - - + -
75F SER* 1.3 73.4 - - - +
77F GLU* 1.3 62.3 + - - +
79F HIS* 3.4 7.6 + - + +
80F LEU* 3.2 29.0 + - + +
104F ASP* 3.6 29.8 - - + +
106F ARG* 3.9 5.2 - - - +
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Residues in contact with GLU 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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75F SER* 3.6 17.7 + - - -
76F VAL* 1.3 82.2 - - - +
78F ASP* 1.3 69.1 + - - +
79F HIS 3.3 0.2 - - - -
80F LEU* 3.8 9.3 + - - +
81F ALA* 3.5 21.7 + - - +
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Residues in contact with ASP 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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42F ASP* 2.9 19.7 - - - +
43F PHE* 3.9 24.5 - - + -
74F ASP* 4.0 15.0 - - + +
75F SER* 3.2 27.2 + - - +
77F GLU* 1.3 89.4 - - - +
79F HIS* 1.3 57.8 + - - +
81F ALA* 4.0 3.8 - - - +
82F TRP* 3.2 22.7 + - - +
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Residues in contact with HIS 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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19F THR* 3.6 18.8 - - + -
42F ASP* 2.9 41.4 + - - -
72F SER* 3.9 14.3 - - - -
74F ASP* 3.4 20.2 + - + -
75F SER 3.0 21.6 + - - +
76F VAL* 3.7 7.9 - - - +
78F ASP* 1.3 78.8 - - - +
80F LEU* 1.3 55.2 + - - +
82F TRP* 4.0 2.2 - - - +
83F SER* 2.5 33.8 + - - -
102F ILE* 3.8 37.5 - - + +
103F ILE 3.2 28.2 + - - -
104F ASP 4.4 1.1 - - - -
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Residues in contact with LEU 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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19F THR* 3.8 39.9 - - + +
76F VAL* 3.2 18.8 + - + +
77F GLU* 4.1 7.6 - - - +
79F HIS* 1.3 77.7 - - - +
81F ALA* 1.3 62.0 + - - +
83F SER* 3.2 19.4 - - - +
84F LYS* 3.7 10.6 - - - +
95F THR 4.3 1.0 - - - +
96F GLU* 4.7 19.9 - - + +
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Residues in contact with ALA 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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213E SER* 5.3 3.1 - - - -
43F PHE* 4.6 12.6 - - + -
77F GLU 3.5 15.7 + - - +
78F ASP* 4.3 3.1 - - - +
79F HIS 3.3 0.2 - - - -
80F LEU* 1.3 76.6 - - - +
82F TRP* 1.3 66.1 + - - +
83F SER 3.1 0.2 - - - -
84F LYS* 3.2 32.6 + - + +
85F ASP* 3.5 8.7 + - - +
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Residues in contact with TRP 82 (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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217E TYR* 3.2 23.6 + - - -
39F HIS* 3.3 31.6 - + - -
42F ASP* 2.7 37.6 + - - +
43F PHE* 3.5 17.5 - + + +
44F THR 4.1 3.8 - - - -
47F CSD 3.2 22.2 - - + -
48F THR* 3.1 40.5 + - - -
51F LEU* 3.6 25.1 - - + -
78F ASP 3.2 19.3 + - - +
79F HIS 4.0 2.0 - - - +
81F ALA* 1.3 76.8 - - - +
83F SER* 1.3 57.8 + - - +
85F ASP* 2.7 24.0 + - + +
86F ILE* 2.8 31.3 + - + +
102F ILE* 4.8 9.2 - - + -
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Residues in contact with SER 83 (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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19F THR* 5.4 0.9 - - - +
79F HIS 2.5 23.2 + - - -
80F LEU* 3.2 14.9 + - - +
81F ALA 3.1 0.2 - - - -
82F TRP* 1.3 79.1 - - - +
84F LYS* 1.3 52.5 + - - +
86F ILE* 3.6 11.7 - - - +
87F ASN* 2.8 34.1 + - - +
95F THR 3.0 16.7 - - - +
96F GLU* 3.8 13.9 + - - -
98F LEU* 3.3 24.9 - - - +
102F ILE* 4.3 0.5 - - - +
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Residues in contact with LYS 84 (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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212E PRO* 3.7 17.3 - - + +
80F LEU 3.7 9.4 - - - +
81F ALA* 3.3 25.6 - - + +
83F SER* 1.3 75.8 - - - +
85F ASP* 1.3 66.7 + - - +
88F ALA* 3.2 23.9 + - - +
94F PRO* 3.9 33.6 + - + +
95F THR* 3.0 16.9 + - - +
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Residues in contact with ASP 85 (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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211E LEU* 3.2 34.5 - - + +
212E PRO* 3.7 6.5 - - - +
213E SER* 2.2 52.1 + - - -
217E TYR* 2.9 33.0 + - - +
43F PHE* 4.3 1.9 - - - -
48F THR* 4.3 3.3 - - - +
81F ALA 3.6 9.3 - - - +
82F TRP* 2.7 22.2 + - + +
84F LYS* 1.3 73.3 - - - +
86F ILE* 1.3 56.0 + - - -
88F ALA* 3.9 1.1 - - - -
89F TYR* 3.5 10.4 + - - +
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Residues in contact with ILE 86 (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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48F THR* 3.6 19.1 - - + +
51F LEU* 3.7 36.8 - - + +
52F GLY* 4.5 4.0 - - - -
82F TRP* 2.8 48.0 + - + +
83F SER* 3.6 9.2 - - - +
85F ASP* 1.3 78.8 - - - +
87F ASN* 1.3 61.1 + - - +
88F ALA 3.0 5.2 - - - -
89F TYR* 3.2 16.2 + - - +
90F ASN* 2.9 20.3 + - - +
98F LEU* 3.7 35.0 - - + -
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Residues in contact with ASN 87 (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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55F ALA* 5.4 4.6 - - - +
83F SER 2.8 14.5 + - - +
84F LYS 4.0 1.6 - - - +
86F ILE* 1.3 77.5 + - - +
88F ALA* 1.3 52.0 + - - +
89F TYR 3.4 0.2 - - - -
90F ASN* 3.7 7.3 + - - +
92F GLU* 2.6 64.5 + - + +
93F GLU 3.4 17.5 - - - +
94F PRO* 4.8 0.4 - - - -
95F THR 3.1 15.1 + - - +
96F GLU 3.8 0.7 - - - -
97F LYS* 3.1 46.6 + - - +
98F LEU* 3.8 10.9 - - - +
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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