Contacts of the helix formed by residues 72 - 80 (chain F) in PDB entry 6S1M
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 LEU 72 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16F LEU* 4.1 8.4 - - + +
19F LEU* 4.1 21.8 - - + -
20F LYS* 4.2 11.8 - - - +
23F ILE* 3.3 54.7 - - + +
24F ASN 2.9 8.1 + - - +
26F ALA* 3.6 16.2 - - + -
28F TRP* 3.4 43.1 - - + +
37F LEU* 4.5 2.2 - - + -
70F VAL* 4.2 4.0 - - + +
71F ASN* 1.3 70.3 - - - +
73F THR* 1.3 57.6 + - - +
75F MET* 3.9 6.8 - - - +
76F SER* 2.9 28.2 + - - -
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Residues in contact with THR 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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20F LYS* 4.6 14.6 + - + +
24F ASN* 3.9 12.0 + - - +
71F ASN* 3.0 15.7 + - - +
72F LEU* 1.3 76.5 - - - +
74F SER* 1.3 62.0 + - - +
76F SER* 3.2 5.4 + - - -
77F LYS* 2.9 38.6 + - + +
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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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71F ASN* 3.0 30.1 + - - +
73F THR* 1.3 76.6 - - - +
75F MET* 1.3 61.0 + - - +
77F LYS* 3.3 2.0 + - - +
78F ILE* 2.9 35.3 + - - +
116F MET* 4.3 11.4 - - - -
175G LEU* 3.7 39.4 - - - +
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Residues in contact with MET 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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12F LEU* 4.5 13.2 - - + -
16F LEU* 3.1 22.7 - - + -
28F TRP* 3.2 49.1 - - + -
70F VAL* 3.8 13.5 - - + -
71F ASN 2.9 13.7 + - - +
72F LEU* 4.1 2.7 - - - +
74F SER* 1.3 77.9 - - - +
76F SER* 1.3 56.8 + - - +
78F ILE* 3.7 3.1 - - - +
79F LEU* 2.9 37.7 + - + +
90F LEU* 4.8 8.7 - - + -
99F LEU* 5.0 9.0 - - + -
101F LEU* 4.6 13.0 - - + -
116F MET* 3.5 29.3 - - + -
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Residues in contact with SER 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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16F LEU* 3.4 16.1 + - - +
17F GLU* 3.7 8.3 + - - -
20F LYS* 3.3 33.8 + - - +
72F LEU 2.9 21.7 + - - -
73F THR* 3.4 7.0 - - - -
74F SER 3.1 0.2 - - - -
75F MET* 1.3 75.1 - - - +
77F LYS* 1.3 67.3 + - - +
79F LEU* 3.0 13.0 + - - +
80F LYS* 3.1 23.4 + - - +
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Residues in contact with LYS 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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73F THR* 2.9 27.4 + - + +
74F SER* 3.7 5.8 - - - +
76F SER* 1.3 76.4 + - - +
78F ILE* 1.3 63.6 + - - +
80F LYS* 3.0 27.4 + - + +
81F CYS* 3.7 9.0 - - - -
152G SER 5.0 1.4 + - - -
153G HIS* 3.3 56.5 + - + +
175G LEU* 4.2 18.8 - - + +
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Residues in contact with ILE 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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74F SER 2.9 19.4 + - - +
75F MET* 3.7 4.5 - - - +
77F LYS* 1.3 77.1 - - - +
79F LEU* 1.3 57.6 + - - +
81F CYS* 3.0 33.4 + - - +
101F LEU* 4.0 21.1 - - + -
103F PHE* 3.9 6.2 - - + -
114F TYR* 3.8 31.6 - - + -
115F GLU 5.0 0.9 - - - +
116F MET* 3.4 42.6 - - + -
154G ILE* 4.1 10.3 - - + -
175G LEU* 3.9 28.5 - - + +
177G ASN 6.0 0.4 - - - +
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Residues in contact with LEU 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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12F LEU* 3.7 25.6 - - + +
13F LYS* 3.6 20.3 - - + +
16F LEU* 3.2 46.2 - - + -
75F MET* 2.9 19.1 + - + +
76F SER* 3.0 6.0 + - - +
78F ILE* 1.3 76.0 - - - +
80F LYS* 1.3 59.8 + - + +
81F CYS 3.1 2.3 + - - -
82F ALA* 3.3 18.2 + - - +
88F ILE* 4.1 17.5 - - + -
101F LEU* 3.7 24.5 - - + -
103F PHE* 4.0 15.9 - - + -
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Residues in contact with LYS 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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13F LYS* 4.6 9.8 + - - +
17F GLU* 3.6 30.9 + - + -
20F LYS* 3.2 23.0 - - - +
76F SER* 3.1 20.3 + - - +
77F LYS* 3.0 18.3 + - + +
79F LEU* 1.3 74.2 - - - +
81F CYS* 1.3 58.6 + - - +
82F ALA 3.1 6.8 - - - +
146G ARG* 2.8 21.1 + - - -
149G ARG* 4.9 5.1 + - - +
150G ASP* 3.9 2.1 - - - +
153G HIS* 4.6 18.2 - - + -
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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