Contacts of the strand formed by residues 46 - 53 (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 SER 46 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1002A LEU* 3.8 6.3 - - - +
22F LEU* 4.2 5.9 - - - +
40F MET* 3.1 9.9 - - - +
41F ASP* 2.7 47.9 + - - +
44F HIS 3.6 0.4 - - - -
45F VAL* 1.3 83.0 - - - +
47F LEU* 1.3 59.3 + - - +
48F VAL* 5.3 0.2 - - - +
211F TYR* 4.4 2.2 - - - -
215F PHE* 3.8 28.5 - - - -
250F TYR 2.8 20.2 - - - -
251F LEU* 4.1 4.7 - - - -
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Residues in contact with LEU 47 (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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1002A LEU* 3.3 20.6 - - + +
38F GLN* 4.1 23.3 - - + +
39F SER* 3.4 25.1 - - - +
40F MET* 3.8 4.9 - - + +
46F SER* 1.3 73.4 - - - +
48F VAL* 1.3 64.2 + - - +
126F LEU* 4.0 34.1 - - + +
128F ILE* 3.4 33.0 - - + -
248F LYS 3.4 3.6 - - - +
249F TYR* 3.5 1.1 - - - -
250F TYR* 2.8 52.4 + - + -
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Residues in contact with VAL 48 (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 LEU* 3.3 28.3 - - + -
22F LEU* 3.6 31.4 - - + -
23F ILE* 3.7 26.7 - - + -
37F LEU* 3.5 3.2 - - + +
38F GLN* 3.0 8.5 - - - +
39F SER 2.8 31.2 + - - +
41F ASP 5.6 1.3 - - - +
46F SER* 5.3 0.4 - - - +
47F LEU* 1.3 76.9 - - - +
49F GLN* 1.3 63.5 + - - +
50F LEU 4.1 0.9 - - - +
247F LEU* 3.7 16.4 - - + -
248F LYS 3.2 3.6 - - - +
249F TYR* 3.7 13.9 - - + -
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Residues in contact with GLN 49 (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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36F ASN* 3.2 15.2 + - - +
37F LEU 3.3 2.7 - - - +
38F GLN* 3.4 31.1 - - + +
48F VAL* 1.3 74.9 - - - +
50F LEU* 1.3 74.8 + - - +
51F THR* 2.6 24.6 + - - -
128F ILE* 5.2 4.7 - - + -
246F HIS* 2.6 30.7 + - - +
247F LEU* 3.3 4.7 - - - -
248F LYS* 2.7 57.4 + - + +
250F TYR* 4.5 11.9 - - + -
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Residues in contact with LEU 50 (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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15F VAL* 3.6 28.5 - - + -
19F LEU* 4.3 9.2 - - + -
28F TRP* 4.5 14.4 - - + -
35F VAL* 5.5 2.2 - - + -
36F ASN* 3.3 5.9 - - - -
37F LEU* 2.7 53.3 + - + +
48F VAL 4.1 0.4 - - - -
49F GLN* 1.3 79.6 + - - +
51F THR* 1.3 64.2 + - - +
52F LEU* 4.1 25.8 - - + +
241F ILE* 3.8 18.4 - - + -
246F HIS 3.2 17.3 - - - +
247F LEU* 3.8 18.8 - - + -
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Residues in contact with THR 51 (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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35F VAL 3.9 3.1 - - - +
36F ASN* 3.4 9.5 + - - +
49F GLN* 2.6 30.8 + - - -
50F LEU* 1.3 70.9 + - - +
52F LEU* 1.3 65.7 + - - +
53F ARG* 4.0 31.6 - - + +
245F GLY* 2.9 9.4 + - - -
246F HIS* 2.9 53.6 + - + +
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Residues in contact with LEU 52 (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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6F LEU* 5.9 1.3 - - + -
11F ILE* 5.1 4.7 - - + -
12F LEU* 4.6 20.0 - - + -
15F VAL* 4.9 6.3 - - + -
28F TRP* 5.2 2.5 - - + -
34F GLY* 3.2 1.1 - - - -
35F VAL* 2.8 56.5 + - + +
50F LEU* 4.1 24.0 - - + -
51F THR* 1.3 78.2 - - - +
53F ARG* 1.3 64.2 + - - +
57F PHE* 3.8 21.4 - - + -
90F LEU* 6.4 1.3 - - + -
241F ILE* 4.0 24.7 - - + -
244F MET* 3.2 27.6 - - + -
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Residues in contact with ARG 53 (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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33F SER 3.6 8.1 - - - +
34F GLY* 4.3 0.2 - - - -
51F THR* 4.0 14.7 - - + +
52F LEU* 1.3 72.5 - - - +
54F SER* 1.3 66.4 + - - +
55F GLU* 4.0 18.2 - - + +
56F GLY* 3.0 16.3 + - - +
57F PHE* 3.4 10.6 - - - -
240F LYS* 4.7 10.5 - - - +
243F ASP* 5.0 8.0 - - - +
244F MET* 2.5 21.6 + - - +
245F GLY* 3.9 17.4 + - - +
246F HIS* 4.0 23.2 + - - -
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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