Contacts of the strand formed by residues 34 - 40 (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 GLY 34 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29F ASP 3.5 10.9 - - - +
31F SER* 3.1 16.6 + - - -
32F SER 3.4 0.2 - - - -
33F SER* 1.3 83.3 + - - +
35F VAL* 1.3 64.5 + - - -
36F ASN* 4.7 2.1 - - - +
52F LEU 3.2 11.4 - - - -
53F ARG* 4.3 0.2 - - - -
54F SER 3.6 4.3 - - - -
60F TYR* 3.2 22.0 - - - -
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Residues in contact with VAL 35 (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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2F PHE* 4.3 12.1 - - + -
28F TRP* 3.7 28.3 - - + -
29F ASP 3.9 3.6 - - - -
30F ILE* 3.3 33.4 - - + -
34F GLY* 1.3 75.3 - - - -
36F ASN* 1.3 70.9 + - - +
50F LEU* 5.5 2.2 - - + -
51F THR* 3.8 1.4 - - - +
52F LEU* 2.8 49.8 + - + +
57F PHE* 4.7 10.8 - - + -
60F TYR* 4.0 12.7 - - + +
90F LEU* 4.9 7.0 - - + -
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Residues in contact with ASN 36 (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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28F TRP* 3.4 3.6 - - - +
29F ASP* 2.8 47.5 + - + +
34F GLY 4.7 1.6 - - - +
35F VAL* 1.3 79.1 - - - +
37F LEU* 1.3 84.2 + - - +
38F GLN* 4.2 7.4 + - - +
49F GLN* 3.2 23.4 + - - +
50F LEU* 3.3 10.9 + - - +
51F THR* 3.4 10.9 + - - +
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Residues in contact with LEU 37 (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* 4.6 16.6 - - + -
23F ILE* 4.5 10.3 - - + -
26F ALA* 3.8 22.4 - - + -
27F CYS 3.6 13.5 - - - +
28F TRP* 3.5 47.8 - - + +
29F ASP* 4.8 1.3 - - - -
36F ASN* 1.3 83.4 + - - +
38F GLN* 1.3 73.1 + - - +
39F SER* 4.4 5.6 - - - +
48F VAL* 3.5 4.6 - - + +
49F GLN* 3.3 3.3 - - - -
50F LEU* 2.7 52.2 + - + +
72F LEU* 4.5 3.4 - - + -
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Residues in contact with GLN 38 (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 CYS* 4.4 11.3 + - - +
29F ASP* 5.0 4.3 + - - +
36F ASN* 4.2 6.7 + - - +
37F LEU* 1.3 77.2 - - - +
39F SER* 1.3 64.8 + - - +
47F LEU* 4.1 23.2 - - + +
48F VAL 3.0 11.2 - - - +
49F GLN* 3.4 25.8 - - + +
123F VAL* 5.2 4.3 - - - +
125F GLN* 3.9 25.5 + - - +
126F LEU 3.2 24.9 - - - +
127F GLY* 4.9 1.7 - - - -
128F ILE* 4.2 19.5 + - - +
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Residues in contact with SER 39 (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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23F ILE* 3.9 25.8 - - - +
25F GLU 4.4 5.4 + - - -
26F ALA* 4.5 10.8 - - - -
27F CYS 5.5 0.9 - - - -
37F LEU* 4.4 6.7 - - - +
38F GLN* 1.3 79.0 - - - +
40F MET* 1.3 76.8 + - - +
47F LEU* 3.8 6.3 - - - +
48F VAL* 2.8 38.4 + - - +
123F VAL* 4.8 13.5 - - - +
124F GLU 6.0 0.4 - - - -
125F GLN* 5.7 0.2 - - - -
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Residues in contact with MET 40 (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* 5.7 0.9 - - + -
1003A LEU* 2.9 35.0 - - + -
23F ILE* 4.1 5.7 - - - +
39F SER* 1.3 90.4 + - - +
41F ASP* 1.3 69.7 + - - +
44F HIS* 2.9 54.7 - - + +
46F SER 3.1 11.9 - - - +
47F LEU* 3.8 6.8 - - + +
123F VAL* 5.9 1.4 - - - +
124F GLU* 4.3 21.7 + - - +
126F LEU* 3.3 33.2 - - + -
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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