Contacts of the strand formed by residues 49 - 57 (chain C) in PDB entry 6W4E
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 GLU 49 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C SER* 5.1 4.0 - - - -
2C THR* 2.9 24.8 + - - +
4C TYR* 2.8 23.9 + - - -
45C VAL* 4.1 3.6 - - - +
46C ILE 2.8 29.8 + - - +
47C ASP 3.6 0.6 - - - -
48C GLY* 1.3 80.7 - - - +
50C THR* 1.3 68.4 + - - +
51C CYS* 3.1 14.2 - - - -
164C ARG* 2.8 37.0 + - - +
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Residues in contact with THR 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C SER* 2.8 44.4 + - - +
2C THR 3.2 7.3 + - - -
43C GLN* 4.0 31.0 - - + +
44C VAL 3.6 8.1 - - - +
45C VAL* 4.2 18.3 - - + +
49C GLU* 1.3 74.0 - - - +
51C CYS* 1.3 61.4 + - - +
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Residues in contact with CYS 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C SER 4.9 0.9 - - - -
2C THR 3.2 3.8 - - - -
4C TYR* 3.5 27.8 - - + -
42C LYS 3.7 0.9 - - - +
43C GLN* 3.5 6.7 - - - +
44C VAL 2.9 31.5 + - - +
46C ILE* 3.4 30.3 - - + -
49C GLU* 3.1 44.2 - - - -
50C THR* 1.3 75.1 - - - +
52C LEU* 1.3 60.6 + - - +
53C LEU* 3.8 6.7 + - + +
160C VAL* 4.3 1.1 - - + -
164C ARG* 3.6 0.9 - - - -
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C SER 4.9 3.7 - - - +
2C THR 2.8 14.5 + - - +
3C GLU* 3.5 25.2 - - + +
4C TYR* 2.9 28.6 + - - -
41C ARG* 4.3 24.2 - - + -
42C LYS 3.6 19.3 - - - +
43C GLN* 4.2 18.2 - - + +
51C CYS* 1.3 70.7 - - - +
53C LEU* 1.3 63.6 + - - +
54C ASP* 3.6 1.4 + - + +
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C TYR* 3.7 5.6 - - + -
6C LEU* 4.0 11.2 - - + -
23C LEU* 4.4 15.0 - - + -
40C TYR 3.4 1.0 - - - +
41C ARG* 3.2 30.9 - - - +
42C LYS* 2.7 39.5 + - + +
44C VAL* 3.7 28.7 - - + -
46C ILE* 4.6 4.3 - - + -
51C CYS* 4.3 11.7 - - + +
52C LEU* 1.3 74.7 - - - +
54C ASP* 1.3 59.8 + - - +
55C ILE* 3.5 15.9 - - + -
156C PHE* 6.0 3.8 - - + -
160C VAL* 3.8 29.8 - - + -
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Residues in contact with ASP 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C GLU* 4.2 10.1 - - + +
4C TYR 2.9 17.0 + - - +
5C LYS* 2.7 46.4 + - + +
6C LEU 2.9 24.1 + - - +
41C ARG* 2.7 40.2 + - + +
52C LEU* 3.6 1.5 + - + -
53C LEU* 1.3 70.7 - - - +
55C ILE* 1.3 61.7 + - - +
56C LEU* 5.1 1.9 - - - +
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Residues in contact with ILE 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 3.3 18.2 - - + +
8C VAL* 3.7 27.1 - - + -
20C THR* 4.1 20.2 - - + +
23C LEU* 3.9 27.8 - - + -
24C ILE* 4.2 16.4 - - + -
39C SER* 3.2 7.4 - - - -
40C TYR* 2.7 45.4 + - + +
42C LYS* 4.9 0.4 - - + -
53C LEU* 4.0 23.8 - - + +
54C ASP* 1.3 77.4 - - - +
56C LEU* 1.3 65.8 + - - +
156C PHE* 6.2 4.0 - - + -
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Residues in contact with LEU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU 3.3 6.9 + - - +
7C VAL* 4.0 13.7 - - + +
8C VAL* 3.2 25.2 + - - +
37C GLU* 3.8 28.9 - - + +
38C ASP 3.3 24.2 - - - +
39C SER* 3.8 13.2 - - - +
54C ASP* 5.1 1.8 - - - +
55C ILE* 1.3 81.4 - - - +
57C ASP* 1.3 67.2 + - - +
58C THR* 3.8 0.6 + - + -
71C TYR* 3.8 40.2 - - + -
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Residues in contact with ASP 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 4.0 7.1 - - + +
16C LYS* 3.3 31.9 - - - +
17C SER* 2.6 8.2 + - - +
20C THR* 5.6 4.5 - - + +
35C THR* 2.7 16.6 + - + -
36C ILE 3.9 0.4 - - - +
37C GLU* 3.6 23.0 - - - +
38C ASP* 2.8 17.3 + - + +
40C TYR* 4.8 9.5 - - + -
55C ILE* 5.2 0.2 - - - +
56C LEU* 1.3 77.6 - - - +
58C THR* 1.3 71.1 + - - +
71C TYR* 5.9 0.3 - - - -
201C GSP 2.5 2.7 + - - -
202C MG 1.5 37.0 - - - -
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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