Contacts of the strand formed by residues 38 - 46 (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 ASP 38 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C THR* 3.6 26.4 - - + +
36C ILE 5.7 0.2 + - - -
37C GLU* 1.3 78.3 + - - +
39C SER* 1.3 65.2 + - - +
40C TYR* 3.8 30.0 + - + +
56C LEU* 3.3 4.4 - - - -
57C ASP 2.8 34.7 + - - -
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Residues in contact with SER 39 (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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37C GLU* 4.4 4.3 + - - -
38C ASP* 1.3 78.8 + - - +
40C TYR* 1.3 71.2 + - - +
41C ARG* 3.5 35.1 + - - -
55C ILE 3.2 9.2 - - - -
56C LEU* 3.8 13.5 - - - +
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Residues in contact with TYR 40 (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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17C SER* 5.5 4.5 + - - -
20C THR* 3.6 28.0 - - + -
21C ILE* 4.5 22.8 - - + +
24C ILE* 3.8 39.3 - - + -
25C GLN* 5.8 7.0 - - + -
33C ASP* 5.6 1.6 + - - -
35C THR* 5.0 3.9 - - + +
38C ASP* 3.8 42.7 - - + +
39C SER* 1.3 78.5 - - - +
41C ARG* 1.3 64.2 + - - +
53C LEU 3.4 1.0 - - - +
55C ILE* 2.7 44.5 + - + +
57C ASP* 4.8 10.1 - - + -
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Residues in contact with ARG 41 (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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24C ILE* 4.2 9.4 - - - +
39C SER* 3.5 37.3 + - - -
40C TYR* 1.3 77.4 - - - +
42C LYS* 1.3 63.2 + - - +
52C LEU* 4.3 24.5 - - + -
53C LEU 3.2 11.2 - - - +
54C ASP* 2.7 40.3 + - - +
55C ILE 4.7 0.2 + - - -
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Residues in contact with LYS 42 (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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23C LEU* 2.8 58.4 + - + +
24C ILE* 3.7 20.9 + - + -
26C ASN* 5.2 6.9 - - - +
40C TYR 4.3 0.2 + - - -
41C ARG* 1.3 76.0 - - - +
43C GLN* 1.3 62.5 + - - +
44C VAL* 3.6 26.7 - - + -
52C LEU* 3.6 4.8 - - - +
53C LEU* 2.7 57.0 + - + +
55C ILE* 4.9 0.9 - - + -
149C ARG* 5.7 1.7 - - - +
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Residues in contact with GLN 43 (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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1C SER 5.6 4.4 - - - +
42C LYS* 1.3 76.1 - - - +
44C VAL* 1.3 68.4 + - - +
50C THR* 4.0 26.0 - - + +
51C CYS 3.5 10.1 - - - +
52C LEU* 4.2 15.7 - - + +
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Residues in contact with VAL 44 (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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23C LEU* 6.0 1.1 - - + -
42C LYS* 3.6 28.9 - - - -
43C GLN* 1.3 79.0 - - - +
45C VAL* 1.3 62.9 + - - +
46C ILE* 3.4 22.1 + - + -
50C THR* 3.6 3.6 - - - +
51C CYS* 2.9 30.0 + - - +
53C LEU* 3.7 29.8 - - + -
157C TYR* 3.9 20.4 - - + +
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Residues in contact with VAL 45 (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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128B LYS* 5.5 4.4 + - - -
44C VAL* 1.3 75.7 - - - +
46C ILE* 1.3 57.3 + - - +
47C ASP 3.0 27.4 + - - +
48C GLY* 4.3 3.8 - - - -
49C GLU 3.5 18.4 - - - +
50C THR* 4.2 17.3 - - + +
157C TYR* 3.5 17.6 + - - -
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Residues in contact with ILE 46 (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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44C VAL* 3.4 25.1 + - + +
45C VAL* 1.3 69.0 - - - +
47C ASP* 1.3 72.1 + - - +
48C GLY 2.9 8.8 + - - -
49C GLU 2.8 11.1 + - - -
51C CYS* 3.4 25.1 - - + -
53C LEU* 4.6 2.5 - - + -
157C TYR* 3.7 30.5 - - + +
160C VAL* 3.8 32.1 - - + -
161C ARG* 3.8 17.5 - - + -
164C ARG* 2.8 36.6 + - - +
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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