Contacts of the strand formed by residues 42 - 49 (chain C) in PDB entry 3P3W
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 HIS 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C ASN 2.9 13.4 + - - +
5C THR* 3.3 10.8 + - - +
6C ILE 3.2 23.2 + - - -
31C ASN* 3.6 36.7 + - + +
41C PHE* 1.3 78.6 - - - +
43C LEU* 1.3 82.2 + - - +
44C ASN* 3.8 16.9 + - - -
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Residues in contact with LEU 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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6C ILE* 3.6 14.8 - - + +
8C ILE* 4.6 15.3 - - + -
27C VAL* 3.9 33.8 - - + +
30C TYR* 3.7 27.4 - - + -
31C ASN* 3.6 18.3 + - - +
41C PHE* 3.9 20.4 + - + -
42C HIS* 1.3 85.7 + - - +
44C ASN* 1.3 79.2 + - - +
45C TYR* 5.4 0.2 - - - -
286C ILE* 4.9 13.2 - - + -
289C ILE* 4.6 21.1 - - + -
290C ALA* 6.2 1.8 - - - -
293C PHE* 6.3 0.2 - - + -
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Residues in contact with ASN 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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5C THR* 3.2 24.5 + - - +
6C ILE 3.1 7.3 + - - +
7C SER* 3.3 19.4 - - - -
8C ILE* 2.8 29.3 + - - +
42C HIS* 3.8 12.6 + - - -
43C LEU* 1.3 82.7 - - - +
45C TYR* 1.3 68.8 + - - +
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Residues in contact with TYR 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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7C SER* 5.2 2.2 - - - -
8C ILE* 3.2 28.0 - - + +
23C PHE* 3.6 21.8 - + + -
24C ARG* 3.1 48.0 + - + +
27C VAL* 4.1 35.2 - - + -
44C ASN* 1.3 80.4 - - - +
46C HIS* 1.3 60.1 + - - +
47C VAL* 3.7 25.1 - - + +
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Residues in contact with HIS 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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7C SER* 6.0 0.4 - - - -
8C ILE 3.5 6.0 + - - +
9C GLY* 5.1 0.4 - - - -
10C GLY* 2.6 33.8 + - - -
45C TYR* 1.3 74.6 - - - +
47C VAL* 1.3 60.9 + - - +
48C ASP* 6.2 0.2 - - - -
65C GLN* 3.0 20.3 + - - +
68C ARG* 3.8 31.0 - - + +
70C VAL* 5.1 6.5 - - + +
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Residues in contact with VAL 47 (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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10C GLY 3.6 2.7 - - - -
12C PHE* 3.9 26.5 - - + -
20C HIS* 3.8 20.0 - - + +
23C PHE* 5.0 1.3 - - + -
45C TYR* 3.7 33.2 - - + -
46C HIS* 1.3 72.7 - - - +
48C ASP* 1.3 70.1 + - - +
49C HIS* 3.6 37.1 + - + +
68C ARG* 5.7 1.6 + - - +
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Residues in contact with ASP 48 (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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10C GLY 3.0 12.8 + - - +
11C LEU* 3.7 5.2 - - + +
12C PHE* 3.1 27.2 + - - +
47C VAL* 1.3 81.3 - - - +
49C HIS* 1.3 62.5 + - - +
50C LEU* 3.6 2.4 + - - +
61C ALA* 3.6 29.2 - - + +
64C SER* 4.3 13.3 + - - -
65C GLN* 2.8 30.8 + - - +
68C ARG* 5.5 7.8 + - - -
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Residues in contact with HIS 49 (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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12C PHE* 3.8 10.3 - - - +
13C MET 5.9 0.9 - - - +
20C HIS* 3.9 20.2 - + - -
47C VAL* 3.6 31.3 + - + +
48C ASP* 1.3 71.6 - - - +
50C LEU* 1.3 60.3 + - - +
61C ALA* 5.9 0.4 - - - -
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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