Contacts of the strand formed by residues 36 - 43 (chain C) in PDB entry 2PZX
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 THR 36 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C ILE* 3.2 9.8 - - - +
3C LEU* 5.4 0.2 - - - +
13C ILE* 3.6 11.4 - - + -
24C TYR* 3.4 36.5 - - + -
31C VAL* 3.4 26.2 - - + -
32C PRO 3.7 4.9 - - - +
33C ALA* 2.6 21.3 + - - +
34C ILE 4.2 3.5 - - - +
35C LEU* 1.3 80.4 - - - +
37C GLY* 1.3 59.0 + - - +
56C ILE* 3.7 9.9 - - - +
57C ARG 3.4 9.2 - - - -
58C GLY* 4.6 0.2 - - - -
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Residues in contact with GLY 37 (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 ASP* 3.6 6.1 - - - -
2C ILE* 3.1 18.0 - - - +
36C THR* 1.3 78.1 - - - +
38C GLU* 1.3 60.6 + - - -
39C TYR* 3.0 10.2 - - - -
56C ILE* 3.1 9.4 - - - +
57C ARG 2.6 31.1 + - - -
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Residues in contact with GLU 38 (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 ASP* 3.0 25.8 + - - +
37C GLY* 1.3 72.1 - - - -
39C TYR* 1.3 69.3 + - - +
54C ARG* 2.7 63.7 + - + +
55C HIS 3.9 5.8 - - - +
56C ILE* 3.7 9.0 - - + +
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Residues in contact with TYR 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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1C ASP* 3.3 30.5 + - + -
2C ILE* 2.9 35.8 + - + +
5C CYS 5.4 2.3 + - - -
7C TYR* 4.5 9.5 - + - -
10C THR* 4.1 11.7 - - + +
37C GLY 3.0 31.6 - - - -
38C GLU* 1.3 77.6 - - - +
40C ASP* 1.3 61.1 + - - +
41C PHE* 3.7 41.3 - + - +
53C ALA 2.9 20.6 - - - +
54C ARG* 3.3 6.0 - - - +
55C HIS* 3.0 26.1 + - + +
57C ARG* 3.2 39.3 - - + -
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Residues in contact with ASP 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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39C TYR* 1.3 73.3 - - - +
41C PHE* 1.3 71.9 + - - +
51C LYS* 3.1 14.4 - - - +
52C VAL* 2.4 47.2 + - - +
53C ALA 4.7 0.9 - - - -
54C ARG* 4.0 27.5 + - - +
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Residues in contact with PHE 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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1C ASP* 4.1 17.5 - - + -
7C TYR* 4.4 14.5 + + + -
39C TYR* 3.7 45.5 - + - +
40C ASP* 1.3 99.5 + - - +
42C ARG* 1.3 70.5 + - - +
43C ILE* 3.6 32.8 - - + -
49C LYS* 4.1 43.3 - - + -
50C GLN 3.0 13.5 - - - +
51C LYS* 5.0 0.2 - - - -
52C VAL* 4.1 4.8 - - - +
55C HIS* 4.6 3.8 - - - -
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Residues in contact with ARG 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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7C TYR* 3.7 19.5 - - + +
41C PHE* 1.3 80.0 - - - +
43C ILE* 1.3 68.3 + - - +
44C LEU* 3.7 5.1 + - + +
50C GLN* 3.0 42.5 + - + +
51C LYS 4.6 3.4 + - - -
52C VAL* 3.3 35.2 - - + +
55C HIS* 5.7 2.2 - - + -
121C ASP 5.8 4.9 - - - +
123C PRO* 6.0 2.0 - - + -
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Residues in contact with ILE 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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7C TYR* 3.8 38.5 - - + -
8C PHE* 4.4 9.2 - - + -
41C PHE* 3.6 24.0 - - + -
42C ARG* 1.3 77.9 - - - +
44C LEU* 1.3 74.9 + - - +
47C ASP* 3.7 17.5 - - + +
48C SER 3.1 20.0 - - - +
49C LYS* 5.0 5.6 - - + -
123C PRO* 2.9 26.4 - - - +
161C ARG* 4.4 16.2 - - - +
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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