Contacts of the strand formed by residues 36 - 43 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D ILE* 3.2 9.8 - - - +
13D ILE* 3.6 11.0 - - + -
24D TYR* 3.4 35.8 - - + -
31D VAL* 3.4 25.8 - - + -
32D PRO 3.7 5.4 - - - +
33D ALA* 2.6 22.2 + - - +
34D ILE 4.2 3.5 - - - +
35D LEU* 1.3 80.5 - - - +
37D GLY* 1.3 59.3 + - - +
56D ILE* 3.7 10.8 - - - +
57D ARG 3.4 9.4 - - - +
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Residues in contact with GLY 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ASP* 3.6 5.8 - - - -
2D ILE* 3.1 19.1 - - - +
36D THR* 1.3 78.5 - - - +
38D GLU* 1.3 61.3 + - - -
39D TYR* 3.0 9.3 - - - -
56D ILE* 3.1 10.0 - - - +
57D ARG 2.6 31.6 + - - -
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Residues in contact with GLU 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ASP* 3.0 26.5 + - - +
37D GLY* 1.3 71.7 - - - -
39D TYR* 1.3 69.6 + - - +
54D ARG* 2.7 62.3 + - + +
55D HIS 3.9 5.6 - - - +
56D ILE* 3.7 9.2 - - + +
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Residues in contact with TYR 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ASP* 3.3 30.9 + - + -
2D ILE* 2.9 36.2 + - + +
5D CYS* 5.4 2.3 + - - -
7D TYR* 4.5 9.0 - + - -
10D THR* 4.1 11.1 - - + +
37D GLY 3.0 31.6 - - - -
38D GLU* 1.3 78.2 - - - +
40D ASP* 1.3 60.7 + - - +
41D PHE* 3.4 39.7 - + - +
53D ALA 2.9 20.6 - - - +
54D ARG* 3.3 6.8 - - - +
55D HIS* 3.0 27.5 + - + +
57D ARG* 3.2 39.0 - - + -
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Residues in contact with ASP 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D TYR* 1.3 74.1 - - - +
41D PHE* 1.3 71.7 + - - +
51D LYS* 3.1 14.3 - - + +
52D VAL* 2.4 45.3 + - - +
53D ALA 4.7 0.9 - - - -
54D ARG* 4.0 27.8 + - - +
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Residues in contact with PHE 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ASP* 4.1 18.6 - - + -
7D TYR* 4.4 13.5 + + + -
39D TYR* 3.7 45.1 - + - +
40D ASP* 1.3 98.9 - - - +
42D ARG* 1.3 68.7 + - - +
43D ILE* 3.6 34.8 - - + -
49D LYS* 4.1 44.2 - - + -
50D GLN 3.0 12.8 - - - +
51D LYS* 5.0 0.4 - - - -
52D VAL* 4.1 6.5 - - - +
55D HIS* 4.6 3.8 - - - -
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Residues in contact with ARG 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D TYR* 3.7 19.5 - - + +
41D PHE* 1.3 79.9 - - - +
43D ILE* 1.3 69.8 + - - +
44D LEU* 3.7 5.0 + - + +
50D GLN* 3.0 42.7 + - + +
51D LYS 4.6 2.6 + - - -
52D VAL* 3.3 35.0 - - + +
55D HIS* 5.7 2.2 - - + -
121D ASP 5.8 5.6 - - - +
123D PRO* 6.0 2.5 - - + -
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Residues in contact with ILE 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D TYR* 3.8 39.3 - - + -
8D PHE* 4.4 9.9 - - + -
41D PHE* 3.6 24.2 - - + -
42D ARG* 1.3 76.4 - - - +
44D LEU* 1.3 75.5 + - - +
47D ASP* 3.7 17.3 - - + +
48D SER 3.1 19.7 - - - +
49D LYS* 5.0 5.8 - - + -
123D PRO* 2.9 26.4 - - - +
161D 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