Contacts of the strand formed by residues 43 - 50 (chain A) in PDB entry 1PZO
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 ARG 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLU* 3.4 5.8 - - - -
42A ALA* 1.3 72.8 - - - +
44A VAL* 1.3 58.7 + - - +
61A ARG* 3.5 31.6 - - - +
64A GLU* 2.9 30.9 + - - +
65A ARG 3.0 30.1 + - - +
66A PHE* 3.5 23.2 - - + +
265A THR* 2.9 19.9 + - - -
266A THR* 3.1 46.9 + - - +
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 3.8 22.4 - - + +
36A ALA* 4.2 11.0 - - + +
37A GLU* 2.9 35.7 + - + +
40A LEU* 4.7 6.3 - - + -
42A ALA 4.1 2.9 - - - +
43A ARG* 1.3 77.5 - - - +
45A GLY* 1.4 66.8 + - - +
46A TYR* 4.9 0.9 - - + -
60A PHE* 3.2 21.8 - - - -
61A ARG* 3.3 8.1 - - - -
66A PHE* 3.7 3.1 - - - -
263A ILE* 4.2 14.6 - - + -
264A TYR 3.2 10.8 - - - +
265A THR* 4.0 13.2 - - - +
282A ILE* 4.8 8.7 - - + -
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Residues in contact with GLY 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 1.4 73.2 - - - +
46A TYR* 1.3 61.2 + - - +
60A PHE 3.2 9.4 - - - -
61A ARG* 4.1 1.8 - - - -
66A PHE* 3.2 23.8 - - - -
183A PRO* 3.7 12.3 - - - -
262A VAL 4.4 0.2 - - - -
263A ILE* 3.4 6.6 - - - +
264A TYR 2.8 32.0 + - - +
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Residues in contact with TYR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A THR* 3.5 21.2 - - + +
30A LEU* 4.1 18.4 - - + -
33A VAL* 3.9 19.1 - - + -
44A VAL* 4.9 0.9 - - + -
45A GLY* 1.3 73.6 - - - +
47A ILE* 1.3 70.5 + - - +
48A GLU* 2.6 47.4 + - + +
58A GLU* 4.2 11.0 - - + -
59A SER* 3.2 1.2 - - - -
60A PHE* 2.7 47.6 + - + +
62A PRO* 4.7 0.7 - - - +
183A PRO* 3.8 4.8 - - - +
261A VAL* 3.8 19.6 - - + +
262A VAL 3.3 3.4 - - - -
263A ILE* 3.7 20.0 - - + -
282A ILE* 3.9 16.4 - - + -
286A LEU* 3.8 12.2 - - + +
301A CBT 5.9 0.2 - - + -
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Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A TYR* 1.3 77.7 - - - +
48A GLU* 1.3 68.2 + - - +
49A LEU* 4.0 18.4 - - + +
56A ILE* 3.9 19.5 - - + -
58A GLU 3.4 13.5 - - - +
59A SER* 3.8 8.7 - - - -
62A PRO* 4.1 7.0 - - + -
183A PRO* 3.4 28.9 - - + +
184A ALA* 3.6 32.3 - - + +
187A ALA* 3.6 15.3 - - + -
261A VAL* 3.3 7.8 - - - +
262A VAL* 3.0 39.2 + - + +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A HIS 4.3 10.7 + - - -
29A THR* 4.1 8.7 + - - +
46A TYR* 2.6 40.7 + - + +
47A ILE* 1.3 72.8 - - - +
49A LEU* 1.3 59.5 + - - +
56A ILE* 3.6 5.2 - - - +
57A LEU* 2.7 45.9 + - + +
58A GLU* 2.9 26.4 + - - +
259A ARG* 2.9 30.9 + - - -
260A ILE 3.4 4.5 - - - -
261A VAL* 4.2 11.0 - - + -
286A LEU* 3.9 11.9 - - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ILE* 4.0 14.1 - - + -
48A GLU* 1.3 81.4 - - - +
50A ASP* 1.3 62.5 + - - +
54A GLY* 3.4 26.9 - - - +
55A LYS 3.4 1.3 - - - -
56A ILE* 3.4 34.1 - - + -
57A LEU* 4.3 0.7 - - - -
187A ALA* 3.7 37.5 - - + +
188A THR* 3.8 16.8 - - - +
191A ARG* 4.8 7.4 - - + -
259A ARG* 3.3 8.2 - - - +
260A ILE* 2.8 45.6 + - + +
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Residues in contact with ASP 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 1.3 70.0 - - - +
51A LEU* 1.3 61.0 + - - +
52A ASN* 3.3 12.5 + - - +
53A SER* 2.8 41.5 + - - +
54A GLY* 2.8 30.3 + - - -
55A LYS* 2.9 15.8 + - + +
57A LEU* 3.8 26.1 - - + +
191A ARG* 4.1 1.4 - - - -
258A SER* 4.0 9.7 - - - +
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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