Contacts of the strand formed by residues 52 - 59 (chain D) in PDB entry 1PXV
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 GLN 52 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D ASN 3.4 5.4 - - - -
10D VAL* 3.8 15.5 - - + +
46D ASP 2.8 23.8 + - - -
47D ASP* 3.4 21.7 + - - +
49D SER* 3.1 31.1 + - - +
50D HIS* 4.1 0.8 - - - -
51D ASN* 1.3 77.3 - - - +
53D TYR* 1.3 63.6 + - - +
69D SER* 3.7 2.4 - - - -
70D PHE* 3.1 60.8 + - + +
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Residues in contact with TYR 53 (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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5D GLN* 3.0 30.4 + - - +
6D PHE 3.5 15.0 + - - -
7D ILE* 3.7 17.5 - - + -
8D ASN 3.0 7.7 + - - +
9D LEU* 3.5 12.3 - - + +
10D VAL 2.9 27.7 + - - +
51D ASN* 3.2 27.3 + - + -
52D GLN* 1.3 75.6 - - - +
54D HIS* 1.3 60.0 + - - +
67D PHE* 3.6 31.0 - + + -
68D SER 3.2 5.6 - - - +
69D SER* 3.5 35.0 - - - -
70D PHE* 3.5 7.2 - - - -
77D TYR* 3.7 21.3 + + - -
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Residues in contact with HIS 54 (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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10D VAL 4.3 8.5 - - - -
53D TYR* 1.3 72.8 - - - +
55D ILE* 1.3 82.2 + - - +
56D LEU* 3.6 21.3 + - + +
67D PHE* 3.1 4.7 - - - +
68D SER* 2.8 36.4 + - - +
70D PHE* 3.6 21.5 - + + -
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Residues in contact with ILE 55 (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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9D LEU* 4.3 24.9 - - + -
10D VAL 4.3 5.6 + - - +
11D TYR* 3.8 26.2 - - + -
16D LEU* 5.7 0.2 - - + -
24D ILE* 3.4 34.5 - - + -
54D HIS* 1.3 94.3 + - - +
56D LEU* 1.3 63.0 + - - +
57D PHE 3.8 8.1 - - - +
58D ILE* 3.7 26.5 - - + -
65D ILE* 4.8 8.1 - - + -
66D LYS 3.7 10.8 - - - +
67D PHE* 4.0 3.4 - - + -
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Residues in contact with LEU 56 (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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334B ASN* 4.0 11.1 - - - +
336B PRO* 4.1 22.2 - - + +
54D HIS* 3.9 24.9 - - + +
55D ILE* 1.3 73.9 - - - +
57D PHE* 1.3 62.1 + - - +
66D LYS* 2.7 14.3 + - + +
67D PHE* 4.0 14.4 - - - +
68D SER* 3.4 27.4 - - - +
76D ILE* 4.0 27.1 - - + -
94D LYS* 6.3 3.4 - - + -
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Residues in contact with PHE 57 (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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332B ASN* 3.4 47.3 - - + -
334B ASN* 3.8 20.2 - - + -
335B ASP* 3.5 29.2 - - + +
336B PRO* 3.9 17.3 - - + -
55D ILE* 3.7 2.5 - - - +
56D LEU* 1.3 82.6 - - - +
58D ILE* 1.3 79.3 + - - +
59D ASP* 3.7 28.0 + - + -
65D ILE* 3.4 4.3 - - - +
66D LYS* 3.0 33.9 + - + +
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Residues in contact with ILE 58 (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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16D LEU* 3.7 37.2 - - + -
20D GLU* 3.7 49.5 - - + +
23D ASN* 4.2 12.1 - - + -
24D ILE* 3.7 18.2 - - + -
55D ILE* 3.7 19.5 - - + -
57D PHE* 1.3 91.9 - - - +
59D ASP* 1.3 62.9 + - - +
60D THR* 3.9 6.7 + - + +
64D ARG 3.8 2.2 - - - +
65D ILE* 4.0 14.8 - - + -
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Residues in contact with ASP 59 (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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335B ASP* 4.4 8.7 - - - +
23D ASN* 4.6 1.3 - - - -
57D PHE* 3.7 23.4 - - + -
58D ILE* 1.3 73.4 - - - +
60D THR* 1.3 67.5 + - - +
61D ALA* 3.5 10.9 + - - +
62D HIS* 3.3 31.5 - - - +
63D GLN* 2.9 17.9 + - - -
64D ARG* 2.8 41.2 + - + +
66D LYS* 6.5 0.7 - - + -
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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