Contacts of the strand formed by residues 72 - 83 (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 ASN 72 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D SER* 3.1 25.5 + - - +
70D PHE 3.5 0.6 - - - -
71D ASP* 1.3 84.3 + - - +
73D GLU* 1.3 63.9 + - - +
74D GLU* 3.0 27.3 + - - +
75D ILE* 3.3 46.1 + - + +
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Residues in contact with GLU 73 (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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68D SER* 4.3 15.0 + - - -
69D SER 4.8 4.3 - - - +
70D PHE 5.4 5.8 - - - +
71D ASP 4.3 0.2 - - - -
72D ASN* 1.3 74.8 + - - +
74D GLU* 1.3 75.1 + - - +
75D ILE 3.3 1.8 + - - -
94D LYS* 3.3 38.1 + - - +
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Residues in contact with GLU 74 (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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285B PHE* 5.8 1.0 - - - -
72D ASN* 3.0 15.0 + - - +
73D GLU* 1.3 95.3 + - - +
75D ILE* 1.3 61.2 + - + +
93D SER* 3.5 7.9 - - - +
94D LYS* 2.8 32.6 + - - +
95D GLN* 3.0 37.0 + - - +
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Residues in contact with ILE 75 (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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281B ASN* 3.4 48.9 - - + +
68D SER* 2.9 25.5 + - - -
72D ASN* 3.3 35.7 + - + +
73D GLU 3.3 0.2 - - - -
74D GLU* 1.3 82.8 - - + +
76D ILE* 1.3 69.4 + - - +
77D TYR* 3.8 37.0 + - + +
91D THR* 4.4 10.3 - - + -
92D SER 3.6 7.2 - - - +
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Residues in contact with ILE 76 (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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336B PRO* 4.0 24.0 - - + -
337B HIS 4.7 6.7 - - - +
338B LEU* 4.4 8.1 - - + -
56D LEU* 4.0 24.5 - - + -
66D LYS* 4.2 9.0 - - + -
67D PHE 3.7 3.6 - - - +
68D SER* 3.8 1.8 - - - +
73D GLU 5.0 0.2 - - - +
75D ILE* 1.3 76.5 - - - +
77D TYR* 1.3 71.4 + - - +
78D ILE* 3.6 15.2 - - + +
91D THR* 3.3 5.7 - - - -
92D SER* 2.8 39.5 + - - +
93D SER 4.0 6.7 - - - +
94D LYS* 3.7 38.8 - - + +
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Residues in contact with TYR 77 (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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281B ASN* 4.6 5.4 + - - -
5D GLN* 3.7 26.7 + - - -
53D TYR* 3.7 27.0 + + - -
66D LYS* 3.1 5.0 - - - -
67D PHE* 2.8 67.4 + + + +
68D SER* 4.4 0.9 - - - -
69D SER* 4.5 8.8 + - - -
75D ILE* 3.8 34.1 - - + +
76D ILE* 1.3 73.9 - - - +
78D ILE* 1.3 62.6 + - - +
79D LEU 4.2 0.7 - - - -
89D MET* 4.5 17.3 - - + -
90D GLN 3.4 3.1 - - - +
91D THR* 3.5 26.9 - - + -
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Residues in contact with ILE 78 (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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338B LEU* 3.9 35.4 - - + -
382B ARG* 5.0 0.2 - - - +
64D ARG* 3.7 23.3 - - + +
65D ILE 3.4 4.3 - - - +
66D LYS* 4.0 16.2 - - + -
76D ILE* 3.6 17.9 - - + +
77D TYR* 1.3 76.9 - - - +
79D LEU* 1.3 62.7 + - - +
80D ASP* 3.6 20.5 - - - +
88D LEU 3.5 1.4 - - - +
89D MET* 3.3 5.0 - - - +
90D GLN* 2.8 68.4 + - + +
92D SER* 3.9 10.5 - - - -
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Residues in contact with LEU 79 (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* 6.0 0.4 - - + -
27D PHE* 3.6 27.8 - - + -
40D ILE* 4.6 2.5 - - + -
42D ILE* 3.7 26.9 - - + -
64D ARG* 3.1 7.1 - - - +
65D ILE* 2.9 42.0 + - + +
67D PHE* 3.6 29.4 - - + -
78D ILE* 1.3 74.8 - - - +
80D ASP* 1.3 61.2 + - - +
87D ILE* 3.9 20.9 - - + -
88D LEU 3.2 12.8 - - - +
89D MET* 3.7 27.1 - - + -
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Residues in contact with ASP 80 (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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382B ARG* 3.6 26.0 + - - +
27D PHE* 3.7 3.6 - - - -
62D HIS 3.6 9.2 - - - +
63D GLN 3.7 2.0 - - - -
64D ARG* 2.6 55.6 + - - +
78D ILE* 3.6 14.4 - - - +
79D LEU* 1.3 73.7 - - - +
81D TYR* 1.3 65.5 + - - +
82D ASP 3.5 0.3 + - - -
87D ILE* 3.3 3.8 - - - +
88D LEU* 2.9 43.2 + - + +
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Residues in contact with TYR 81 (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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26D LEU* 3.6 43.1 - - + +
27D PHE* 3.6 14.9 - - + -
62D HIS 4.6 3.8 - - - +
63D GLN* 2.9 68.1 + - + +
80D ASP* 1.3 73.9 - - - +
82D ASP* 1.3 69.8 + - - +
83D ASP* 3.4 31.9 - - - +
84D THR* 3.7 25.7 + - + +
87D ILE* 4.3 6.3 - - + -
88D LEU* 5.0 1.2 - - - +
107D ARG* 6.2 0.2 - - - -
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Residues in contact with ASP 82 (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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219A PHE* 5.1 11.4 - - - -
63D GLN* 5.2 1.4 - - - +
80D ASP 3.5 1.4 + - - -
81D TYR* 1.3 85.5 - - - +
83D ASP* 1.3 70.8 + - - +
86D HIS* 3.0 39.1 + - + +
88D LEU* 3.8 18.1 - - + +
104D VAL* 5.8 1.7 - - - +
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Residues in contact with ASP 83 (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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31D TRP* 4.9 0.2 - - - -
81D TYR* 3.4 23.1 - - - +
82D ASP* 1.3 87.0 - - - +
84D THR* 1.3 66.1 + - - +
85D GLN* 2.9 11.8 + - - +
86D HIS* 2.9 44.9 + - - +
87D ILE* 4.8 1.7 - - - +
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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