Contacts of the strand formed by residues 72 - 83 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C SER* 3.1 25.9 + - - +
70C PHE 3.5 0.6 - - - -
71C ASP* 1.3 88.4 + - - +
73C GLU* 1.3 61.6 + - - +
74C GLU* 3.1 26.9 + - - +
75C ILE* 3.3 47.9 + - + +
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Residues in contact with GLU 73 (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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68C SER* 4.2 17.1 + - - -
69C SER 4.2 2.0 + - - +
70C PHE 5.3 1.0 + - - +
71C ASP 4.2 0.4 - - - -
72C ASN* 1.3 71.5 + - - +
74C GLU* 1.3 82.4 + - + +
75C ILE 3.2 4.0 + - - +
76C ILE* 4.7 2.1 - - - +
94C LYS* 2.9 47.3 + - - +
95C GLN* 5.0 0.9 - - - +
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Residues in contact with GLU 74 (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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281A ASN 5.6 0.2 - - - +
72C ASN* 3.1 16.8 + - - +
73C GLU* 1.3 100.7 - - + +
75C ILE* 1.3 62.5 + - + +
93C SER* 3.2 11.4 - - - -
94C LYS* 3.0 32.3 + - - +
95C GLN* 2.8 40.9 + - - +
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Residues in contact with ILE 75 (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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281A ASN* 3.6 46.4 - - + +
68C SER* 2.9 24.8 + - - -
69C SER* 6.0 0.4 - - - +
72C ASN* 3.3 34.9 + - + +
73C GLU 3.2 0.4 - - - -
74C GLU* 1.3 82.8 - - + +
76C ILE* 1.3 66.7 + - - +
77C TYR* 3.8 36.8 + - + +
91C THR* 4.7 10.1 - - + -
92C SER 3.5 8.3 - - - +
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Residues in contact with ILE 76 (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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336A PRO* 4.1 27.1 - - + -
337A HIS 5.4 1.3 - - - +
338A LEU* 4.4 12.1 - - + -
56C LEU* 4.1 18.4 - - + -
66C LYS* 4.5 6.7 - - + -
67C PHE 3.7 2.7 - - - -
68C SER* 3.9 8.7 - - - +
73C GLU 4.7 4.5 - - - +
74C GLU 4.1 0.2 - - - -
75C ILE* 1.3 77.0 - - - +
77C TYR* 1.3 71.6 + - - +
78C ILE* 3.7 15.8 - - + +
91C THR* 3.3 5.4 - - - -
92C SER* 2.9 37.0 + - - +
93C SER 3.9 7.2 - - - +
94C LYS* 3.8 32.3 - - + +
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Residues in contact with TYR 77 (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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281A ASN* 5.1 4.6 + - - -
5C GLN* 3.7 27.5 + - - -
53C TYR* 3.8 16.5 + + - -
66C LYS* 3.2 6.2 - - - +
67C PHE* 2.8 75.6 + + + +
68C SER* 4.3 1.6 - - - -
69C SER* 4.4 9.1 + - - -
75C ILE* 3.8 33.2 - - + +
76C ILE* 1.3 74.1 - - - +
78C ILE* 1.3 62.3 + - - +
79C LEU 4.1 0.4 - - - -
89C MET* 4.2 19.1 - - + -
90C GLN 3.4 4.9 - - - +
91C THR* 3.7 26.5 - - + -
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Residues in contact with ILE 78 (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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338A LEU* 3.8 31.0 - - + -
382A ARG* 4.8 1.5 + - - +
64C ARG* 3.5 37.0 - - + +
65C ILE 3.5 3.1 - - - +
66C LYS* 3.9 17.0 - - + -
76C ILE* 3.7 22.2 - - + +
77C TYR* 1.3 78.8 - - - +
79C LEU* 1.3 63.6 + - - +
80C ASP* 3.6 9.2 + - - +
88C LEU 3.5 1.6 - - - +
89C MET* 3.4 2.8 - - - -
90C GLN* 2.7 65.5 + - + +
92C SER* 4.2 7.4 - - - -
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Residues in contact with LEU 79 (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 ILE* 5.5 0.2 - - + -
9C LEU* 6.1 0.2 - - + -
27C PHE* 3.5 21.2 - - + -
40C ILE* 4.8 1.8 - - + -
42C ILE* 3.8 25.1 - - + -
64C ARG* 3.1 7.1 - - - +
65C ILE* 2.9 47.3 + - + -
67C PHE* 3.5 30.7 - - + -
77C TYR 4.1 0.4 - - - -
78C ILE* 1.3 72.2 - - - +
80C ASP* 1.3 61.8 + - - +
87C ILE* 3.8 24.0 - - + -
88C LEU 3.2 14.4 - - - +
89C MET* 3.7 24.9 - - + -
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Residues in contact with ASP 80 (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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382A ARG* 3.2 29.2 + - - +
27C PHE* 3.5 3.8 - - - -
62C HIS* 4.3 7.6 - - - +
63C GLN 3.6 3.4 - - - +
64C ARG* 2.8 47.8 + - - -
78C ILE* 3.6 9.2 - - - +
79C LEU* 1.3 78.0 - - - +
81C TYR* 1.3 66.0 + - - +
87C ILE* 3.4 3.5 - - - +
88C LEU* 2.8 44.8 + - + +
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Residues in contact with TYR 81 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C LEU* 3.8 50.0 - - + +
27C PHE* 3.5 9.3 - - + -
31C TRP* 5.5 0.9 - + - -
62C HIS 4.9 1.7 - - - +
63C GLN* 2.9 54.1 + - + +
80C ASP* 1.3 76.5 - - - +
82C ASP* 1.3 65.5 + - - +
83C ASP* 3.1 31.2 - - - -
84C THR* 2.8 37.9 + - - +
87C ILE* 4.0 12.6 - - + -
88C LEU* 6.1 0.2 - - - -
107C ARG* 5.7 0.7 - - - -
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Residues in contact with ASP 82 (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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219B PHE* 4.4 20.7 - - - -
63C GLN* 5.5 0.3 - - - +
80C ASP 3.7 1.6 + - - -
81C TYR* 1.3 82.3 - - - +
83C ASP* 1.3 76.2 + - - +
86C HIS* 3.1 29.0 + - + +
87C ILE* 4.7 2.2 - - - +
88C LEU* 5.1 13.6 - - + +
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Residues in contact with ASP 83 (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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81C TYR* 3.1 18.3 - - - -
82C ASP* 1.3 89.9 - - - +
84C THR* 1.3 60.2 + - + +
85C GLN* 3.0 7.1 + - - +
86C HIS* 2.7 65.0 + - - +
87C ILE* 4.7 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