Contacts of the strand formed by residues 86 - 93 (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 HIS 86 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C TRP* 3.8 1.7 - - - -
82C ASP* 3.1 32.3 + - + +
83C ASP* 2.7 56.6 + - - +
84C THR 3.5 0.6 - - - -
85C GLN* 1.3 93.5 + - + +
87C ILE* 1.3 67.7 + - - +
88C LEU* 6.1 0.4 - - + -
104C VAL* 3.9 23.6 - - + -
105C TYR 3.4 5.6 - - - +
106C GLU* 3.6 28.5 + - + +
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Residues in contact with ILE 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU 4.5 0.7 - - - +
27C PHE* 3.9 23.8 - - + -
31C TRP* 3.6 59.4 - - + +
40C ILE* 4.4 3.6 - - + -
42C ILE* 4.2 6.5 - - + -
79C LEU* 3.8 23.3 - - + -
80C ASP 3.4 9.2 - - - +
81C TYR* 4.0 15.7 - - + -
82C ASP 4.3 0.9 - - - +
86C HIS* 1.3 81.6 - - - +
88C LEU* 1.3 65.1 + - - +
104C VAL* 3.7 3.8 - - - +
105C TYR* 2.9 40.1 + - + +
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Residues in contact with LEU 88 (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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380A PHE* 3.6 28.7 - - + -
382A ARG* 3.7 21.0 + - - +
219B PHE* 4.2 11.9 - - + -
78C ILE 3.5 1.4 - - - +
79C LEU* 3.2 8.3 - - - +
80C ASP* 2.8 43.6 + - + +
81C TYR 6.1 0.2 - - - -
82C ASP* 5.1 11.9 - - + +
86C HIS* 6.1 0.4 - - + -
87C ILE* 1.3 75.3 - - - +
89C MET* 1.3 60.2 + - - +
102C PRO* 3.9 12.6 - - + -
103C ILE 3.2 3.1 - - - +
104C VAL* 3.1 44.2 - - + +
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Residues in contact with MET 89 (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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5C GLN* 3.7 21.1 - - - +
7C ILE* 4.6 11.4 - - - -
40C ILE* 4.2 17.0 - - + -
67C PHE* 4.7 2.0 - - - -
77C TYR* 4.2 23.1 - - + -
78C ILE 3.4 4.7 - - - +
79C LEU* 3.7 23.6 - - + -
88C LEU* 1.3 74.1 - - - +
90C GLN* 1.3 72.1 + - - +
91C THR* 5.1 3.8 - - + -
100C SER* 4.5 0.2 + - - -
102C PRO* 4.3 0.4 - - - -
103C ILE* 2.8 38.0 + - - +
105C TYR* 4.0 34.9 - - + +
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Residues in contact with GLN 90 (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* 4.0 8.3 - - - +
362A TRP* 3.3 27.1 - - - -
382A ARG* 3.3 22.3 + - - +
384A TYR* 4.4 2.0 + - - -
77C TYR* 3.4 4.2 - - - -
78C ILE* 2.7 57.6 + - + +
88C LEU 5.7 0.2 - - - -
89C MET* 1.3 76.9 - - - +
91C THR* 1.3 66.3 + - - +
99C THR* 3.3 20.3 - - + +
100C SER* 2.9 34.2 + - - +
101C ARG 4.2 0.2 - - - -
102C PRO* 3.6 18.3 - - + +
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Residues in contact with THR 91 (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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239A ASP* 5.0 2.4 - - - -
240A ASN 4.8 4.0 + - - -
241A SER* 4.1 9.2 + - - -
281A ASN* 4.2 16.8 + - - +
75C ILE* 4.7 5.2 - - + -
76C ILE 3.3 5.6 - - - -
77C TYR* 3.7 33.0 - - + -
78C ILE* 4.4 0.4 - - - -
89C MET* 5.1 5.8 - - + -
90C GLN* 1.3 79.5 - - - +
92C SER* 1.3 65.9 + - - +
99C THR* 3.6 2.4 - - - +
100C SER* 2.8 44.7 + - - +
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Residues in contact with SER 92 (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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241A SER* 4.1 6.5 - - - -
281A ASN 5.7 1.0 - - - +
338A LEU* 3.8 28.8 - - - +
339A GLY 4.2 2.9 + - - -
75C ILE* 3.5 9.9 - - - +
76C ILE* 2.9 30.5 + - - -
78C ILE* 4.2 2.2 - - - -
91C THR* 1.3 77.4 - - - +
93C SER* 1.3 72.2 + - - +
96C GLY 5.6 0.5 + - - -
98C GLY 3.6 9.7 + - - -
99C THR* 2.8 26.4 + - - -
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Residues in contact with SER 93 (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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241A SER* 4.6 0.8 + - - -
281A ASN 4.8 7.4 - - - -
283A ALA* 3.2 30.8 - - - +
337A HIS 5.5 2.1 - - - +
338A LEU* 5.2 1.7 - - - +
339A GLY 5.5 1.9 + - - -
74C GLU* 3.2 13.2 - - - -
75C ILE* 4.7 0.2 - - - +
76C ILE* 3.9 9.0 - - - +
92C SER* 1.3 85.5 + - - +
94C LYS* 1.3 60.4 + - - +
95C GLN 4.4 0.4 - - - -
96C GLY* 2.9 32.2 + - - +
98C GLY 4.0 4.3 + - - -
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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