Contacts of the strand formed by residues 84 - 93 (chain C) in PDB entry 1PR1
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 LYS 84 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C ASP 2.9 4.4 + - - -
15C VAL* 3.4 30.0 - - + -
16C VAL 3.0 25.6 + - - -
82C VAL* 3.4 7.5 - - - +
83C LYS* 1.3 87.6 - - + +
85C ILE* 1.3 63.5 + - - +
86C ILE* 4.3 1.3 - - + -
130C ASP* 5.7 0.2 - - - -
132C ASP* 6.3 0.8 - - - +
133C MET* 4.0 36.7 - - + +
136C ASN* 4.2 10.3 - - - +
195C LYS* 3.5 18.4 - - + +
232C VAL* 5.0 9.8 + - + +
235C GLY* 4.1 26.7 + - - -
236C ASP* 5.6 1.6 + - - -
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Residues in contact with ILE 85 (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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16C VAL* 3.6 12.1 - - + +
18C MET* 4.2 17.7 - - + -
73C THR* 3.5 44.2 - - + +
76C LEU* 4.8 6.5 - - + -
77C ILE* 4.1 20.6 - - + -
82C VAL* 4.0 13.7 - - + -
83C LYS 5.7 0.4 - - - -
84C LYS* 1.3 80.9 - - - +
86C ILE* 1.3 69.5 + - - +
87C ARG* 4.6 2.0 - - - +
133C MET* 3.7 1.6 - - - +
185C ILE* 4.3 14.6 - - + -
189C ALA* 6.5 0.4 - - + -
194C ALA* 5.9 0.9 - - + -
195C LYS 3.0 11.0 + - - +
196C ALA* 3.1 12.4 - - + +
197C LEU 2.9 25.5 + - - +
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Residues in contact with ILE 86 (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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15C VAL* 4.5 7.2 - - + -
16C VAL 3.2 6.7 + - - -
17C LEU* 3.2 19.5 - - + +
18C MET 2.8 23.6 + - - -
84C LYS* 6.0 0.7 - - + -
85C ILE* 1.3 73.1 - - - +
87C ARG* 1.3 66.7 + - - +
88C VAL* 3.4 2.9 + - + -
133C MET* 3.5 26.0 - - + -
197C LEU* 3.1 13.2 - - + +
199C ILE* 3.8 28.0 - - + -
228C ALA* 3.9 20.0 - - + +
231C SER* 4.2 8.1 - - - +
232C VAL* 3.6 30.7 - - + -
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Residues in contact with ARG 87 (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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18C MET* 3.3 16.4 - - + +
20C GLY 4.1 0.2 - - - +
62C HIS* 3.2 16.1 + - + +
85C ILE* 4.0 3.2 - - + +
86C ILE* 1.3 72.3 - - - +
88C VAL* 1.3 56.3 + - - +
89C GLY* 3.5 7.1 - - - -
90C SER 3.5 10.7 + - - -
179C GLU* 3.1 23.8 + - - +
181C GLU* 2.9 35.8 + - - -
182C ALA 4.4 0.9 - - - +
185C ILE* 3.5 20.8 - - + +
197C LEU 2.7 10.0 + - - +
198C THR* 3.6 25.1 - - + +
199C ILE* 2.7 35.2 + - - +
200C CYS* 3.7 8.2 - - - -
247C FMB 3.2 5.9 + - - -
250C PO4 2.8 42.4 + - - -
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Residues in contact with VAL 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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17C LEU* 4.4 8.1 - - + -
18C MET 3.1 11.0 + - - +
19C PRO* 3.2 29.5 - - + +
24C ARG* 2.7 23.4 + - - -
28C ILE* 4.2 4.7 - - + -
86C ILE* 4.1 8.3 - - + +
87C ARG* 1.3 75.2 - - - +
89C GLY* 1.3 50.5 + - - +
199C ILE* 3.3 7.0 - - + -
224C MET* 3.3 32.8 - - + +
225C ILE* 4.2 18.2 - - + -
228C ALA* 3.8 29.8 - - + -
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Residues in contact with GLY 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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24C ARG* 3.1 13.2 - - - -
87C ARG* 3.5 12.1 - - - +
88C VAL* 1.3 76.5 - - - +
90C SER* 1.3 61.6 + - - -
199C ILE 3.0 8.7 + - - -
200C CYS* 3.0 7.6 - - - -
201C THR* 2.9 22.2 + - - -
221C PHE* 5.5 0.7 - - - -
224C MET* 3.1 8.4 - - - +
250C PO4 3.1 11.7 - - - -
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Residues in contact with SER 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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24C ARG* 5.0 1.6 - - - -
87C ARG* 3.5 8.1 + - - -
89C GLY* 1.3 75.0 - - - -
91C CYS* 1.3 66.5 + - - +
179C GLU* 3.6 0.9 - - - +
200C CYS* 4.3 0.4 - - - -
201C THR 3.2 11.7 - - - -
203C SER* 3.4 21.3 + - - -
215C ALA* 5.3 4.3 - - - +
221C PHE* 4.1 12.8 - - - -
247C FMB 3.3 27.8 + - - -
250C PO4 2.6 28.8 + - - -
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Residues in contact with CYS 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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90C SER* 1.3 78.4 - - - +
92C GLY* 1.3 60.0 + - - +
104C VAL* 5.1 2.9 - - - -
153C LEU* 4.7 2.2 - - - -
177C GLY* 4.0 17.3 - - - -
178C VAL 3.3 22.7 - - - +
179C GLU* 3.9 6.1 - - + -
200C CYS* 3.6 25.4 - - + -
201C THR 3.1 6.5 + - - -
202C VAL* 3.5 28.0 - - - -
203C SER* 2.8 23.9 + - - -
204C ASP 3.4 5.0 + - - -
247C FMB 3.3 11.0 + - - -
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Residues in contact with GLY 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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91C CYS* 1.3 74.3 - - - +
93C ALA* 1.3 62.0 + - - -
177C GLY* 3.2 5.9 - - - -
178C VAL* 2.6 40.9 + - - +
202C VAL* 4.6 1.3 - - - -
204C ASP* 3.3 12.1 - - - -
206C ILE* 4.2 7.2 - - - -
247C FMB 3.2 21.5 + - - -
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Residues in contact with ALA 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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92C GLY* 1.3 73.2 - - - -
94C VAL* 1.3 62.1 + - - +
98C VAL* 3.4 33.4 - - + -
176C LEU 4.2 7.0 - - - +
202C VAL* 3.5 15.2 - - + +
204C ASP 2.9 7.9 + - - -
205C HIS* 3.5 24.3 + - + +
206C ILE* 2.9 27.6 + - - +
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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