Contacts of the strand formed by residues 84 - 93 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASP 3.0 3.6 + - - -
15B VAL* 3.3 30.8 - - + -
16B VAL 3.0 24.6 + - - -
82B VAL* 3.3 5.7 - - - +
83B LYS* 1.3 86.3 - - + +
85B ILE* 1.3 63.1 + - - +
86B ILE* 6.1 0.4 - - + -
130B ASP* 5.6 0.2 - - - -
132B ASP* 6.2 1.4 - - - +
133B MET* 3.9 38.4 - - + +
136B ASN* 4.2 10.3 - - - +
195B LYS* 3.3 25.1 - - + +
232B VAL* 5.1 11.3 + - + +
235B GLY* 4.2 25.5 + - - -
236B ASP* 5.6 1.8 + - - -
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL* 3.4 9.4 - - + +
18B MET* 4.0 25.4 - - + -
73B THR* 3.4 49.8 - - + +
76B LEU* 4.6 5.2 - - + -
77B ILE* 4.2 15.7 - - + -
82B VAL* 3.9 13.5 - - + -
83B LYS 5.7 0.4 - - - -
84B LYS* 1.3 80.7 - - - +
86B ILE* 1.3 71.2 + - - +
87B ARG* 4.6 2.5 - - + +
133B MET* 3.8 0.7 - - - +
185B ILE* 4.3 11.9 - - + -
194B ALA* 6.2 0.2 - - + -
195B LYS 3.0 10.6 + - - +
196B ALA* 3.2 8.7 - - + +
197B LEU 2.9 24.9 + - - +
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL* 4.7 7.0 - - + -
16B VAL 2.9 8.6 + - - +
17B LEU* 3.2 25.9 - - + +
18B MET 2.7 30.5 + - - -
84B LYS* 6.1 0.4 - - + -
85B ILE* 1.3 74.6 - - - +
87B ARG* 1.3 64.6 + - - +
88B VAL* 3.7 14.2 + - + +
133B MET* 3.4 29.2 - - + -
197B LEU* 3.1 13.9 - - + +
199B ILE* 4.2 13.0 - - + -
228B ALA* 3.9 16.8 - - + +
231B SER* 4.0 8.7 - - - +
232B VAL* 3.8 22.9 - - + -
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Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B MET* 3.3 15.5 - - + +
20B GLY 4.3 0.8 - - - +
62B HIS* 3.1 32.2 + - + +
85B ILE* 4.1 4.6 - - + +
86B ILE* 1.3 74.9 - - - +
88B VAL* 1.3 60.9 + - - +
89B GLY* 3.7 12.8 - - - -
90B SER 3.6 12.3 + - - -
179B GLU* 3.1 23.6 + - - +
181B GLU* 3.4 20.6 + - - +
182B ALA 4.6 1.6 - - - +
185B ILE* 4.7 11.4 - - + +
197B LEU 2.7 9.6 + - - +
198B THR* 3.3 27.0 + - + -
199B ILE 2.8 29.6 + - - -
200B CYS* 3.6 12.1 - - - -
246B FMB 3.2 12.3 + - - -
249B PO4 2.7 31.9 + - - -
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU* 4.5 5.6 - - + -
18B MET 3.1 12.5 + - - +
19B PRO* 3.4 35.0 - - + +
28B ILE* 4.1 10.1 - - + -
86B ILE* 4.1 8.5 - - + +
87B ARG* 1.3 79.2 - - - +
89B GLY* 1.3 58.0 + - - +
199B ILE* 3.4 6.1 - - + +
221B PHE* 4.8 3.7 - - + -
224B MET* 3.9 20.4 - - + +
225B ILE* 3.7 30.3 - - + -
228B ALA* 3.9 27.6 - - + -
249B PO4 4.1 0.5 + - - -
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Residues in contact with GLY 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ARG* 3.7 9.4 - - - +
88B VAL* 1.3 75.6 - - - +
90B SER* 1.3 61.3 + - - -
199B ILE 3.1 8.5 + - - -
200B CYS* 3.2 6.3 - - - -
201B THR* 3.1 22.0 + - - -
221B PHE* 5.3 5.3 - - - -
224B MET* 3.4 11.2 - - - +
249B PO4 3.2 21.1 - - - -
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Residues in contact with SER 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ARG* 3.6 10.9 + - - -
89B GLY* 1.3 75.6 - - - -
91B CYS* 1.3 66.5 + - - +
179B GLU* 3.7 1.4 - - - +
200B CYS* 4.3 1.1 - - - -
201B THR* 3.4 9.9 - - - -
203B SER* 3.5 21.3 + - - -
221B PHE* 6.4 1.3 - - - -
246B FMB 2.8 34.9 + - - -
249B PO4 2.8 24.7 + - - -
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Residues in contact with CYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B SER* 1.3 78.0 - - - +
92B GLY* 1.3 59.5 + - - +
104B VAL* 4.7 5.6 - - - -
153B LEU* 4.9 0.9 - - + -
177B GLY* 3.7 20.4 - - - -
178B VAL 3.1 24.2 - - - +
179B GLU* 4.2 4.3 - - + -
200B CYS* 3.6 24.7 - - + -
201B THR 3.3 4.9 + - - -
202B VAL* 3.4 28.7 - - - -
203B SER* 3.0 26.7 + - - -
246B FMB 3.5 9.6 - - - -
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Residues in contact with GLY 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B CYS* 1.3 75.0 - - - +
93B ALA* 1.3 61.0 - - - -
177B GLY* 3.4 4.8 - - - -
178B VAL* 2.7 39.8 + - - +
202B VAL* 4.6 0.7 - - - -
204B ASP* 2.9 21.5 - - - -
205B HIS* 5.1 0.2 - - - -
246B FMB 3.3 13.3 + - - -
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Residues in contact with ALA 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B GLY* 1.3 72.9 - - - -
94B VAL* 1.3 63.2 + - - +
98B VAL* 3.6 27.6 - - + -
176B LEU 4.1 7.0 - - - +
202B VAL* 3.7 12.6 - - + -
204B ASP 2.9 7.9 + - - -
205B HIS* 3.4 28.0 + - + +
206B ILE* 3.1 27.2 + - - +
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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