Contacts of the strand formed by residues 195 - 205 (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 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B LYS* 3.0 10.2 + - + +
84B LYS* 3.3 27.2 - - + +
85B ILE* 3.0 23.9 + - - +
130B ASP* 3.3 36.3 + - + +
132B ASP* 5.4 6.3 + - - +
133B MET* 3.6 15.0 - - - +
189B ALA* 4.4 1.1 - - - -
194B ALA* 1.3 84.4 - - - +
196B ALA* 1.3 62.3 + - - +
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Residues in contact with ALA 196 (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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85B ILE* 3.2 12.8 - - + +
129B ALA* 3.4 6.8 - - - -
130B ASP* 3.1 26.3 + - - +
133B MET* 4.0 2.7 - - - -
185B ILE* 3.6 31.2 - - + -
186B TYR* 4.0 9.6 - - + -
189B ALA* 3.8 19.4 - - + +
195B LYS* 1.3 77.3 - - - +
197B LEU* 1.3 61.9 + - - +
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Residues in contact with LEU 197 (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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85B ILE 2.9 5.5 + - - +
86B ILE* 3.1 15.4 - - + +
87B ARG 2.7 23.9 + - - -
105B ILE* 3.9 15.3 - - + -
106B GLY 4.3 2.2 - - - +
129B ALA* 3.7 8.3 - - + -
133B MET* 3.5 42.2 - - + +
134B VAL* 3.6 30.7 - - + +
137B ALA* 3.8 18.2 - - + -
185B ILE* 5.9 0.7 - - - +
186B TYR* 4.0 4.0 - - - -
196B ALA* 1.3 78.0 - - - +
198B THR* 1.3 74.4 + - - +
199B ILE* 4.1 15.0 - - + -
231B SER* 5.3 1.6 - - - +
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Residues in contact with THR 198 (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* 3.3 30.0 + - + -
105B ILE* 4.0 1.0 - - - -
106B GLY* 3.1 23.9 + - - -
153B LEU* 3.2 22.0 - - - +
182B ALA* 3.6 23.3 - - + +
185B ILE* 5.0 4.9 - - + -
186B TYR* 3.2 33.9 + - + +
197B LEU* 1.3 78.6 - - - +
199B ILE* 1.3 62.2 + - - +
200B CYS* 4.2 7.8 - - - -
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Residues in contact with ILE 199 (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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86B ILE* 4.2 13.7 - - + -
87B ARG 2.8 10.2 + - - +
88B VAL* 3.4 3.0 - - + -
89B GLY 3.1 22.7 + - - -
103B VAL* 3.8 23.8 - - + -
104B VAL 3.4 11.4 - - - +
105B ILE* 4.1 10.5 - - + -
137B ALA* 4.3 7.2 - - + -
197B LEU* 4.1 21.1 - - + -
198B THR* 1.3 78.3 - - - +
200B CYS* 1.3 66.1 + - - +
224B MET* 3.5 18.9 - - + +
227B ILE* 4.2 22.7 - - + -
228B ALA* 4.2 21.8 - - + +
231B SER* 5.4 0.2 - - - +
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Residues in contact with CYS 200 (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 27.8 - - - -
89B GLY 3.2 7.0 - - - +
90B SER 4.0 8.1 - - - -
91B CYS* 3.6 23.1 - - + -
103B VAL* 3.5 4.5 - - - +
104B VAL* 2.7 46.7 + - + +
153B LEU* 4.6 7.2 - - + +
179B GLU* 4.1 14.8 - - - -
198B THR* 4.2 12.1 - - - -
199B ILE* 1.3 79.1 - - - +
201B THR* 1.3 61.4 + - - +
202B VAL 4.1 0.2 - - - -
224B MET* 4.0 2.5 - - - -
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Residues in contact with THR 201 (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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89B GLY 3.1 10.1 + - - -
90B SER* 3.4 7.3 - - - -
91B CYS* 3.3 15.8 + - - -
101B ARG* 4.0 13.0 - - + -
102B ASP 3.4 4.9 - - - +
103B VAL* 4.2 3.1 - - - +
200B CYS* 1.3 73.5 + - - +
202B VAL* 1.3 67.9 + - - +
203B SER* 3.1 6.2 + - - -
217B ARG* 5.3 5.2 - - + +
220B THR* 3.6 37.1 + - + +
221B PHE* 4.2 7.9 - - + +
224B MET* 3.5 31.5 - - - +
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Residues in contact with VAL 202 (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* 3.4 15.5 - - - +
93B ALA* 3.7 17.7 - - + +
98B VAL* 3.9 22.2 - - + -
99B LYS 3.8 16.2 - - - +
100B LEU* 3.8 9.0 - - + +
101B ARG* 2.9 24.9 + - - +
102B ASP* 3.0 20.0 + - + +
104B VAL* 3.9 15.9 - - + -
176B LEU 5.0 0.7 - - - +
201B THR* 1.3 72.4 - - - +
203B SER* 1.3 57.3 + - - +
204B ASP 3.2 26.0 - - - +
205B HIS* 5.0 0.2 - - + -
217B ARG* 6.1 0.7 - - - +
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Residues in contact with SER 203 (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* 3.5 26.8 + - - -
91B CYS 3.0 11.6 + - - -
100B LEU* 4.3 11.2 - - - +
201B THR* 3.1 3.4 + - - -
202B VAL* 1.3 73.3 - - - +
204B ASP* 1.3 68.6 + - - +
217B ARG* 5.5 17.8 + - - +
246B FMB 3.9 5.4 + - - -
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Residues in contact with ASP 204 (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 3.4 2.6 - - - +
92B GLY* 2.9 25.3 - - - -
93B ALA 2.9 19.5 + - - -
100B LEU* 3.9 9.0 - - - -
159B PHE* 5.8 3.1 - - - -
202B VAL* 3.2 10.1 - - - +
203B SER* 1.3 84.0 + - - +
205B HIS* 1.3 63.8 + - - +
208B THR* 6.0 3.1 - - + +
246B FMB 3.4 16.9 + - - +
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Residues in contact with HIS 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLY* 5.1 0.2 - - - -
93B ALA* 3.4 25.5 - - + +
94B VAL 4.1 2.0 - - - -
95B LEU 2.6 31.7 + - - -
96B PRO* 4.1 8.9 + - + +
98B VAL 2.9 24.8 + - - -
99B LYS* 4.9 3.6 - - - -
100B LEU* 3.9 15.5 - - + +
204B ASP* 1.3 79.8 - - - +
206B ILE* 1.3 102.1 + - + +
207B ARG* 3.3 10.9 + - + +
208B THR* 3.4 21.8 + - + +
209B HIS* 6.2 1.6 - - - +
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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