Contacts of the strand formed by residues 195 - 204 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A ILE* 5.9 0.3 - - - +
83A LYS* 2.9 15.2 + - + +
84A LYS* 3.3 23.0 - - + +
85A ILE* 2.9 24.8 + - - +
130A ASP* 3.6 33.7 + - + +
132A ASP* 5.6 4.4 + - - +
133A MET* 3.7 16.4 - - - -
189A ALA* 4.3 1.0 - - - +
194A ALA* 1.3 80.6 - - - +
196A ALA* 1.3 63.9 + - - +
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Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ILE* 3.2 12.1 - - + +
129A ALA* 3.3 6.6 - - - +
130A ASP* 3.1 26.9 + - - +
133A MET* 3.9 5.3 - - - +
185A ILE* 3.6 30.1 - - + -
186A TYR* 3.9 11.4 - - + -
189A ALA* 3.9 16.8 - - + +
195A LYS* 1.3 78.4 - - - +
197A LEU* 1.3 63.7 + - - +
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Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ILE 2.9 6.1 + - - +
86A ILE* 3.1 11.7 - - + +
87A ARG* 2.8 23.7 + - - +
105A ILE* 3.6 24.5 - - + -
106A GLY 4.1 3.6 - - - +
129A ALA* 3.9 7.2 - - + -
133A MET* 3.4 45.8 - - + +
134A VAL* 3.9 19.7 - - + -
137A ALA* 3.8 16.8 - - + -
185A ILE* 5.9 0.6 - - - +
186A TYR* 3.7 4.9 - - - -
196A ALA* 1.3 77.7 - - - +
198A THR* 1.3 75.1 + - - +
199A ILE* 4.0 14.6 - - + -
231A SER* 5.4 2.0 - - - +
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Residues in contact with THR 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ARG* 3.2 33.6 + - + -
104A VAL 4.3 0.2 - - - +
105A ILE* 4.0 0.2 - - - -
106A GLY 3.2 22.5 + - - -
153A LEU* 3.0 27.2 - - - +
182A ALA* 3.6 29.7 - - + +
185A ILE* 4.5 5.8 - - + -
186A TYR* 3.2 19.0 + - + +
197A LEU* 1.3 81.8 - - - +
199A ILE* 1.3 63.1 + - - +
200A CYS* 4.3 4.1 + - - -
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Residues in contact with ILE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ILE* 4.2 14.4 - - + -
87A ARG 2.8 9.6 + - - +
88A VAL* 3.4 5.3 - - + -
89A GLY 3.0 22.5 + - - -
103A VAL* 3.9 22.2 - - + -
104A VAL 3.5 10.1 - - - +
105A ILE* 4.4 10.3 - - + -
137A ALA* 4.0 23.3 - - + -
197A LEU* 4.0 17.3 - - + -
198A THR* 1.3 78.4 - - - +
200A CYS* 1.3 66.0 + - - +
224A MET* 3.5 19.7 - - + +
227A ILE* 4.2 17.7 - - + -
228A ALA* 4.3 13.7 - - + -
231A SER* 5.3 0.7 - - - +
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Residues in contact with CYS 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ARG* 4.0 25.4 - - - -
89A GLY 3.1 9.9 - - - +
90A SER 4.1 5.6 - - - -
91A CYS* 3.7 23.1 - - + -
103A VAL* 3.6 3.8 - - - +
104A VAL* 2.7 43.5 + - + +
153A LEU* 4.6 6.7 - - + -
179A GLU* 4.3 14.6 - - - -
198A THR* 4.3 13.7 - - - -
199A ILE* 1.3 82.4 - - - +
201A THR* 1.3 63.1 + - - +
224A MET* 4.1 1.1 - - - -
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Residues in contact with THR 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLY 2.9 11.3 + - - -
90A SER* 3.3 5.7 - - - -
91A CYS* 3.1 16.6 + - - -
102A ASP 3.3 5.6 - - - -
103A VAL* 4.4 12.6 - - + -
200A CYS* 1.3 76.4 - - - +
202A VAL* 1.3 65.3 + - - +
203A SER 3.1 4.2 + - - -
217A ARG* 3.4 14.3 + - - -
220A THR* 3.3 35.1 - - + +
221A PHE* 5.1 2.3 - - - +
224A MET* 3.7 34.6 - - + +
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Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A CYS* 3.5 20.6 - - - +
93A ALA* 3.9 15.0 - - + -
98A VAL* 3.6 25.6 - - + -
99A LYS 3.5 21.8 - - - +
100A LEU* 3.6 9.4 - - + -
101A ARG* 2.7 28.3 + - - +
102A ASP* 2.9 20.5 + - + +
104A VAL* 4.1 7.6 - - + -
176A LEU 5.0 0.4 - - - +
201A THR* 1.3 68.6 - - - +
203A SER* 1.3 59.1 + - - +
204A ASP 3.3 25.4 - - - +
205A HIS* 5.2 0.7 - - + -
217A ARG* 3.5 5.8 + - - -
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Residues in contact with SER 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A SER* 3.6 16.0 + - - -
91A CYS 2.9 14.7 + - - -
100A LEU* 4.0 15.0 - - - +
201A THR 3.1 2.0 + - - -
202A VAL* 1.3 73.7 - - - +
204A ASP* 1.3 66.1 + - - +
217A ARG* 3.6 24.2 + - - +
245A FMB 3.4 17.7 + - - -
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Residues in contact with ASP 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A CYS 3.4 2.3 - - - +
92A GLY* 3.0 20.6 - - - -
93A ALA 3.0 17.7 + - - -
100A LEU* 4.3 8.5 - - - -
159A PHE* 5.8 2.6 - - - -
202A VAL* 3.3 9.8 - - - +
203A SER* 1.3 84.3 + - - +
205A HIS* 1.3 63.5 + - - +
245A FMB 3.2 16.6 + - - +
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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