Contacts of the strand formed by residues 103 - 111 (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 VAL 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ARG 4.1 7.6 - - - +
102A ASP* 1.3 74.9 - - - +
104A VAL* 1.3 65.0 + - - +
105A ILE* 4.8 1.6 - - + -
146A ILE* 3.9 22.9 - - + -
147A ASP 4.1 12.1 + - - +
148A ALA* 3.3 15.2 - - + -
149A ARG* 2.9 25.6 + - - +
199A ILE* 3.9 25.6 - - + -
200A CYS 3.6 5.2 - - - +
201A THR* 4.4 13.0 - - + -
220A THR* 5.2 3.6 - - + -
223A ASP* 5.6 4.7 - - + -
224A MET* 5.6 1.3 - - + -
227A ILE* 4.2 20.4 - - + -
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Residues in contact with VAL 104 (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* 4.8 5.8 - - - -
98A VAL* 4.7 0.9 - - + -
102A ASP 4.6 1.1 - - - +
103A VAL* 1.3 78.4 - - - +
105A ILE* 1.3 69.1 + - - +
106A GLY 4.2 0.7 + - - -
149A ARG* 3.4 18.6 - - + -
151A GLY 5.8 0.2 - - - +
153A LEU* 4.0 21.4 - - + +
176A LEU* 3.4 46.7 - - + +
199A ILE* 3.5 3.5 - - - +
200A CYS* 2.7 41.9 + - + +
202A VAL* 4.1 24.0 - - + -
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Residues in contact with ILE 105 (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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103A VAL* 4.8 1.8 - - + -
104A VAL* 1.3 81.9 - - - +
106A GLY* 1.3 61.9 + - - +
107A MET 3.3 2.6 + - - -
134A VAL* 4.2 19.7 - - + -
137A ALA* 3.8 18.6 - - + +
138A VAL* 3.8 24.5 - - + +
141A ALA* 5.5 0.7 - - + -
148A ALA* 3.6 27.4 - - + -
149A ARG 2.7 14.3 + - - +
150A VAL* 3.3 6.0 - - + -
151A GLY 3.0 25.5 + - - -
197A LEU* 3.6 29.6 - - + -
198A THR 4.0 3.6 - - - +
199A ILE* 4.4 15.3 - - + -
227A ILE* 5.7 1.6 - - + -
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Residues in contact with GLY 106 (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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104A VAL 4.1 1.0 + - - -
105A ILE* 1.3 73.1 - - - +
107A MET* 1.3 64.5 + - - -
108A GLY 3.0 4.2 + - - -
129A ALA* 3.6 5.0 - - - +
151A GLY 3.4 8.1 - - - -
153A LEU* 3.8 29.2 - - - +
186A TYR* 2.6 25.3 + - - -
197A LEU* 4.1 1.4 - - - +
198A THR 3.2 13.8 + - - -
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Residues in contact with MET 107 (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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105A ILE* 3.3 4.6 + - - +
106A GLY* 1.3 73.2 - - - -
108A GLY* 1.3 57.5 + - - +
128A ILE* 3.4 13.4 - - + +
129A ALA* 2.9 24.2 + - + +
131A PHE* 5.8 9.6 - - + -
134A VAL* 4.4 22.4 - - + -
150A VAL* 3.8 25.5 - - + +
151A GLY* 2.9 13.6 + - - +
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Residues in contact with GLY 108 (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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106A GLY* 3.9 3.5 - - - -
107A MET* 1.3 82.1 - - - +
109A ALA* 1.3 62.6 + - - +
127A ALA 3.4 10.8 - - - -
128A ILE* 4.2 6.7 - - - -
151A GLY 3.4 5.5 + - - +
152A ASN* 3.1 16.1 - - - +
153A LEU* 2.9 22.9 + - - +
186A TYR* 4.2 3.4 - - - -
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A GLY* 1.3 75.2 - - - +
110A CYS* 1.3 62.8 + - - +
111A THR* 4.9 1.4 - - - +
127A ALA* 2.9 27.4 + - - +
152A ASN* 3.4 1.2 + - - -
153A LEU* 3.3 8.7 - - + +
155A SER* 4.1 3.8 - - - +
182A ALA* 3.6 17.5 - - + -
183A ALA* 3.5 34.1 - - + +
186A TYR* 3.9 7.2 - - + -
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Residues in contact with CYS 110 (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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109A ALA* 1.3 74.7 - - - +
111A THR* 1.3 59.8 + - - +
152A ASN* 3.7 32.1 - - - -
153A LEU 2.7 14.1 + - - +
154A PHE* 3.8 17.3 - - + -
155A SER* 2.7 30.5 + - - -
175A ILE* 4.4 12.1 - - - -
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Residues in contact with THR 111 (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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66A ILE* 3.8 5.2 - - + +
109A ALA 4.9 0.9 - - - +
110A CYS* 1.3 81.1 - - - +
112A ASP* 1.3 67.3 + - - +
113A SER* 3.0 33.2 + - - +
115A VAL* 6.2 1.3 - - + -
116A ASN* 4.9 11.9 - - + +
117A ARG* 5.8 1.7 + - - -
127A ALA* 6.2 0.4 - - + -
154A PHE* 4.0 11.6 - - - -
155A SER 2.8 17.6 + - - -
183A ALA* 3.7 21.8 - - + -
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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