Contacts of the strand formed by residues 103 - 111 (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 VAL 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B ARG 3.7 1.1 + - - +
102B ASP* 1.3 73.1 - - - +
104B VAL* 1.3 61.6 + - - +
105B ILE* 4.8 0.7 - - + -
146B ILE* 4.3 20.9 - - + -
147B ASP 5.2 4.2 + - - +
148B ALA* 3.4 22.4 - - + -
149B ARG* 3.0 26.5 + - - +
199B ILE* 3.8 25.8 - - + -
200B CYS 3.5 3.8 - - - +
201B THR* 4.2 8.3 - - - +
220B THR* 4.0 26.5 - - + +
223B ASP* 5.5 0.9 - - + -
224B MET* 4.8 4.7 - - + +
227B ILE* 4.3 17.9 - - + -
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Residues in contact with VAL 104 (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* 4.7 2.2 - - - -
98B VAL* 5.0 0.7 - - + -
102B ASP 4.3 0.7 - - - +
103B VAL* 1.3 77.2 - - - +
105B ILE* 1.3 68.3 + - - +
106B GLY* 4.1 0.9 + - - -
149B ARG* 3.5 17.5 - - - -
151B GLY 5.8 0.2 - - - +
153B LEU* 3.8 24.2 - - + +
176B LEU* 3.6 44.9 - - + +
177B GLY 4.6 0.2 - - - +
199B ILE* 3.4 4.7 - - - +
200B CYS* 2.7 46.4 + - + +
202B VAL* 3.9 26.5 - - + -
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Residues in contact with ILE 105 (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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103B VAL* 5.3 0.7 - - + -
104B VAL* 1.3 78.7 - - - +
106B GLY* 1.3 61.5 + - - +
107B MET 3.1 3.1 + - - -
134B VAL* 4.1 20.9 - - + -
137B ALA* 3.7 27.1 - - + +
138B VAL* 4.1 19.3 - - + +
148B ALA* 3.9 25.6 - - + -
149B ARG 2.7 14.0 + - - +
150B VAL* 3.4 5.9 - - + -
151B GLY 3.1 24.8 + - - +
197B LEU* 3.9 25.8 - - + -
198B THR 4.0 4.0 - - - +
199B ILE* 4.1 16.4 - - + -
227B ILE* 5.3 2.5 - - + -
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Residues in contact with GLY 106 (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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104B VAL 4.0 1.4 + - - -
105B ILE* 1.3 71.6 - - - +
107B MET* 1.3 63.0 + - - -
108B GLY 3.0 3.9 + - - -
129B ALA* 3.6 4.7 - - - +
151B GLY 3.4 8.5 - - - -
153B LEU* 3.7 30.6 - - - +
186B TYR* 2.5 25.8 + - - -
197B LEU* 4.3 1.2 - - - +
198B THR 3.1 13.7 + - - -
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Residues in contact with MET 107 (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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105B ILE 3.1 4.8 + - - -
106B GLY* 1.3 74.1 - - - -
108B GLY* 1.3 59.5 + - - +
128B ILE* 3.3 10.4 - - + +
129B ALA* 2.9 30.6 + - - +
131B PHE* 6.2 4.0 - - + -
134B VAL* 4.4 14.1 - - + -
150B VAL* 3.7 28.9 - - + +
151B GLY* 2.9 28.2 + - - +
152B ASN* 5.5 0.4 - - - +
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Residues in contact with GLY 108 (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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106B GLY* 3.8 5.4 - - - -
107B MET* 1.3 87.2 - - - +
109B ALA* 1.3 61.9 + - - +
127B ALA 3.4 10.5 - - - -
128B ILE* 4.2 6.1 - - - -
151B GLY 3.3 2.6 + - - +
152B ASN* 3.0 17.3 - - - +
153B LEU* 3.0 21.1 + - - +
186B TYR* 4.1 3.1 - - - -
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Residues in contact with ALA 109 (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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108B GLY* 1.3 74.8 - - - +
110B CYS* 1.3 63.6 + - - +
111B THR* 4.1 1.4 + - - +
127B ALA* 2.9 27.3 + - - +
152B ASN* 3.4 1.8 + - - -
153B LEU* 3.3 8.3 - - + +
155B SER* 4.0 3.1 - - - +
182B ALA* 3.6 17.7 - - + -
183B ALA* 3.5 34.8 - - + +
186B TYR* 3.9 8.1 - - + -
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Residues in contact with CYS 110 (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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109B ALA* 1.3 75.1 - - - +
111B THR* 1.3 57.3 + - - +
152B ASN* 3.7 29.6 - - - -
153B LEU 2.6 14.3 + - - +
154B PHE* 3.7 18.8 - - + -
155B SER* 2.6 34.2 + - - -
175B ILE* 4.2 14.4 - - - -
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Residues in contact with THR 111 (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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66B ILE* 3.7 3.6 - - - +
109B ALA 5.0 0.9 - - - +
110B CYS* 1.3 79.3 - - - +
112B ASP* 1.3 67.4 + - - +
113B SER* 2.8 35.8 + - - +
115B VAL* 5.8 1.3 - - + -
116B ASN* 4.7 14.1 - - + +
117B ARG* 6.0 0.2 + - - -
154B PHE* 4.0 9.6 - - - -
155B SER 2.9 17.0 + - - -
183B ALA* 3.5 22.9 - - + -
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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