Contacts of the strand formed by residues 103 - 111 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ARG 4.2 8.1 - - - +
102C ASP* 1.3 77.2 - - - +
104C VAL* 1.3 66.9 + - - +
105C ILE* 4.9 1.3 - - + -
146C ILE* 4.4 14.4 - - + -
147C ASP 3.7 19.7 + - - +
148C ALA* 3.1 12.8 - - + -
149C ARG* 3.1 22.5 + - - +
199C ILE* 3.9 25.6 - - + -
200C CYS 3.4 4.0 - - - +
201C THR* 4.7 6.1 - - - +
220C THR* 4.6 7.6 - - + +
223C ASP* 4.6 14.4 - - + -
224C MET* 4.7 3.8 - - - +
227C ILE* 4.1 17.0 - - + -
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Residues in contact with VAL 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C CYS* 5.1 2.0 - - - -
98C VAL* 5.4 1.6 - - + -
102C ASP 4.9 0.7 - - - -
103C VAL* 1.3 79.2 - - - +
105C ILE* 1.3 70.7 + - - +
106C GLY* 4.0 0.6 + - - -
149C ARG* 3.5 14.4 - - + +
153C LEU* 3.9 21.9 - - + +
176C LEU* 3.4 50.9 - - + +
198C THR 4.0 0.3 - - - +
199C ILE* 3.4 6.1 - - - +
200C CYS* 2.8 41.1 + - + +
202C VAL* 4.2 22.9 - - + -
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Residues in contact with ILE 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C VAL* 4.9 1.1 - - + -
104C VAL* 1.3 79.1 - - - +
106C GLY* 1.3 60.9 + - - +
107C MET 3.3 2.4 + - - -
134C VAL* 3.9 20.0 - - + -
137C ALA* 4.0 22.4 - - + +
138C VAL* 3.9 25.1 - - + -
148C ALA* 4.0 24.2 - - + -
149C ARG 2.8 13.5 + - - +
150C VAL* 3.3 8.5 - - + +
151C GLY 2.9 26.5 + - - -
197C LEU* 3.8 30.1 - - + -
198C THR 3.8 3.8 - - - +
199C ILE* 4.7 12.1 - - + -
227C ILE* 5.4 3.4 - - + -
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Residues in contact with GLY 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C VAL 4.0 1.2 - - - -
105C ILE* 1.3 73.1 - - - +
107C MET* 1.3 62.9 + - - -
108C GLY 3.1 9.2 - - - -
129C ALA* 3.6 5.4 - - - +
151C GLY 3.2 9.4 - - - -
153C LEU* 4.1 19.4 - - - +
186C TYR* 2.7 25.7 + - - -
197C LEU* 4.0 2.6 - - - +
198C THR 3.0 16.0 + - - -
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Residues in contact with MET 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ILE 3.3 4.6 + - - -
106C GLY* 1.3 72.4 - - - -
108C GLY* 1.3 57.6 + - - +
128C ILE* 3.3 10.2 - - + +
129C ALA* 2.9 34.1 + - - +
131C PHE* 5.6 11.2 - - - -
134C VAL* 4.4 18.8 - - + -
150C VAL* 4.0 25.8 - - + +
151C GLY* 2.9 15.7 + - - +
186C TYR* 4.7 0.2 - - - -
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Residues in contact with GLY 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C GLY* 3.8 7.1 - - - -
107C MET* 1.3 82.9 - - - +
109C ALA* 1.3 62.3 + - - +
127C ALA 3.4 9.4 - - - -
128C ILE* 4.3 5.8 - - - -
151C GLY 3.3 7.1 + - - +
152C ASN* 2.9 17.7 - - - +
153C LEU* 3.1 18.9 + - - +
186C TYR* 4.4 2.6 - - - -
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Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C GLY* 1.3 75.8 - - - +
110C CYS* 1.3 63.9 + - - +
111C THR* 5.0 1.2 - - - +
127C ALA* 3.0 28.1 + - - +
152C ASN* 3.1 3.5 + - - -
153C LEU* 3.2 10.5 - - + +
155C SER* 4.2 2.9 - - - +
182C ALA* 3.9 15.7 - - + -
183C ALA* 3.7 31.5 - - + +
186C TYR* 4.0 8.5 - - + -
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Residues in contact with CYS 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C ALA* 1.3 76.3 - - - +
111C THR* 1.3 58.4 + - - +
152C ASN* 3.9 29.8 - - - -
153C LEU 2.7 10.8 + - - +
154C PHE* 3.5 22.0 - - + -
155C SER* 2.7 30.7 + - - -
175C ILE* 4.5 11.7 - - - -
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Residues in contact with THR 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ILE* 3.8 5.9 - - - +
109C ALA 5.0 1.6 - - - +
110C CYS* 1.3 79.3 - - - +
112C ASP* 1.3 64.4 + - - +
113C SER* 3.1 33.6 + - - +
116C ASN* 4.6 15.9 - - + +
127C ALA* 6.2 0.2 - - + -
154C PHE* 4.0 9.8 - - - -
155C SER 2.9 19.5 + - - -
183C ALA* 3.5 21.1 - - + -
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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