Contacts of the strand formed by residues 113 - 120 (chain A) in PDB entry 1P01
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 THR 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ALA* 3.1 32.7 + - + +
16A ILE* 2.7 34.4 + - - -
50A LYS* 4.8 0.7 - - - +
111A ALA 4.3 5.0 + - - -
112A GLN* 1.3 72.6 - - - +
114A LEU* 1.3 61.7 + - - +
115A LEU* 3.9 23.2 - - + +
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Residues in contact with LEU 114 (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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16A ILE* 4.1 7.6 - - + -
47A SER* 4.0 15.3 - - - +
48A VAL* 3.3 40.8 - - - +
50A LYS* 3.8 31.9 - - + +
51A GLY 3.7 9.4 - - - +
108A LEU* 3.7 30.5 - - + -
112A GLN* 4.0 1.5 + - + -
113A THR* 1.3 76.6 - - - +
115A LEU* 1.3 69.5 + - - +
116A PRO* 4.5 1.4 - - - +
242A VAL* 4.0 16.0 - - + +
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Residues in contact with LEU 115 (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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15A ASN* 3.7 37.9 - - + +
16A ILE 3.2 14.4 + - - +
17A VAL* 4.1 15.5 - - + -
47A SER* 3.0 20.1 + - - -
113A THR* 3.9 19.1 - - + +
114A LEU* 1.3 82.9 - - - +
116A PRO* 1.3 70.7 - - + +
117A ARG* 2.9 38.0 + - + +
242A VAL* 4.0 4.3 - - - -
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Residues in contact with PRO 116 (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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114A LEU 4.5 0.9 - - - +
115A LEU* 1.3 90.9 - - + +
117A ARG* 1.3 81.8 + - + +
123A THR* 3.5 4.0 - - - +
124A VAL* 2.7 27.1 + - + +
242A VAL* 3.6 19.9 - - + +
243A THR* 3.3 35.7 - - - +
244A GLY* 3.4 18.2 - - - +
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Residues in contact with ARG 117 (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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17A VAL* 3.5 9.5 - - + +
18A GLY* 2.7 28.2 + - - -
46A PHE* 5.9 0.5 - - - -
115A LEU* 2.9 32.8 + - + +
116A PRO* 1.3 104.0 + - - +
118A VAL* 1.3 60.7 - - - +
121A PHE* 3.9 42.0 - - + -
122A VAL 3.2 8.5 - - - +
123A THR* 4.2 18.4 + - - +
124A VAL* 4.0 2.6 - - - +
244A GLY* 5.8 0.6 + - - -
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Residues in contact with VAL 118 (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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17A VAL* 3.9 2.7 - - - -
18A GLY* 3.5 7.0 - - - +
46A PHE* 3.8 18.8 - - + -
117A ARG* 1.3 80.0 - - - +
119A ALA* 1.3 67.6 + - - +
121A PHE* 3.4 4.5 - - - -
122A VAL* 2.8 38.8 + - + +
124A VAL* 4.1 3.8 - - + -
139A SER* 3.5 28.0 - - - -
157A TYR* 4.5 4.5 - - + -
198A SER* 3.6 30.5 - - - +
200A ILE* 4.0 24.5 - - + -
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Residues in contact with ALA 119 (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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17A VAL* 3.6 13.3 - - + +
18A GLY 2.8 18.2 + - - +
19A GLY* 4.9 2.7 - - - -
29A ILE* 4.7 10.8 - - + -
118A VAL* 1.3 73.9 - - - +
120A ASN* 1.3 76.3 + - - +
121A PHE* 4.5 3.8 - - + -
139A SER* 2.8 26.1 + - - +
157A TYR* 3.3 11.8 - - - +
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Residues in contact with ASN 120 (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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118A VAL 3.7 0.2 + - - -
119A ALA* 1.3 73.3 - - - +
120A GLY* 1.3 108.4 + - + +
121A PHE 4.7 1.9 + - - +
122A VAL* 4.3 12.6 - - + +
157A TYR* 3.4 47.0 - - + +
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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