Contacts of the strand formed by residues 112 - 119 (chain A) in PDB entry 1V9P
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 LEU 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PRO 4.1 0.2 + - - -
111A PHE* 1.3 75.3 - - - +
113A TYR* 1.3 80.1 + - - +
260A LYS* 4.2 28.7 - - + +
261A ALA 3.4 21.3 - - - +
262A LEU* 3.9 13.0 - - + +
292A LEU* 3.9 7.1 - - - +
293A ASP* 3.1 34.3 + - + +
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Residues in contact with TYR 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 6.1 0.7 - - + -
97A PHE* 4.3 12.9 - + - -
98A GLU* 3.0 45.8 - - + +
101A LEU* 3.3 17.7 - - + +
111A PHE* 3.0 27.8 - - + +
112A LEU* 1.3 84.2 - - - +
114A THR* 1.3 68.3 + - - +
115A VAL* 4.7 1.3 - - + -
260A LYS* 3.5 4.3 - - - +
261A ALA 2.7 31.2 + - - +
263A GLY* 4.2 4.3 - - - -
264A ALA* 4.3 1.6 - - - -
267A VAL* 3.4 29.4 - - + -
290A VAL* 4.0 13.7 - - + -
291A LYS 3.3 7.6 - - - +
292A LEU* 3.3 42.0 - - + -
293A ASP* 3.9 3.8 - - - +
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Residues in contact with THR 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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113A TYR* 1.3 72.7 + - - +
115A VAL* 1.3 66.8 + - - +
116A GLU* 4.1 8.1 - - - +
240A GLN* 3.5 27.4 - - + -
241A TYR* 3.5 15.4 + - + +
244A LEU* 4.0 19.5 - - + -
258A TYR* 4.5 6.7 - - + -
259A GLU 3.6 7.0 - - - +
260A LYS* 4.4 1.6 - - - +
289A VAL 3.2 3.1 - - - +
291A LYS* 2.9 32.4 + - - +
293A ASP* 2.6 29.6 + - - -
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Residues in contact with VAL 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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113A TYR* 4.7 1.8 - - + -
114A THR* 1.3 78.6 - - - +
116A GLU* 1.3 63.8 + - - +
258A TYR* 3.1 2.1 - - - +
259A GLU* 2.6 47.3 + - - +
261A ALA* 3.8 28.0 - - + -
267A VAL* 4.3 24.0 - - + +
270A VAL* 3.9 27.4 - - + -
271A TYR 5.5 0.2 - - - +
274A PHE* 4.8 1.8 - - + -
288A VAL* 4.0 28.9 - - + -
289A VAL 3.5 7.4 - - - +
290A VAL* 4.9 2.5 - - - +
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Residues in contact with GLU 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 THR* 4.1 6.1 - - - +
115A VAL* 1.3 76.0 - - - +
117A HIS* 1.3 61.0 - - - +
226A TYR* 3.6 7.1 - - - +
240A GLN* 3.1 23.7 - - - +
244A LEU* 3.6 13.6 - - - +
256A HIS* 3.1 19.7 + - + -
257A GLY 3.0 13.5 - - - +
258A TYR* 3.4 9.9 - - + +
274A PHE* 4.1 6.7 - - - -
288A VAL* 3.3 6.6 - - - +
289A VAL* 2.9 39.7 + - + +
291A LYS* 4.1 7.8 - - + +
700A AMP 2.7 39.5 + - - +
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Residues in contact with HIS 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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116A GLU* 1.3 77.4 - - - +
118A LYS* 1.3 60.8 + - - +
119A VAL 3.5 2.4 + - - -
256A HIS* 3.7 7.1 - - + -
257A GLY* 2.8 46.5 + - - +
274A PHE* 3.4 47.8 + + + +
277A GLN* 5.4 5.4 - - - +
281A LEU* 3.2 36.6 - - + +
283A PHE* 4.3 15.3 - - + -
285A ALA* 4.7 7.0 - - + -
287A GLY 4.3 4.9 - - - -
288A VAL* 5.3 0.2 - - + -
316A PHE* 5.7 3.4 - + - -
700A AMP 3.4 19.6 + - - -
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Residues in contact with LYS 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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87A ASN* 4.3 2.0 - - - +
117A HIS* 1.3 71.4 - - - +
119A VAL* 1.3 59.3 + - - +
120A ASP* 3.0 11.1 + - - -
285A ALA* 3.3 20.6 - - - +
286A ASP* 3.8 4.6 + - - +
287A GLY* 3.3 25.2 + - - +
288A VAL 3.3 29.6 - - - +
289A VAL* 3.2 26.2 - - + -
313A ALA* 3.6 18.5 - - + +
315A LYS* 3.3 14.2 - - + +
700A AMP 2.6 65.0 + - - -
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Residues in contact with VAL 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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117A HIS 3.5 0.6 + - - +
118A LYS* 1.3 67.4 - - - +
120A ASP* 1.3 53.6 + - - +
121A GLY 2.7 16.1 + - - -
174A GLU* 2.8 29.4 - - + +
176A TYR* 3.9 38.6 - - + -
224A THR* 3.8 15.3 - - + -
226A TYR* 5.8 0.9 - - + -
256A HIS* 3.2 43.7 - - + -
283A PHE* 4.2 15.3 - - + -
700A AMP 3.6 20.8 + - - +
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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