Contacts of the strand formed by residues 281 - 287 (chain A) in PDB entry 4ITY
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 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A PHE* 3.6 33.0 - - + -
238A VAL* 3.1 15.6 - - - +
240A VAL* 3.5 27.8 - - + -
275A ILE* 3.9 19.2 + - + +
276A ALA* 5.6 1.8 - - - -
278A CYS* 4.8 2.2 - - - -
279A GLY* 3.7 3.3 - - - +
280A ARG* 1.3 75.1 - - - +
282A VAL* 1.3 57.9 + - - +
283A ALA 3.2 23.8 - - - +
284A LEU* 4.4 3.4 - - + -
314A MET* 4.0 41.3 - - + +
315A MET* 4.3 2.0 - - - -
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 3.4 13.2 - - + -
107A PRO* 3.4 18.6 - - + +
124A VAL* 3.8 22.3 - - + +
128A HIS* 3.3 37.5 - - + +
131A ALA* 4.6 3.1 - - + -
237A PRO* 3.9 21.8 - - + -
238A VAL 2.6 26.1 + - - +
239A MET* 4.4 1.6 - - + -
280A ARG 3.1 1.1 + - - +
281A LEU* 1.3 73.2 - - - +
283A ALA* 1.3 61.6 + - + +
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Residues in contact with ALA 283 (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 PHE* 3.4 11.9 - - - -
107A PRO* 3.7 11.7 - - + +
124A VAL* 3.5 37.7 - - + -
238A VAL 3.8 0.4 + - - -
239A MET* 4.1 11.4 - - + -
240A VAL 3.1 22.5 + - - -
281A LEU* 3.2 10.4 - - - +
282A VAL* 1.3 82.9 - - - +
284A LEU* 1.3 62.8 + - - +
285A ASP* 5.7 0.7 - - - +
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 3.7 13.4 - - + -
107A PRO 3.3 6.2 + - - +
108A LEU* 3.4 15.6 - - + +
109A THR 2.9 25.8 + - - +
239A MET* 5.1 0.2 - - - +
240A VAL* 3.1 35.7 - - + +
242A TYR* 4.3 6.5 - - + -
281A LEU* 4.4 3.8 - - + -
283A ALA* 1.3 77.2 - - - +
285A ASP* 1.3 77.5 + - - +
286A VAL* 3.9 18.6 - - + -
310A ILE* 4.6 0.9 - - + +
311A ALA* 4.3 12.3 - - - -
314A MET* 3.7 41.7 - - + -
315A MET* 4.9 2.0 - - - -
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Residues in contact with ASP 285 (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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107A PRO 5.4 0.2 - - - +
109A THR* 3.2 12.4 + - - +
116A ILE* 5.2 1.1 - - + -
117A ALA* 4.3 2.2 - - - +
120A THR* 2.7 47.4 + - + +
121A VAL* 4.8 0.2 - - - +
239A MET* 3.3 15.2 - - - +
240A VAL 2.9 5.9 + - - -
241A SER* 2.8 28.2 + - - +
242A TYR* 2.7 31.2 + - - +
283A ALA* 5.7 0.3 - - - +
284A LEU* 1.3 82.5 + - - +
286A VAL* 1.3 61.6 + - - +
287A VAL* 4.0 13.7 - - + -
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Residues in contact with VAL 286 (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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38A LEU* 5.6 3.4 - - + -
108A LEU* 4.5 2.7 - - + -
109A THR 2.9 7.1 + - - -
110A ILE* 3.6 26.9 - - + +
111A GLY 3.0 23.6 + - - +
242A TYR* 3.4 4.9 - - + +
244A VAL* 4.3 19.7 - - + -
284A LEU* 3.9 24.0 - - + -
285A ASP* 1.3 78.8 - - - +
287A VAL* 1.3 61.0 + - - +
289A CYS* 5.1 5.7 - - - -
307A GLY* 4.3 23.3 - - - +
310A ILE* 4.4 19.1 - - + -
311A ALA* 5.1 3.4 - - + +
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Residues in contact with VAL 287 (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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111A GLY* 4.5 1.1 - - - +
112A GLY 3.4 9.9 - - - +
113A ASP 4.2 3.4 - - - +
114A HIS* 3.5 38.6 - - + +
116A ILE* 3.5 37.7 - - + -
241A SER* 5.3 0.2 - - - +
242A TYR 2.9 19.7 + - - +
243A ASP* 3.7 5.8 - - - -
244A VAL* 3.1 28.4 + - - +
285A ASP* 4.2 8.5 - - + -
286A VAL* 1.3 84.8 - - - +
288A GLU* 1.3 72.8 + - + +
289A CYS* 3.5 4.0 - - - -
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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