Contacts of the strand formed by residues 117 - 123 (chain A) in PDB entry 5JQE
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 ALA 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A PHE* 3.5 33.7 - - + -
91A ILE* 3.4 16.8 - - - +
106A TRP* 4.0 0.2 - - - -
109A VAL* 3.2 30.9 - - + +
116A ILE* 1.3 78.4 - - + +
118A TYR* 1.3 59.8 + - - +
119A PRO* 3.8 1.6 - - - +
275A SER* 3.7 10.8 - - - -
276A ALA 3.3 16.6 - - - +
277A GLY* 3.9 0.9 - - - -
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Residues in contact with TYR 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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91A ILE* 3.5 43.0 - - + +
92A THR 4.5 0.3 + - - -
93A PRO* 4.2 4.8 - - + +
97A PHE* 3.8 23.3 - + - -
106A TRP* 4.5 3.4 - + - -
117A ALA* 1.3 71.1 - - - +
119A PRO* 1.3 67.6 - - - +
120A ILE* 3.5 6.2 + - + +
275A SER* 3.2 4.7 - - - -
276A ALA* 2.9 39.5 + - + +
278A ILE* 4.0 5.6 - - + -
289A LYS* 3.8 18.7 - - - +
292A LEU* 3.8 30.1 - - + -
293A GLU* 3.0 41.5 + - + +
297A LEU* 3.9 22.9 - - + -
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Residues in contact with PRO 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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101A LEU* 3.5 21.6 - - + +
105A THR* 3.2 50.7 - - - +
106A TRP* 3.5 32.5 - - + -
109A VAL* 4.3 4.9 - - + -
117A ALA 3.8 2.9 - - - +
118A TYR* 1.3 83.9 - - + +
120A ILE* 1.3 67.2 + - - +
273A VAL* 3.8 12.6 - - + -
274A LEU 4.0 3.8 - - - +
275A SER* 4.2 2.2 - - - +
297A LEU* 3.6 6.9 - - - +
315A ALA* 3.9 8.2 - - + +
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Residues in contact with ILE 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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73A PHE* 3.7 25.1 - - + -
118A TYR* 3.5 15.7 - - + +
119A PRO* 1.3 85.8 - - - +
121A ALA* 1.3 58.3 + - - +
273A VAL* 4.4 0.2 - - - +
274A LEU* 2.8 31.0 + - + +
275A SER* 4.0 1.1 - - - -
276A ALA* 3.9 10.1 - - + +
292A LEU* 5.1 0.2 - - + -
296A LEU* 3.9 20.6 - - + -
297A LEU* 3.8 21.0 - - + +
302A LEU* 4.2 22.2 - - + +
311A LEU* 4.4 11.7 - - + -
314A VAL* 3.7 10.7 - - - +
315A ALA* 3.2 18.7 + - - +
316A LEU 4.8 0.9 + - - -
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Residues in contact with ALA 121 (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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120A ILE* 1.3 80.5 - - + +
122A VAL* 1.3 65.8 + - - +
273A VAL* 3.2 14.9 - - - +
274A LEU* 3.1 42.3 + - + -
311A LEU* 3.3 35.4 - - + +
313A ALA 3.5 5.4 - - - +
314A VAL* 4.0 1.8 - - - +
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Residues in contact with VAL 122 (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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104A PHE* 4.3 9.0 - - + -
105A THR* 3.8 29.4 - - + -
121A ALA* 1.3 83.5 - - - +
123A GLU* 1.3 64.4 + - - +
241A PRO* 5.7 1.4 - - - +
271A VAL* 3.7 13.2 - - + -
272A GLY 3.4 3.6 - - - -
273A VAL* 4.6 5.2 - - + -
311A LEU 4.5 2.1 - - - +
312A GLY* 4.9 1.6 - - - -
313A ALA* 2.7 36.8 + - + +
314A VAL 4.7 0.9 - - - +
315A ALA* 4.4 12.3 - - + -
332A THR* 5.0 5.1 + - - +
333A MET* 4.7 8.7 - - + -
336A ALA* 3.4 32.8 - - + -
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Residues in contact with GLU 123 (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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122A VAL* 1.3 76.4 - - - +
124A ALA* 1.3 67.2 + - - +
167A TYR* 4.8 4.7 + - - +
241A PRO* 4.1 21.4 - - + +
242A TRP* 3.3 39.7 + - + -
270A PHE 3.9 0.9 - - - +
271A VAL* 3.4 6.6 - - - +
272A GLY* 2.8 42.2 + - - +
332A THR* 5.1 1.6 - - - -
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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