Contacts of the strand formed by residues 479 - 486 (chain A) in PDB entry 1ISR
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 TYR 479 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PRO* 4.1 15.2 + - + +
207A SER 3.6 15.2 + - - -
208A ASP* 4.6 0.7 + - - -
210A LEU* 3.9 23.5 - - + +
211A GLN* 3.4 44.6 + - + +
214A ALA* 4.9 2.2 - - + -
340A ILE* 3.5 26.7 - - + -
341A LYS 3.2 16.2 - - - +
342A LEU* 4.0 22.9 - - + -
343A GLN* 4.2 0.8 + - - +
478A ARG* 1.3 85.0 - - - +
480A ASP* 1.3 68.0 + - - +
481A ILE* 5.0 2.5 - - + -
499A THR* 3.3 5.2 - - - -
500A TRP* 2.9 59.4 + + + +
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Residues in contact with ASP 480 (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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340A ILE* 4.0 0.2 - - - -
341A LYS* 2.7 48.3 + - + +
342A LEU 4.4 0.3 - - - +
343A GLN* 3.1 44.8 + - - +
344A SER 4.4 1.0 + - - -
479A TYR* 1.3 74.6 - - - +
481A ILE* 1.3 64.0 + - - +
482A MET* 3.8 10.1 + - - +
496A HIS* 3.8 19.5 + - + +
498A GLY 3.4 7.2 - - - +
499A THR* 3.5 19.9 - - - +
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Residues in contact with ILE 481 (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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214A ALA* 5.5 2.5 - - + -
218A ILE* 3.8 15.5 - - + -
338A ILE* 3.7 23.1 - - + -
339A THR 3.6 8.3 - - - +
340A ILE* 3.6 30.5 - - + -
479A TYR* 5.0 1.8 - - + -
480A ASP* 1.3 76.3 - - - +
482A MET* 1.3 66.6 + - - +
496A HIS* 4.3 0.3 - - - -
497A VAL* 3.1 31.2 + - + +
498A GLY* 2.8 30.8 + - - +
499A THR* 4.3 4.9 - - - +
500A TRP* 4.9 9.0 - - + -
505A LEU* 4.4 18.8 - - + -
507A ILE* 5.0 11.2 - - + -
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Residues in contact with MET 482 (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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322A ASP* 4.2 15.3 - - + +
338A ILE* 3.2 10.4 - - - +
339A THR* 2.9 50.2 + - - +
341A LYS* 4.4 20.9 - - + -
480A ASP* 4.1 20.9 - - - +
481A ILE* 1.3 85.2 - - - +
483A ASN* 1.3 60.1 + - - +
484A LEU 4.2 0.4 - - - -
494A TYR* 3.9 41.3 - - + +
495A VAL 3.6 11.9 - - - +
496A HIS* 4.1 12.3 - - + +
497A VAL* 4.1 2.0 - - - -
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Residues in contact with ASN 483 (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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336A GLY* 4.2 8.3 + - - -
337A GLY 2.9 19.3 + - - -
338A ILE* 4.3 7.8 - - + +
482A MET* 1.3 75.7 - - - +
484A LEU* 1.3 72.1 + - - +
485A GLN* 3.4 16.6 + - - +
494A TYR* 4.5 0.9 - - - -
495A VAL* 3.1 31.5 + - - +
497A VAL* 3.6 24.0 - - + +
512A ILE* 3.1 41.2 - - + +
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Residues in contact with LEU 484 (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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320A TRP* 5.1 4.5 - - + -
327A ILE* 3.5 38.8 - - + -
331A GLU* 4.7 3.6 - - - +
334A ALA* 3.2 35.2 - - + +
335A ASN* 3.8 5.8 - - - +
336A GLY* 3.0 27.0 + - - -
337A GLY* 2.9 19.7 + - - +
339A THR* 6.3 1.3 - - + +
482A MET 4.2 0.8 - - - -
483A ASN* 1.3 75.7 + - - +
485A GLN* 1.3 60.7 + - - +
492A TYR* 4.3 8.3 - - + -
493A ASP* 3.6 34.5 - - - +
494A TYR* 4.0 21.3 - - + +
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Residues in contact with GLN 485 (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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335A ASN* 3.1 10.8 - - - +
336A GLY* 6.0 0.2 - - - -
483A ASN* 3.9 20.6 + - - +
484A LEU* 1.3 75.3 - - - +
486A TYR* 1.3 68.8 + - - +
487A THR* 3.3 7.1 + - + +
492A TYR* 4.2 3.8 - - - -
493A ASP 3.3 28.3 + - - +
495A VAL* 3.6 38.6 - - + +
497A VAL* 4.7 0.4 - - - +
511A LYS 3.1 27.5 + - - +
512A ILE* 5.5 2.5 - - - -
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Residues in contact with TYR 486 (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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335A ASN* 3.5 9.2 + - - +
485A GLN* 1.3 76.4 - - - +
487A THR* 1.3 81.5 + - - +
488A GLU 5.3 2.5 - - - -
489A ALA 3.5 7.3 - - - -
490A ASN* 2.9 34.8 + - - +
491A ARG* 3.4 29.4 - - - -
492A TYR* 3.5 41.3 - + + -
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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