Contacts of the strand formed by residues 485 - 490 (chain A) in PDB entry 3SXS
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 ILE 485 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A LYS 3.3 3.5 - - - +
446A MET* 3.5 2.4 - - - -
447A ILE* 2.8 48.2 + - + +
454A GLU* 3.7 17.9 - - - +
457A PHE* 3.4 50.7 - - + -
478A VAL* 4.8 0.2 - - + -
479A CYS 3.4 12.6 - - - +
480A SER* 3.8 19.3 - - - +
482A GLU 3.9 7.4 - - - +
483A TYR* 3.5 32.7 - - + +
484A PRO* 1.3 72.1 - - - +
486A TYR* 1.3 65.8 + - - +
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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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414A ARG* 3.4 43.6 + - + +
417A ILE* 3.7 32.1 + - + -
419A LEU* 3.4 22.3 - - + +
444A VAL* 3.5 11.0 - - + -
445A LYS 3.5 3.4 - - - -
446A MET* 3.7 29.4 - - - -
478A VAL* 3.2 11.1 - - - +
479A CYS* 3.0 54.3 + - + +
484A PRO* 3.6 11.9 - - + -
485A ILE* 1.3 75.5 - - - +
487A ILE* 1.3 60.2 + - - +
488A VAL* 4.2 5.2 - - + -
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Residues in contact with ILE 487 (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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1A PP2 3.6 26.8 - - + -
443A ALA 3.6 1.6 - - - +
444A VAL* 3.3 3.9 - - - -
445A LYS* 2.9 37.9 + - + +
447A ILE* 3.5 22.0 - - + -
457A PHE* 3.7 20.9 - - + -
461A ALA* 6.3 0.7 - - + -
464A MET* 4.5 4.7 - - - -
475A PHE* 4.0 28.9 - - + -
477A GLY 4.0 2.0 - - - -
478A VAL* 4.4 1.6 - - + -
486A TYR* 1.3 72.8 - - - +
488A VAL* 1.3 62.8 + - - +
489A THR* 3.9 3.9 + - + -
555A PHE* 3.4 40.2 - - + -
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Residues in contact with VAL 488 (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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412A LEU* 3.8 25.6 - - + -
417A ILE* 4.1 21.5 - - + -
436A TRP* 5.1 2.0 - - + -
442A VAL* 3.6 35.9 - - + -
443A ALA 3.8 2.7 - - - -
444A VAL* 4.2 15.5 - - + +
475A PHE* 3.8 2.1 - - - -
476A TYR* 2.8 37.9 + - + -
477A GLY 2.9 20.7 + - - +
479A CYS* 4.7 2.9 - - - -
486A TYR* 4.2 9.6 - - + -
487A ILE* 1.3 74.3 - - - +
489A THR* 1.3 60.2 + - - +
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Residues in contact with THR 489 (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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1A PP2 3.1 51.3 + - + -
442A VAL* 3.3 9.7 - - - +
443A ALA 2.9 34.1 + - - -
464A MET* 3.7 28.0 - - + -
473A VAL* 3.7 8.1 - - + -
474A LYS 3.1 13.9 - - - +
475A PHE* 4.3 1.1 - - - -
476A TYR* 3.7 8.1 - - - -
487A ILE* 4.3 4.7 - - + -
488A VAL* 1.3 78.6 - - - +
490A GLU* 1.3 60.0 + - - +
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Residues in contact with GLU 490 (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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1A PP2 2.9 24.1 + - - -
441A ASP 4.3 1.6 - - - -
443A ALA 4.1 0.2 - - - -
472A LEU 3.9 1.4 - - - +
473A VAL* 3.7 1.6 - - + -
474A LYS* 2.8 48.0 + - + +
476A TYR* 3.6 28.5 - - + +
489A THR* 1.3 73.0 + - - +
491A TYR* 1.3 62.6 + - - +
492A ILE* 3.6 18.6 + - + +
545A ASP* 6.1 0.2 - - - +
551A LYS* 3.1 38.7 + - - +
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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