Contacts of the strand formed by residues 478 - 483 (chain B) in PDB entry 5X61
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 478 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B LEU* 4.1 22.9 - - + -
382B ALA* 3.3 14.6 - - + +
384B LEU* 4.0 9.0 - - + -
476B THR 4.2 0.4 - - - +
477B GLU* 1.3 79.9 - - - +
479B LEU* 1.3 59.8 + - - +
480B THR* 4.8 6.1 - - + -
567B PHE* 4.0 22.7 - - + -
568B ALA* 4.2 13.9 - - - -
571B TYR* 3.8 48.9 - - + -
577B ASN 3.1 4.5 + - - +
578B VAL* 3.4 16.3 - - + +
579B TYR* 3.0 24.3 + - - -
636B PHE* 3.6 4.1 - - - -
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Residues in contact with LEU 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B ALA 3.1 6.9 + - - -
383B ILE* 3.2 14.5 - - + +
384B LEU* 2.7 31.9 + - - -
478B ILE* 1.3 71.5 - - - +
480B THR* 1.3 57.7 - - - +
579B TYR* 3.4 12.8 - - + +
581B TYR* 3.9 7.2 - - + -
632B TYR 4.5 3.4 - - - +
633B TRP* 3.8 30.1 - - + -
636B PHE* 3.4 47.9 - - + -
642B PRO* 4.1 14.4 - - + -
654B TRP* 3.7 31.6 - - + -
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Residues in contact with THR 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B LEU* 2.7 36.8 + - - +
387B GLY 4.4 2.8 + - - -
478B ILE* 4.1 6.7 - - + -
479B LEU* 1.3 74.8 - - - +
481B GLY* 1.3 60.4 + - - +
564B VAL* 3.4 16.6 + - + +
567B PHE* 5.5 2.9 - - + -
568B ALA* 3.6 31.9 - - + +
578B VAL* 4.6 5.8 - - + -
579B TYR 2.9 14.6 + - - +
580B MET* 3.2 12.7 - - - -
581B TYR* 2.9 30.7 + - - -
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Residues in contact with GLY 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B LEU 3.4 2.2 + - - -
386B SER* 2.9 27.4 + - - -
480B THR* 1.3 82.5 + - - +
482B SER* 1.3 61.3 + - - -
564B VAL* 3.8 4.2 - - - +
580B MET* 3.8 10.3 - - - -
581B TYR* 3.2 30.5 + - - -
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Residues in contact with SER 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B SER* 4.1 1.3 - - - +
481B GLY* 1.3 74.9 + - - -
483B ASN* 1.3 68.5 + - - +
486B GLU* 3.4 14.3 + - - -
561B THR* 3.4 42.6 + - - +
564B VAL* 3.9 14.2 - - - +
565B ASN* 4.9 1.6 + - - -
580B MET* 5.1 0.7 - - - -
581B TYR* 3.3 9.3 + - - -
582B LEU* 3.6 10.7 - - - +
583B TYR 2.9 23.4 + - - -
678B PRO* 5.3 2.7 - - - +
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Residues in contact with ASN 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B SER* 4.0 6.0 + - - -
482B SER* 1.3 85.8 - - - +
484B THR* 1.3 64.3 + - - +
485B GLU 3.5 0.9 - - - +
486B GLU* 3.1 25.7 + - - +
561B THR* 4.1 4.5 + - - +
581B TYR* 4.3 1.4 - - - -
582B LEU* 4.1 6.3 - - - +
583B TYR* 3.4 30.9 - - - +
598B VAL* 3.7 14.1 - - + +
599B MET 2.8 24.3 + - - +
600B HIS* 3.9 1.6 - - - +
601B GLY 3.3 8.1 - - - +
602B ASP* 3.7 3.6 - - - +
603B GLU* 2.9 31.7 + - - +
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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