Contacts of the strand formed by residues 537 - 545 (chain B) in PDB entry 6RUT
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 MET 537 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469B GLY 3.9 2.8 - - - +
482B LEU* 3.3 14.8 - - - +
483B SER* 3.0 35.3 + - - +
505B TYR* 4.4 14.1 - - + -
509B PHE* 4.4 13.0 - - + -
536B ARG* 1.3 77.6 - - - +
538B ALA* 1.3 59.2 + - - +
539B VAL* 3.7 17.3 - - + -
551B LEU* 4.0 35.2 - - + +
552B ALA* 4.1 28.3 - - - +
553B GLY 4.5 2.5 - - - +
554B THR 3.4 20.6 - - - +
555B LEU* 3.8 19.7 - - + -
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Residues in contact with ALA 538 (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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470B ASN* 3.9 26.2 - - + +
482B LEU* 3.9 13.9 - - + +
537B MET* 1.3 69.6 - - - +
539B VAL* 1.3 64.6 + - - +
540B SER* 4.8 0.2 - - - -
553B GLY* 3.4 1.7 - - - -
554B THR* 2.9 47.9 + - - +
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Residues in contact with VAL 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASN 5.3 0.5 - - - +
73B ASN* 6.2 0.2 - - - -
456B ASN* 3.4 20.2 + - + +
467B PHE* 3.5 14.8 - - + +
468B GLY 3.4 13.9 - - - +
469B GLY* 3.2 6.2 + - - +
470B ASN* 3.9 16.8 + - - +
483B SER* 3.4 24.9 - - - +
505B TYR* 4.3 2.2 - - - +
537B MET* 3.8 20.2 - - + -
538B ALA* 1.3 71.7 - - - +
540B SER* 1.3 64.8 + - - +
541B GLY* 3.6 11.4 - - - +
542B VAL* 4.5 3.1 - - + -
551B LEU* 3.7 17.9 - - + -
552B ALA 3.6 10.5 - - - +
553B GLY* 4.5 0.2 - - - -
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Residues in contact with SER 540 (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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73B ASN 4.7 5.9 - - - +
456B ASN* 3.4 13.6 + - - +
538B ALA 3.7 2.4 + - - -
539B VAL* 1.3 72.6 - - - +
541B GLY* 1.3 59.8 + - - +
552B ALA* 2.8 28.7 + - - +
553B GLY* 3.8 7.6 - - - -
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Residues in contact with GLY 541 (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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456B ASN* 3.6 18.6 - - - -
539B VAL* 3.6 2.4 - - - +
540B SER* 1.3 81.9 + - - +
542B VAL* 1.3 66.9 + - - +
543B LYS* 4.2 9.9 - - - -
550B VAL 3.8 1.1 - - - +
551B LEU* 3.6 0.2 - - - -
552B ALA* 3.0 27.2 + - - +
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Residues in contact with VAL 542 (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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456B ASN* 4.7 6.1 - - + +
457B MET 4.6 4.0 - - - +
458B VAL* 3.6 37.5 - - + +
467B PHE* 3.5 45.1 - - + -
539B VAL* 4.5 1.1 - - + -
541B GLY* 1.3 79.4 - - - +
543B LYS* 1.3 70.5 + - - +
549B LEU* 4.0 18.4 - - + -
550B VAL 3.2 14.4 - - - +
551B LEU* 3.5 24.7 - - + -
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Residues in contact with LYS 543 (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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456B ASN* 5.5 3.2 + - - -
457B MET 5.7 2.6 + - - -
458B VAL* 5.3 0.9 - - - -
541B GLY* 4.2 6.4 - - - -
542B VAL* 1.3 84.6 + - - +
544B TRP* 1.4 66.9 + - - +
545B VAL* 3.4 7.1 + - + +
549B LEU* 4.4 4.7 - - - -
550B VAL* 2.9 35.1 + - - +
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Residues in contact with TRP 544 (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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195B PRO* 6.3 0.8 - - - +
458B VAL* 4.9 7.3 - - + +
459B ALA 4.7 6.9 + - - -
460B ILE* 4.1 36.7 - - + +
543B LYS* 1.4 74.4 - - - +
545B VAL* 1.3 62.9 + - - +
546B GLY 3.4 14.1 + - - +
547B ASN* 3.1 31.0 - - - -
548B GLN 3.5 3.6 - - - -
549B LEU* 3.6 42.7 - - + +
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Residues in contact with VAL 545 (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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543B LYS* 3.4 6.7 + - + +
544B TRP* 1.3 71.2 - - - +
546B GLY* 1.3 62.1 + - - +
547B ASN 3.2 4.2 + - - -
548B GLN* 2.7 29.9 + - + +
550B VAL* 3.8 28.9 - - + -
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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