Contacts of the strand formed by residues 540 - 546 (chain B) in PDB entry 5XOU
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 ARG 540 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470B PRO* 3.8 33.0 + - - +
471B ALA* 3.4 15.9 - - + +
472B GLU* 3.4 13.0 + - - +
473B LEU 3.9 2.1 + - - -
538B PRO* 3.4 4.1 - - - +
539B SER* 1.3 84.4 + - - +
541B VAL* 1.3 70.5 + - - +
566B ILE* 4.7 0.2 - - - -
567B ALA* 3.1 35.6 - - + +
568B TYR 4.1 8.3 + - - +
569B ASP* 3.4 15.7 + - - +
625B ASP* 3.1 28.9 + - - -
626B THR* 3.3 19.8 + - - -
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Residues in contact with VAL 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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471B ALA* 3.7 3.8 - - - -
473B LEU* 3.3 41.3 - - + +
475B VAL* 5.5 0.2 - - + -
523B LEU* 5.2 2.9 - - + -
527B LEU* 4.1 8.5 - - + -
538B PRO* 4.0 12.6 - - + -
540B ARG* 1.3 78.4 - - - +
542B LEU* 1.3 60.7 + - - +
543B LEU* 3.8 17.9 + - + -
561B LEU* 3.6 30.5 - - + -
566B ILE* 4.2 4.3 - - + -
567B ALA 2.9 15.0 + - - +
568B TYR* 3.4 4.3 - - + -
569B ASP* 3.0 26.5 + - - +
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Residues in contact with LEU 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ALA* 3.5 14.5 - - + +
473B LEU 2.8 11.6 + - - +
474B ALA* 3.2 4.2 - - + -
475B VAL* 2.6 34.3 + - - +
541B VAL* 1.3 71.4 - - - +
543B LEU* 1.3 59.4 + - - +
544B LEU* 3.8 22.3 + - + +
569B ASP* 3.9 7.4 - - + +
571B VAL* 4.0 11.7 - - + -
631B LEU* 3.9 27.4 - - + +
634B GLN* 3.8 33.0 - - + +
635B ILE* 4.1 16.4 - - + -
638B LEU* 4.1 15.5 - - + -
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Residues in contact with LEU 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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475B VAL* 3.5 8.1 - - + -
477B PHE* 3.9 13.0 - - + -
523B LEU* 3.8 32.3 - - + -
541B VAL* 4.1 13.9 - - + -
542B LEU* 1.3 78.0 - - - +
544B LEU* 1.3 64.3 + - - +
554B PHE* 3.9 25.1 - - + -
558B LEU* 4.1 21.1 - - + -
561B LEU* 4.2 13.9 - - + -
568B TYR* 4.9 1.8 - - + -
569B ASP 2.9 19.2 + - - +
570B LEU* 3.5 13.8 - - + +
571B VAL 2.9 25.1 + - - -
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Residues in contact with LEU 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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474B ALA* 5.1 0.9 - - + -
475B VAL 2.6 18.7 + - - +
476B GLY* 3.3 0.7 - - - -
477B PHE* 2.9 32.5 + - - -
542B LEU* 3.8 25.1 - - + +
543B LEU* 1.3 80.9 - - - +
545B ARG* 1.3 60.7 + - - +
570B LEU* 5.3 0.4 - - - -
571B VAL* 3.5 22.9 - - + +
573B VAL* 4.5 4.5 - - + -
635B ILE* 4.0 14.8 - - + -
638B LEU* 4.7 7.0 - - + -
653B PRO* 4.0 28.9 - - + -
655B PRO* 4.5 18.8 - - + -
656B LEU* 3.8 17.7 - - + +
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Residues in contact with ARG 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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477B PHE* 3.7 24.3 + - - -
478B ASP* 4.2 9.1 + - - +
479B ALA* 4.5 0.6 - - - +
512B GLU* 3.1 39.8 + - - +
514B ILE* 4.0 12.9 - - - +
543B LEU 4.3 0.2 + - - -
544B LEU* 1.3 73.9 - - - +
546B ASN* 1.3 81.5 + - - +
547B GLY 3.3 2.6 + - - +
548B ARG 3.8 13.8 + - - +
549B VAL* 3.5 32.8 - - + -
550B PRO* 3.9 7.9 - - - +
553B GLU* 2.9 38.3 + - - -
554B PHE* 4.2 8.7 - - + -
570B LEU* 5.1 1.1 - - + -
571B VAL 3.0 10.5 + - - +
572B SER* 4.5 0.7 - - - -
573B VAL* 2.9 27.2 + - - +
656B LEU* 4.1 3.6 - - - +
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Residues in contact with ASN 546 (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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477B PHE 3.1 15.2 + - - +
478B ASP* 3.3 38.5 + - - +
512B GLU* 4.5 2.3 - - - +
545B ARG* 1.3 91.5 + - - +
547B GLY* 1.3 65.2 + - - +
548B ARG 4.0 0.3 + - - -
573B VAL 3.8 4.8 - - - +
575B LYS* 3.3 24.9 + - - +
652B LEU* 4.3 20.8 - - - +
656B LEU* 3.7 16.6 + - + +
660B ASP* 4.3 7.3 + - - +
9F C 3.9 7.1 + - - +
10F T 3.7 7.4 + - - -
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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