Contacts of the strand formed by residues 533 - 540 (chain B) in PDB entry 2XPH
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 HIS 533 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A MET* 4.5 18.6 - - + -
529B HIS* 3.5 3.3 - - - -
530B LEU* 2.5 47.6 + - + +
531B GLY 3.3 0.6 - - - -
532B VAL* 1.3 83.2 - - + +
534B TRP* 1.3 70.5 + - - +
535B CYS* 3.4 24.7 - - - -
550B ASP* 2.8 23.9 + - - -
551B SER* 4.7 0.8 + - - -
552B MET* 3.5 34.7 - - + +
597B GLN* 3.4 26.6 + - - -
600B GLY 5.0 0.4 + - - -
603B CYS* 3.5 19.7 - - + +
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Residues in contact with TRP 534 (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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465B TRP* 6.3 0.7 - + - -
466B LEU 3.8 14.4 + - - -
468B ASP* 3.9 15.3 - - - -
471B ILE* 3.5 23.0 - - + +
495B THR* 3.6 39.3 - - + -
527B PRO* 4.4 11.4 - - + -
528B ILE 3.5 18.8 - - - -
529B HIS* 3.3 56.0 + + + -
532B VAL 4.5 3.5 + - - -
533B HIS* 1.3 97.2 + - - +
535B CYS* 1.3 67.3 + - - +
550B ASP* 4.5 0.3 - - - +
551B SER* 5.0 3.6 + - - -
603B CYS* 3.8 31.6 - - - +
604B GLY* 3.9 23.1 - - - +
607B ALA* 4.3 9.9 - - + +
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Residues in contact with CYS 535 (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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552A MET* 5.8 0.2 - - - -
527B PRO* 3.8 2.8 - - - +
528B ILE* 2.9 33.3 + - + +
530B LEU* 4.1 7.2 - - - -
533B HIS* 3.4 12.8 - - - -
534B TRP* 1.3 79.2 - - - +
536B LEU* 1.3 62.5 + - - +
548B TYR* 3.3 34.3 - - + +
549B TYR 3.2 11.7 - - - +
550B ASP* 3.2 34.8 - - - +
607B ALA* 4.3 10.6 - - - +
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Residues in contact with LEU 536 (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 MET* 4.3 18.2 - - + -
525B LEU* 4.5 9.6 - - + -
526B VAL 3.6 25.4 - - - +
527B PRO* 4.1 6.5 - - + -
528B ILE* 4.1 4.7 - - - -
535B CYS* 1.3 76.0 - - - +
537B ALA* 1.3 64.6 + - - +
538B VAL* 3.7 24.0 - - + -
548B TYR* 3.5 2.5 - - - -
549B TYR* 2.7 48.8 + - + +
607B ALA* 3.7 26.4 - - + +
610B TYR* 4.0 5.2 - - + -
611B ALA* 3.9 11.4 - - + +
614B ILE* 3.9 16.8 - - + -
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Residues in contact with ALA 537 (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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524B LEU 3.9 0.2 - - - +
526B VAL* 2.7 43.6 + - - +
528B ILE* 3.7 13.8 - - + +
536B LEU* 1.3 79.7 - - - +
538B VAL* 1.3 61.8 + - - +
546B ILE* 4.9 1.6 - - + -
547B THR 3.2 9.2 - - - +
548B TYR* 4.6 8.7 - - + -
559B ALA* 5.7 1.6 - - + -
560B CYS* 5.9 2.0 - - - -
563B LEU* 3.4 31.0 - - + -
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Residues in contact with VAL 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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523B ILE* 4.4 11.2 - - + -
524B LEU 3.5 3.8 - - - -
525B LEU* 4.3 6.1 - - + -
536B LEU* 3.7 22.7 - - + -
537B ALA* 1.3 76.9 - - - +
539B VAL* 1.3 71.6 + - - +
540B ASP* 3.8 9.3 + - + +
545B ASN 3.7 1.7 - - - +
546B ILE* 3.4 4.2 - - - +
547B THR* 2.8 36.2 + - - +
549B TYR* 3.6 30.3 - - + +
614B ILE* 3.8 28.3 - - + -
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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
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522B ASP 3.7 0.9 - - - +
523B ILE* 3.3 7.6 - - - +
524B LEU* 2.9 62.1 + - + +
526B VAL* 4.7 5.2 - - + -
538B VAL* 1.3 71.8 - - - +
540B ASP* 1.3 62.1 + - - +
541B PHE* 3.8 17.2 + - + +
545B ASN 4.0 3.4 - - - -
546B ILE* 3.8 35.4 - - + -
563B LEU* 4.7 16.6 - - + -
567B LEU* 4.0 19.3 - - + -
584B TRP* 5.0 1.1 - - + -
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Residues in contact with ASP 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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522B ASP 3.6 4.1 - - - +
523B ILE* 4.3 12.2 - - + +
538B VAL* 3.8 8.3 + - + +
539B VAL* 1.3 72.9 - - - +
541B PHE* 1.3 58.2 + - - +
542B ARG* 2.9 38.6 + - - -
543B LYS* 2.6 67.9 + - + +
544B LYS* 2.8 31.7 + - - -
545B ASN* 3.3 12.6 + - + +
547B THR* 6.2 0.2 - - - +
584B TRP* 3.8 3.5 - - - -
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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