Contacts of the helix formed by residues 531 - 544 (chain B) in PDB entry 2XYN
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 SER 531 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401B GLU* 3.4 15.7 - - - -
465B LYS* 3.7 11.9 - - - +
468B VAL* 4.8 1.3 - - - -
530B PRO* 1.3 73.6 - - - +
532B PHE* 1.3 58.4 + - - +
533B ALA* 2.9 12.6 + - - +
534B GLU* 2.9 41.0 + - - +
535B THR* 3.0 31.0 + - - -
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Residues in contact with PHE 532 (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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394B SER* 4.2 6.6 - - - +
397B MET* 3.4 64.6 - - + +
398B GLU* 3.7 10.1 - - - +
401B GLU* 2.8 28.0 + - + +
410B LEU* 4.3 0.4 - - + -
464B ILE* 4.0 6.5 - - + -
467B ASP* 3.5 37.5 - - + -
468B VAL* 3.7 19.2 - - + +
471B PHE* 3.7 31.0 - + + -
530B PRO 4.0 0.4 + - - -
531B SER* 1.3 71.8 - - - +
533B ALA* 1.3 55.6 + - - +
535B THR* 3.8 11.2 - - - -
536B HIS* 3.1 29.1 + - - +
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Residues in contact with ALA 533 (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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398B GLU* 3.5 27.2 - - + +
401B GLU* 3.0 12.6 + - - +
531B SER* 2.9 9.3 + - - +
532B PHE* 1.3 74.7 - - - +
534B GLU* 1.3 65.6 + - - +
536B HIS* 3.3 2.9 + - - +
537B GLN* 3.1 23.1 + - - +
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Residues in contact with GLU 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 LYS* 5.3 1.0 + - - -
517B LEU* 5.8 0.7 - - + -
529B ARG 5.1 0.2 - - - +
530B PRO* 3.2 23.9 - - + +
531B SER* 2.9 37.1 + - - +
533B ALA* 1.3 75.6 - - + +
535B THR* 1.3 64.3 + - - +
537B GLN* 3.1 9.9 + - - +
538B ALA* 2.9 21.9 + - - +
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Residues in contact with THR 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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394B SER* 4.3 4.5 - - - -
468B VAL* 5.4 1.0 - - - +
471B PHE* 3.4 34.4 - - + -
517B LEU* 3.9 14.1 - - + +
521B CYS* 5.0 3.9 - - - -
530B PRO* 3.9 18.7 + - - +
531B SER 3.0 15.9 + - - -
532B PHE* 3.8 12.5 - - + -
534B GLU* 1.3 79.7 - - - +
536B HIS* 1.3 63.0 + - - +
538B ALA* 3.1 15.9 + - - +
539B PHE* 3.1 28.6 + - + -
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Residues in contact with HIS 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B THR* 3.5 21.0 + - + +
394B SER* 3.8 16.1 + - - +
395B SER* 3.4 39.0 + - - -
398B GLU* 3.2 26.9 + - - +
532B PHE 3.1 20.0 + - - +
533B ALA 3.8 3.4 - - - +
535B THR* 1.3 72.1 - - - +
537B GLN* 1.3 69.3 + - - +
539B PHE* 3.3 1.8 + - - +
540B GLU* 2.9 51.3 + - - +
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Residues in contact with GLN 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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533B ALA 3.1 13.3 + - - +
534B GLU* 3.4 12.1 - - - +
536B HIS* 1.3 79.7 - - - +
538B ALA* 1.3 63.5 + - - +
540B GLU* 3.4 4.8 + - - +
541B THR* 3.0 28.2 + - - +
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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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517B LEU* 4.2 26.5 - - + -
534B GLU 2.9 12.9 + - - +
535B THR 3.1 9.4 + - - +
537B GLN* 1.3 77.8 - - - +
539B PHE* 1.3 57.3 + - - +
541B THR* 3.7 4.9 - - - -
542B MET* 3.0 37.6 + - + +
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Residues in contact with PHE 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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387B LEU* 3.9 27.3 - - + +
390B ALA* 3.8 18.6 - - + -
391B THR* 3.3 23.6 + - - +
394B SER* 4.0 10.1 - - - +
471B PHE* 4.0 7.0 - + - -
475B LEU* 3.6 30.3 - - + -
514B VAL* 4.3 19.1 - - + -
517B LEU* 3.2 29.8 - - + -
535B THR* 3.1 34.8 + - + +
536B HIS 3.9 3.4 - - - +
538B ALA* 1.3 75.9 - - - +
540B GLU* 1.3 61.2 + - - +
542B MET* 3.7 6.1 - - - +
543B PHE* 2.8 32.9 + - - +
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Residues in contact with GLU 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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391B THR* 4.1 18.1 - - + +
536B HIS* 2.9 40.8 + - - +
537B GLN* 4.0 5.6 - - - +
539B PHE* 1.3 76.4 - - - +
541B THR* 1.3 61.3 + - - +
543B PHE* 3.7 3.8 - - + +
544B HIS* 3.1 57.2 + - + +
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Residues in contact with THR 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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537B GLN 3.0 17.8 + - - -
538B ALA* 3.7 6.1 - - - +
540B GLU* 1.3 75.3 - - - +
542B MET* 1.3 68.4 + - + +
544B HIS* 3.6 3.9 + - - +
545B ASP* 3.1 28.6 - - - +
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Residues in contact with MET 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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387B LEU* 3.8 21.7 - - + +
511B PRO* 4.7 11.4 - - + -
513B LYS* 3.5 33.0 - - + -
514B VAL* 3.7 30.3 - - + -
517B LEU* 6.1 2.2 - - - -
538B ALA* 3.0 24.7 + - + +
539B PHE* 3.3 11.9 + - - +
541B THR* 1.3 79.2 - - + +
543B PHE* 1.3 64.9 + - - +
545B ASP* 3.2 22.4 + - - +
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Residues in contact with PHE 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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384B VAL* 4.2 23.0 - - + +
387B LEU* 3.7 16.0 - - + +
388B TYR* 3.6 56.5 - + + -
391B THR* 4.0 17.5 - - + +
539B PHE 2.8 21.7 + - - +
540B GLU* 3.7 4.0 - - + +
542B MET* 1.3 70.7 - - - +
544B HIS* 1.3 83.6 + + - +
545B ASP 2.9 21.0 + - - +
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Residues in contact with HIS 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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540B GLU* 3.1 47.4 + - + +
541B THR* 3.6 2.7 + - - +
542B MET 3.5 0.4 - - - -
543B PHE* 1.3 100.8 - + - +
545B ASP* 1.3 65.8 + - - +
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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