Contacts of the helix formed by residues 531 - 541 (chain B) in PDB entry 2OBF
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 GLU 531 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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529B ARG 3.9 10.0 - - - +
530B PHE* 1.3 75.5 - - - +
532B PRO* 1.3 69.2 - - - +
533B ARG* 3.2 3.1 - - + +
534B ALA* 3.0 13.9 + - + +
535B TYR* 2.9 20.8 + - - +
724B ALA 2.8 15.8 + - - +
725B GLY* 3.5 17.7 - - - -
726B GLU* 3.7 21.7 + - - +
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Residues in contact with PRO 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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530B PHE* 3.4 23.3 - - + +
531B GLU* 1.3 81.0 - - + +
533B ARG* 1.3 53.7 + - + +
535B TYR* 3.2 3.0 + - + +
536B LEU* 2.7 42.0 + - - +
582B PRO* 4.3 12.3 - - + -
605B VAL* 3.7 30.3 - - + +
606B ASN* 3.3 22.9 - - - +
609B GLU* 4.4 16.8 - - + +
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Residues in contact with ARG 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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531B GLU* 3.2 2.6 - - + -
532B PRO* 1.3 80.8 - - + +
534B ALA* 1.3 57.4 + - - +
536B LEU* 3.8 8.7 - - - +
537B ARG* 3.1 38.8 + - - +
609B GLU* 2.7 39.6 + - - +
612B ARG* 4.2 9.2 - - - +
619B GLY 2.5 30.2 + - - -
620B ALA* 3.5 1.6 + - - +
621B PHE* 3.4 33.0 - - - +
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Residues in contact with ALA 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B GLU* 3.0 15.0 + - + +
533B ARG* 1.3 76.4 - - - +
535B TYR* 1.3 57.4 + - - +
537B ARG* 3.4 22.0 + - - +
538B ASN* 2.8 44.2 + - - +
725B GLY* 3.4 36.1 - - - +
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Residues in contact with TYR 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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530B PHE* 3.4 27.6 - + + -
531B GLU 2.9 11.5 + - - +
532B PRO 3.3 7.6 - - - +
534B ALA* 1.3 76.6 - - - +
536B LEU* 1.3 66.2 + - - +
538B ASN* 3.2 5.4 + - - +
539B ASN* 3.0 51.3 + - - +
540B TYR* 3.8 11.2 - + - -
582B PRO* 3.8 22.7 - - + -
722B TYR* 3.8 24.7 - + - -
723B LEU 4.8 0.4 - - - -
724B ALA* 4.4 7.5 - - + +
2002B F83 3.3 18.7 - + + +
3002B SAH 2.8 61.5 + - + +
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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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532B PRO 2.7 28.8 + - - +
533B ARG* 3.8 12.8 - - - +
535B TYR* 1.3 73.3 - - + +
537B ARG* 1.3 56.6 + - - +
540B TYR* 2.7 40.4 + - + +
541B ALA 3.4 2.3 + - - -
582B PRO* 3.5 43.3 - - + +
583B THR* 3.9 7.0 - - + -
609B GLU* 4.3 13.5 - - + -
621B PHE* 3.7 40.7 - - + -
623B TRP* 3.8 20.6 - - + -
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Residues in contact with ARG 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 ARG* 3.1 25.9 + - - +
534B ALA* 3.4 32.8 + - - +
536B LEU* 1.3 75.2 - - - +
538B ASN* 1.3 75.2 + - - +
539B ASN 3.3 0.5 + - - -
541B ALA* 3.4 33.6 + - + +
542B PRO 4.8 1.9 - - - +
621B PHE* 4.9 2.6 - - - -
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Residues in contact with ASN 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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534B ALA* 2.8 30.6 + - - +
535B TYR 3.6 3.6 - - - +
537B ARG* 1.3 91.9 + - - +
539B ASN* 1.3 67.2 + - - +
541B ALA 5.0 0.5 - - - +
543B PRO* 6.2 0.2 - - - +
544B ARG* 3.6 18.7 - - - +
723B LEU* 2.9 37.5 + - - +
724B ALA* 4.5 0.8 - - - +
725B GLY 4.5 1.4 - - - +
764B THR* 4.8 1.4 + - - -
766B VAL* 3.6 35.4 - - + +
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Residues in contact with ASN 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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535B TYR* 3.0 49.7 + - - +
538B ASN* 1.3 86.8 - - - +
540B TYR* 1.3 67.5 + - + +
541B ALA 3.7 1.6 - - - -
544B ARG* 3.1 40.8 + - - +
722B TYR* 5.1 2.8 - - - -
723B LEU 5.0 2.4 + - - -
766B VAL* 4.5 2.3 - - - +
767B ASP* 4.1 1.9 - - - +
2002B F83 3.0 61.7 + - + +
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Residues in contact with TYR 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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535B TYR* 3.8 7.0 - + - -
536B LEU* 2.7 30.7 + - - +
539B ASN* 1.3 88.6 - - + +
541B ALA* 1.3 59.3 + - - +
542B PRO* 4.7 0.5 - - - +
545B GLY* 3.5 6.6 - - - -
583B THR* 3.5 16.4 - - + -
585B TYR* 3.2 32.1 + + - -
621B PHE* 4.0 19.5 - - + -
623B TRP* 3.9 18.2 - + + -
626B TYR* 2.8 38.4 + + - +
682B PHE* 3.9 0.7 - - - -
2002B F83 3.3 43.9 - + - -
3002B SAH 2.6 30.6 + - - -
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Residues in contact with ALA 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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536B LEU 3.4 2.4 + - - +
537B ARG* 3.4 35.1 + - + +
538B ASN 5.0 0.9 - - - +
539B ASN 4.5 0.2 - - - -
540B TYR* 1.3 78.8 + - - +
542B PRO* 1.3 80.7 - - + +
544B ARG* 3.5 6.2 + - - +
545B GLY 2.9 14.1 + - - -
621B PHE* 5.0 8.1 - - + -
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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