Contacts of the helix formed by residues 531 - 544 (chain B) in PDB entry 5Y7G
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 GLN 531 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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524B LYS* 4.6 3.1 - - - +
528B ASP* 5.2 6.7 + - - +
529B ARG 4.5 5.6 - - - +
530B LEU* 1.3 77.5 - - - +
532B ASP* 1.3 61.0 - - - +
533B ASN* 3.4 25.8 + - - +
534B GLN* 3.0 26.7 + - - +
535B LEU* 2.9 26.3 + - - +
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Residues in contact with ASP 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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322B ALA* 5.1 2.6 - - + +
325B GLN* 2.9 40.8 + - - +
326B GLY 4.9 0.5 + - - -
329B ARG* 2.7 44.0 + - - -
530B LEU 4.7 2.4 - - - +
531B GLN* 1.3 74.0 - - - +
533B ASN* 1.3 61.8 + - - +
535B LEU* 3.3 6.1 + - - +
536B ARG* 2.9 38.8 + - - +
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Residues in contact with ASN 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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493B ARG* 4.5 2.1 + - - -
500B GLY 4.7 5.3 + - - +
503B ALA* 3.8 15.5 + - - +
504B GLY* 3.5 26.0 - - - +
531B GLN* 3.4 29.2 + - - +
532B ASP* 1.3 76.0 - - - +
534B GLN* 1.3 71.1 + - - +
536B ARG* 3.2 34.5 + - - +
537B TRP* 2.9 30.2 + - + +
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Residues in contact with GLN 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B GLY* 3.2 25.2 - - - +
505B LEU 4.3 5.6 + - - -
507B ASP* 5.4 0.2 + - - -
522B GLU* 3.7 25.0 + - + +
524B LYS* 2.8 37.2 + - - +
530B LEU* 3.6 5.1 - - + +
531B GLN* 3.0 35.8 + - + +
533B ASN* 1.3 92.3 + - - +
535B LEU* 1.3 57.0 + - - +
537B TRP* 3.2 2.4 + - - +
538B LEU* 2.9 41.3 + - + +
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Residues in contact with LEU 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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325B GLN* 3.7 20.4 - - - +
351B ILE* 5.5 4.9 - - + -
530B LEU* 3.5 49.8 - - + +
531B GLN 2.9 13.0 + - - +
532B ASP* 3.5 10.3 - - - +
533B ASN 3.3 0.2 - - - -
534B GLN* 1.3 73.0 - - - +
536B ARG* 1.3 67.0 + - - +
538B LEU* 3.5 8.7 + - + +
539B GLN* 3.1 36.7 + - - +
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Residues in contact with ARG 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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321B ASP* 3.9 26.2 - - + +
322B ALA* 3.2 33.7 - - - +
325B GLN* 3.3 18.3 + - - +
493B ARG* 3.7 20.0 + - - +
500B GLY 4.3 11.3 + - - -
501B ASN* 4.3 8.7 + - - -
532B ASP* 2.9 20.3 + - - +
533B ASN* 3.2 47.9 + - - +
535B LEU* 1.3 75.6 - - - +
537B TRP* 1.3 58.9 + - - +
539B GLN* 3.5 4.1 + - - +
540B PHE* 2.9 27.4 + - - +
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Residues in contact with TRP 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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390B ILE* 5.4 1.3 - - + -
490B TRP* 4.0 35.4 - + + +
493B ARG* 3.5 40.6 - - + +
494B LEU* 4.1 13.0 - - + -
501B ASN* 2.8 42.2 - - + -
503B ALA 3.8 16.4 - - - -
504B GLY 4.1 9.4 - - - +
505B LEU* 3.3 42.3 - - + +
506B PRO* 5.5 1.8 - - + -
533B ASN* 2.9 15.6 + - + +
534B GLN 3.6 4.0 - - - +
536B ARG* 1.3 74.7 - - - +
538B LEU* 1.3 68.8 + - + +
540B PHE* 2.8 21.1 + + - +
541B CYS* 2.9 25.6 + - - -
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Residues in contact with LEU 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ILE* 4.5 14.7 - - + +
506B PRO* 4.5 20.4 - - + -
522B GLU* 5.5 6.5 - - + -
530B LEU* 4.4 14.8 - - + -
534B GLN* 2.9 32.6 + - + +
535B LEU* 3.9 8.3 - - + +
537B TRP* 1.3 73.1 - - + +
539B GLN* 1.3 61.2 + - + +
541B CYS* 3.3 7.0 + - - +
542B ARG* 2.9 28.2 + - - +
548B VAL* 4.0 28.2 - - + +
549B ALA 5.3 1.8 - - - +
550B VAL* 3.3 34.3 - - + -
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Residues in contact with GLN 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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348B ALA* 3.9 28.5 - - - +
349B PRO* 4.6 24.6 + - + +
351B ILE 5.8 3.1 - - - +
535B LEU* 3.1 27.2 + - - +
536B ARG* 4.1 3.6 - - - +
538B LEU* 1.3 74.8 - - + +
540B PHE* 1.3 65.7 + - - +
542B ARG* 4.1 4.9 - - + +
543B GLU* 3.0 46.9 + - + +
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Residues in contact with PHE 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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489B ALA* 3.8 22.2 - - + -
490B TRP* 3.7 24.5 - + - -
493B ARG* 3.6 42.0 - - + +
536B ARG 2.9 15.1 + - - +
537B TRP* 2.8 23.2 + - - +
539B GLN* 1.3 77.6 - - - +
541B CYS* 1.3 64.9 + - - +
543B GLU* 3.9 8.4 + - - +
544B ARG* 2.8 79.9 + - - -
546B MET* 4.6 2.0 - - + -
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Residues in contact with CYS 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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490B TRP* 4.0 10.5 - - - -
520B MET* 4.8 6.3 - - - -
537B TRP* 2.9 34.6 + - - -
538B LEU* 3.6 6.1 - - - +
540B PHE* 1.3 78.7 - - - +
542B ARG* 1.3 59.0 + - - +
544B ARG* 3.0 16.3 + - - -
546B MET* 3.0 49.2 + - + +
548B VAL* 3.6 33.4 - - + -
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Residues in contact with ARG 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B PRO* 3.7 35.4 - - + +
350B GLU* 3.9 20.8 + - - +
351B ILE 5.3 5.4 - - - +
352B ASP* 5.5 4.4 - - + +
538B LEU 2.9 16.7 + - - +
539B GLN* 3.2 8.0 + - + +
541B CYS* 1.3 77.7 - - - +
543B GLU* 1.3 61.5 + - - +
545B GLU* 3.4 38.6 + - - +
546B MET 4.7 7.0 - - - +
548B VAL* 4.7 10.1 - - + +
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Residues in contact with GLU 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B PRO* 5.5 11.6 - - + +
539B GLN* 3.0 38.1 + - + +
540B PHE* 4.2 10.6 - - - +
542B ARG* 1.3 78.4 - - - +
544B ARG* 1.3 65.7 + - - +
545B GLU* 3.2 7.8 + - - +
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Residues in contact with ARG 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B HIS* 4.8 4.7 + - + -
489B ALA* 3.8 14.2 - - + +
540B PHE* 2.8 64.2 + - - +
541B CYS 3.0 8.2 + - - +
543B GLU* 1.3 87.5 + - - +
545B GLU* 1.3 72.3 + - - +
546B MET* 3.3 21.8 + - + +
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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