Contacts of the helix formed by residues 541 - 549 (chain B) in PDB entry 2YIC
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 GLY 541 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493B GLU* 4.7 1.3 - - - -
506B PHE* 3.1 18.0 + - - +
508B LEU* 3.9 27.9 - - - +
537B MET* 4.0 2.5 - - - -
539B HIS 3.1 0.8 + - - -
540B ARG* 1.3 71.6 - - - +
542B ARG* 1.3 57.8 + - - +
543B LEU 3.4 2.7 - - - -
544B ASN* 3.1 11.5 + - - +
545B VAL* 2.9 31.2 + - - +
578B TYR* 6.0 0.2 - - - -
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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
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537B MET* 3.4 38.0 + - - +
538B PRO 3.9 4.6 + - - +
539B HIS 3.0 19.9 + - - +
540B ARG 3.2 1.4 - - - -
541B GLY* 1.3 76.0 - - - +
543B LEU* 1.3 59.1 + - - +
545B VAL* 3.3 4.2 + - - +
546B LEU* 3.0 32.0 + - - +
577B LYS 3.9 6.4 + - - -
578B TYR* 3.1 46.5 + - + +
579B HIS 3.6 5.9 + - - -
580B LEU 2.8 25.8 + - - -
599B LEU* 3.3 22.1 - - + +
600B THR 3.1 22.4 + - - -
602B ASN* 2.6 25.1 + - - +
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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
----------------------------------------------------------
492B PHE* 3.4 24.7 - - + -
496B LEU* 4.3 10.3 - - + -
541B GLY 3.4 0.2 - - - -
542B ARG* 1.3 73.7 - - + +
544B ASN* 1.4 60.1 + - - +
546B LEU* 3.3 27.4 + - + +
547B ALA* 3.1 24.1 + - - +
557B ILE* 4.1 19.3 - - + +
558B PHE* 4.4 3.1 - - + -
561B PHE* 3.6 28.3 - - + -
577B LYS* 4.1 24.7 - - + +
578B TYR* 3.4 39.8 - - + +
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Residues in contact with ASN 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ALA* 2.9 31.8 + - - +
492B PHE* 3.4 19.9 - - + +
493B GLU* 2.9 31.6 + - - +
508B LEU* 4.1 7.8 - - + +
515B ILE* 3.7 18.0 - - + +
541B GLY* 3.1 14.1 + - - +
543B LEU* 1.4 75.5 - - - +
545B VAL* 1.4 55.1 + - - +
547B ALA 3.4 0.3 + - - -
548B ASN* 2.9 59.3 + - - +
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Residues in contact with VAL 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B LEU* 5.8 0.2 - - + -
514B VAL* 5.7 2.5 - - + -
515B ILE* 3.9 10.5 - - + -
518B MET* 3.8 41.3 - - + -
535B ILE* 4.3 9.4 - - + -
537B MET* 3.8 28.7 - - + -
541B GLY* 2.9 16.1 + - - +
542B ARG 3.3 7.8 + - - +
544B ASN* 1.4 71.5 - - - +
546B LEU* 1.3 61.5 + - - +
549B ILE* 2.9 42.5 + - + +
550B VAL* 3.0 15.8 + - + -
599B LEU* 5.2 4.3 - - + -
642B LEU* 5.1 0.2 - - + -
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Residues in contact with LEU 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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542B ARG* 3.0 19.3 + - - +
543B LEU* 3.3 34.3 + - + +
545B VAL* 1.3 76.1 - - - +
547B ALA* 1.3 57.4 + - - +
550B VAL* 3.5 9.5 - - + +
551B GLY 2.9 11.3 + - - -
552B LYS* 2.8 33.4 + - + +
557B ILE* 4.0 22.0 - - + -
577B LYS* 4.6 11.0 - - + +
580B LEU 5.6 0.9 - - - +
582B ALA* 3.6 31.4 - - + -
599B LEU* 3.7 19.3 - - + -
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Residues in contact with ALA 547 (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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492B PHE* 3.8 10.8 - - + -
543B LEU 3.1 12.5 + - - +
544B ASN 4.0 1.8 - - - +
546B LEU* 1.3 77.5 - - - +
548B ASN* 1.3 67.7 + - - +
551B GLY* 3.6 17.5 - - - -
552B LYS 3.8 6.6 - - - +
554B TYR* 3.7 23.8 - - + -
557B ILE* 3.6 21.3 - - + -
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Residues in contact with ASN 548 (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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485B LYS* 2.8 32.3 + - - +
488B ALA* 3.4 42.0 + - + +
489B ALA 4.0 0.4 - - - +
492B PHE* 4.1 7.3 - - - +
515B ILE* 3.8 19.5 - - + -
544B ASN* 2.9 38.7 + - - +
547B ALA* 1.3 83.3 - - - +
549B ILE* 1.4 63.6 + - - +
551B GLY* 4.8 0.7 - - - -
554B TYR* 4.8 7.1 + - - -
586B TYR* 5.8 0.7 - - - -
799B GLN* 5.3 0.3 + - - -
802B ARG* 5.6 2.8 + - - -
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Residues in contact with ILE 549 (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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515B ILE* 3.4 40.8 - - + +
518B MET* 3.8 13.0 - - + -
519B ASP* 3.6 23.6 - - + +
522B ILE* 3.4 30.1 - - + -
535B ILE* 3.8 20.2 - - + -
545B VAL* 2.9 28.6 + - + +
547B ALA 3.6 0.2 - - - -
548B ASN* 1.4 87.7 - - - +
550B VAL* 1.3 62.6 + - - +
551B GLY* 3.2 1.8 + - - -
585B THR 5.5 0.2 - - - +
586B TYR* 4.1 23.2 - - + +
597B VAL* 4.4 7.2 - - + +
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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