Contacts of the helix formed by residues 534 - 541 (chain C) in PDB entry 1C2O
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 ARG 534 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385B TRP* 4.2 32.6 - - + +
526C ALA 5.6 0.2 + - - -
529C CYS 5.3 0.6 + - - -
530C ALA* 2.7 40.0 + - + +
533C ASN* 1.3 80.2 - - + +
535C PHE* 1.3 60.5 + - + +
536C LEU 3.8 0.2 - - - -
537C PRO* 3.8 5.8 - - - +
538C LYS* 3.0 25.7 + - - +
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Residues in contact with PHE 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B LEU* 3.9 28.9 - - + -
376B GLU* 4.8 18.4 - - + -
377B ALA* 4.9 17.7 - - + -
380B LEU* 4.1 23.6 - - + -
535B PHE* 5.4 8.1 - + - -
539B LEU* 5.2 5.2 - - + -
377C ALA* 4.7 4.7 - - + -
530C ALA 3.3 2.9 + - - +
531C PHE* 3.2 34.1 + + - +
534C ARG* 1.3 76.5 - - + +
536C LEU* 1.4 69.8 + - - +
537C PRO* 3.2 2.9 - - - -
538C LYS* 2.8 30.9 + - + +
539C LEU* 3.0 37.7 + - + -
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Residues in contact with LEU 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367C VAL* 5.1 4.9 - - + -
374C ALA* 3.8 29.8 - - + +
378C VAL* 4.6 5.6 - - + -
405C HIS* 5.4 2.5 - - + -
531C PHE* 2.7 44.3 + - + +
532C TRP* 3.5 37.5 - - + +
535C PHE* 1.4 72.4 - - - +
537C PRO* 1.3 63.7 - - + +
539C LEU* 2.9 20.8 + - + +
540C LEU* 2.8 47.4 + - + +
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Residues in contact with PRO 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532C TRP 2.9 27.4 - - - +
533C ASN* 3.8 13.0 - - - +
534C ARG 3.8 8.3 - - - +
535C PHE 3.3 4.5 - - - -
536C LEU* 1.3 87.7 - - + +
538C LYS* 1.3 60.9 + - + +
540C LEU* 2.8 12.3 + - + +
541C SER* 2.8 30.2 + - - -
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Residues in contact with LYS 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B LEU* 5.4 10.4 - - + +
376B GLU* 5.0 17.8 + - + +
534C ARG 3.0 23.0 + - - +
535C PHE* 2.8 32.1 + - + +
537C PRO* 1.3 76.0 - - + +
539C LEU* 1.3 61.3 + - - +
541C SER* 3.2 11.6 + - - +
542C ALA* 3.2 22.7 + - - +
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Residues in contact with LEU 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B LEU* 4.6 19.7 - - + -
535B PHE* 5.3 3.8 - - + -
539B LEU* 5.2 4.0 - - + -
373C LEU* 4.1 29.8 - - + +
374C ALA* 3.7 20.2 - - + +
377C ALA* 3.7 30.1 - - + -
535C PHE* 3.0 30.6 + - + +
536C LEU* 2.9 20.2 + - + +
538C LYS* 1.3 76.9 - - - +
540C LEU* 1.3 63.7 + - - +
542C ALA* 3.1 6.5 + - + +
543C THR* 2.8 35.2 + - + +
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Residues in contact with LEU 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C GLN* 4.0 29.4 - - + +
370C ALA* 3.8 7.0 - - + -
371C SER* 3.6 18.4 - - - +
374C ALA* 3.2 29.6 - - + -
536C LEU* 2.8 37.6 + - + +
537C PRO* 3.4 11.2 - - + +
539C LEU* 1.3 78.1 - - - +
541C SER* 1.3 56.2 + - - +
542C ALA 3.1 2.1 + - - -
543C THR* 3.1 30.0 + - - +
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Residues in contact with SER 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537C PRO 2.8 23.6 + - - -
538C LYS* 3.2 14.7 + - - +
540C LEU* 1.3 70.1 - - - +
542C ALA* 1.3 59.6 + - - +
543C THR 5.0 0.7 - - - -
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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