Contacts of the strand formed by residues 552 - 560 (chain C) in PDB entry 2O1S
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 ALA 552 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505C LYS 3.4 2.9 + - - +
506C LEU* 3.6 21.6 - - + +
507C ALA 3.2 21.3 + - - -
550C HIS* 3.4 1.6 - - - +
551C GLU* 1.3 82.2 - - + +
553C LEU* 1.3 68.4 + - - +
580C VAL* 4.1 2.7 - - - -
581C PRO* 3.2 19.1 - - + +
618C TRP* 3.7 24.0 - - + -
619C LEU* 5.1 4.7 - - + -
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Residues in contact with LEU 553 (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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507C ALA* 3.3 21.3 - - + +
509C LEU* 4.2 23.3 - - + -
543C ILE* 4.3 18.4 - - + +
546C MSE 3.8 30.7 - - + +
547C ALA* 3.9 8.1 - - + +
550C HIS* 4.6 1.1 - - + -
552C ALA* 1.3 81.1 - - - +
554C VAL* 1.3 69.5 + - - +
569C VAL* 4.5 2.9 - - + -
573C LEU* 4.0 24.7 - - + -
580C VAL* 4.6 5.4 - - + -
581C PRO 2.9 6.9 + - - +
582C VAL* 3.3 19.0 - - + -
583C LEU 3.0 22.7 + - - -
618C TRP* 4.1 2.1 - - - -
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Residues in contact with VAL 554 (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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506C LEU* 4.8 15.0 - - + -
507C ALA 2.8 13.9 + - - +
508C ILE* 3.3 15.4 - - + +
509C LEU* 2.5 34.2 + - - +
553C LEU* 1.3 81.8 - - - +
555C THR* 1.3 63.0 + - - +
556C VAL* 4.3 8.1 - - + -
583C LEU* 3.4 21.8 - - + +
585C ILE* 3.8 27.4 - - + -
615C ILE* 4.3 24.9 - - + -
618C TRP* 4.8 5.4 - - + -
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Residues in contact with THR 555 (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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509C LEU* 3.2 18.2 - - + -
511C PHE* 4.4 5.8 - - + -
553C LEU 4.3 0.2 - - - -
554C VAL* 1.3 76.1 - - - +
556C VAL* 1.3 61.5 + - - +
557C GLU* 4.9 1.6 + - - -
566C GLY* 3.3 17.7 - - - -
569C VAL* 3.9 30.3 - - + -
582C VAL* 4.0 17.7 - - + -
583C LEU 3.0 4.9 + - - +
584C ASN* 3.0 25.5 + - - -
585C ILE* 2.8 33.9 + - - +
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Residues in contact with VAL 556 (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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508C ILE* 4.0 24.0 - - + -
509C LEU 2.9 9.4 + - - +
510C ASN* 4.0 14.1 - - + +
511C PHE* 2.8 32.4 + - - +
514C LEU* 3.8 21.8 - - + -
518C ALA* 4.5 5.2 - - + -
554C VAL* 4.3 9.0 - - + -
555C THR* 1.3 79.1 - - - +
557C GLU* 1.3 65.2 - - - +
585C ILE* 3.7 6.3 - - + -
611C MSE 3.1 42.4 - - + -
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Residues in contact with GLU 557 (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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437C LEU* 3.7 6.8 - - + +
511C PHE* 3.7 22.2 - - + +
514C LEU* 3.9 9.6 - - - +
555C THR* 4.9 1.5 + - - -
556C VAL* 1.3 79.3 - - - +
558C GLU* 1.3 58.8 + - - +
559C ASN* 3.1 28.1 + - - +
560C ALA 4.1 11.7 - - - +
561C ILE* 4.5 6.8 - - - +
564C GLY* 3.6 4.7 - - - -
565C ALA* 2.8 27.6 + - + +
566C GLY* 2.9 27.4 + - - -
584C ASN* 5.5 1.9 - - - +
585C ILE 3.3 13.9 + - - +
586C GLY* 3.3 16.9 - - - -
606C LEU* 5.1 0.3 - - - +
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Residues in contact with GLU 558 (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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421C ALA 4.3 3.5 - - - +
422C GLY* 3.5 19.5 - - - -
423C ILE* 3.2 36.8 + - + +
433C GLY 4.2 0.7 - - - +
437C LEU* 5.1 0.4 - - - +
475C ARG* 2.5 35.8 + - - +
477C PRO* 4.4 0.9 - - - +
511C PHE 4.4 5.3 + - - -
513C THR* 4.0 16.4 + - - +
514C LEU* 4.0 26.0 - - + +
557C GLU* 1.3 71.4 - - - +
559C ASN* 1.3 55.1 + - - +
587C LEU* 4.5 6.7 - - + +
601C ARG* 2.8 43.7 + - - -
606C LEU* 4.8 4.5 - - + -
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Residues in contact with ASN 559 (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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434C ALA 3.1 19.5 + - - +
435C PHE* 3.3 5.0 - - - -
436C ASP 3.5 0.9 + - - -
437C LEU* 3.0 45.9 + - + +
438C SER* 3.0 21.2 + - - +
475C ARG* 3.6 4.6 + - - +
557C GLU* 3.1 19.0 + - - +
558C GLU* 1.3 78.0 - - - +
560C ALA* 1.3 90.8 + - - +
561C ILE 3.3 0.3 + - - -
564C GLY* 3.7 3.4 - - - -
586C GLY* 3.7 4.3 - - - -
587C LEU* 2.8 30.3 + - - +
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Residues in contact with ALA 560 (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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434C ALA 2.9 20.1 + - - +
435C PHE* 3.9 21.1 - - + -
438C SER* 4.3 1.6 - - - +
557C GLU* 3.9 2.1 - - - +
559C ASN* 1.3 90.6 + - - +
561C ILE* 1.3 65.0 + - - +
562C MSE 4.0 14.6 - - + +
564C GLY* 3.5 8.7 + - - -
587C LEU* 3.7 14.9 - - + +
588C PRO 5.5 2.7 - - - +
442D CYS* 4.5 6.7 - - + +
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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