Contacts of the strand formed by residues 485 - 491 (chain C) in PDB entry 2YWB
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 ILE 485 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401C ILE* 3.8 19.1 - - + -
405C ALA* 3.6 30.5 - - + -
429C LEU* 4.2 9.4 - - + -
446C TYR* 3.6 7.0 - - + +
448C LEU* 3.8 24.7 - - + +
478C ILE* 3.8 11.9 - - + -
479C THR* 3.9 16.0 - - + +
482C VAL* 2.9 29.0 + - + +
483C PRO 3.7 5.9 - - - +
484C GLU* 1.3 79.9 - - - +
486C GLY* 1.3 59.4 + - - +
487C ARG 3.5 24.2 - - - +
488C VAL* 4.1 11.4 - - + -
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Residues in contact with GLY 486 (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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445C GLY* 5.7 0.8 - - - -
446C TYR 3.0 11.0 + - - +
479C THR* 4.3 5.9 - - - +
483C PRO 5.1 1.6 - - - -
484C GLU 3.7 3.2 + - - -
485C ILE* 1.3 73.9 - - - +
487C ARG* 1.3 63.2 + - - +
493D THR* 3.7 13.9 - - - +
497D PRO* 5.0 4.0 - - - +
498D ALA* 4.0 11.3 - - - +
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Residues in contact with ARG 487 (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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446C TYR 3.6 2.0 + - - -
447C VAL* 3.3 17.5 - - + +
448C LEU 2.9 24.8 + - - -
479C THR* 4.5 0.6 - - - +
485C ILE* 3.5 4.3 - - - +
486C GLY* 1.3 80.0 - - - +
488C VAL* 1.3 63.3 + - - +
489C VAL* 4.8 1.3 - - + -
451D ARG* 3.6 9.5 - - - +
491D ASP* 2.8 30.9 + - - +
493D THR* 3.1 22.8 - - - +
498D ALA* 3.6 17.9 - - - +
499D THR* 3.4 34.8 + - - +
501D GLU 3.5 13.5 + - - -
502D TRP* 3.1 59.4 + - + +
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Residues in contact with VAL 488 (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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448C LEU* 3.3 12.6 - - + +
450C LEU* 3.7 34.3 - - + -
475C ALA* 4.1 22.7 - - + +
478C ILE* 3.8 33.2 - - + -
479C THR* 3.9 15.5 - - + -
485C ILE* 4.1 4.3 - - + -
487C ARG* 1.3 78.6 - - - +
489C VAL* 1.3 66.2 + - - +
491D ASP* 3.5 1.0 - - - +
492D LEU* 2.9 27.6 + - + +
493D THR* 2.9 12.9 + - - +
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Residues in contact with VAL 489 (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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447C VAL* 4.2 11.7 - - + -
448C LEU 3.0 9.0 + - - +
449C ALA* 3.6 26.0 - - + +
450C LEU* 2.8 35.5 + - - +
487C ARG* 4.8 1.1 - - + -
488C VAL* 1.3 78.8 - - - +
490C TYR* 1.3 55.6 + - - +
502C TRP* 5.4 0.7 - - + -
489D VAL* 3.8 27.6 - - + -
490D TYR 3.1 14.4 - - - +
491D ASP* 3.9 8.7 - - - +
492D LEU* 4.2 4.3 - - - +
502D TRP* 3.8 34.1 - - + -
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Residues in contact with TYR 490 (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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409C PHE* 5.3 1.8 - + - -
450C LEU* 3.3 30.3 - - + -
451C ARG* 4.6 0.2 - - - -
452C ALA* 3.6 18.2 + - + +
463C TRP* 3.5 23.3 - + - -
464C ALA* 2.7 46.5 + - - +
466C LEU* 3.5 16.7 - - + +
471C LEU* 3.9 32.5 - - + -
489C VAL* 1.3 74.7 - - - +
491C ASP* 1.3 70.5 + - - +
492C LEU* 3.4 8.8 + - + +
468D LEU* 6.2 0.2 - - + -
489D VAL* 3.2 4.9 - - - -
490D TYR* 2.8 38.4 + - + +
492D LEU* 3.8 22.9 - - + +
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Residues in contact with ASP 491 (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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449C ALA 5.5 0.2 - - - -
450C LEU 2.9 13.8 + - - +
451C ARG* 3.2 33.9 + - + +
452C ALA 5.2 0.5 - - - +
463C TRP* 3.5 16.5 - - - +
489C VAL* 5.3 0.4 - - - +
490C TYR* 1.3 83.6 - - - +
492C LEU* 1.3 58.7 + - - +
493C THR* 2.8 33.8 + - - -
502C TRP* 2.8 38.3 + - + +
487D ARG* 2.9 16.1 + - - +
488D VAL 3.4 2.1 - - - +
489D VAL* 4.0 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