Contacts of the strand formed by residues 434 - 443 (chain C) in PDB entry 2Y1X
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 THR 434 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376C LYS* 4.1 29.0 - - - +
377C PHE 2.9 9.6 - - - +
378C HIS* 3.6 28.3 - - + +
432C GLY 4.9 0.4 - - - +
433C ASP* 1.3 75.7 - - - +
435C LEU* 1.3 59.7 + - - +
457C VAL* 4.0 2.4 - - - -
458C ASP* 2.6 53.5 + - - +
459C GLN* 3.2 12.0 + - - +
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Residues in contact with LEU 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C PRO* 3.9 29.2 - - + -
375C PHE* 4.5 2.5 - - + -
376C LYS* 3.4 0.7 - - - -
377C PHE* 2.6 59.5 + - + +
379C MET* 4.1 15.0 - - + +
385C VAL* 4.3 14.6 - - + -
388C LEU* 4.8 5.8 - - + -
423C PHE* 5.5 0.7 - - + -
427C LEU* 3.8 22.4 - - + -
433C ASP 4.1 0.8 + - - -
434C THR* 1.3 71.6 - - - +
436C SER* 1.3 60.0 + - - +
455C ALA* 4.0 12.6 - - + -
456C GLN 3.0 35.4 - - - +
457C VAL* 3.9 10.3 - - + +
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Residues in contact with SER 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C PHE* 3.1 16.6 - - - -
376C LYS* 4.0 14.1 - - - -
434C THR 4.0 0.8 + - - -
435C LEU* 1.3 75.3 - - - +
437C GLY* 1.3 58.5 + - - +
455C ALA* 3.3 1.0 - - - -
456C GLN* 2.8 41.7 + - - +
458C ASP* 2.8 30.6 + - - -
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Residues in contact with GLY 437 (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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374C PRO* 3.5 2.6 - - - +
375C PHE* 2.9 37.7 + - - +
436C SER* 1.3 76.7 - - - +
438C THR* 1.3 66.6 + - - -
454C VAL* 3.1 14.8 - - - -
456C GLN* 5.8 0.4 - - - -
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Residues in contact with THR 438 (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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372C GLU* 3.8 34.8 + - + +
373C ILE 3.6 6.7 - - - +
374C PRO* 4.4 6.1 - - - +
375C PHE* 3.4 5.5 - - - -
437C GLY* 1.3 78.7 + - - -
439C CYS* 1.3 73.6 + - - +
440C LEU* 4.1 10.7 - - + +
452C SER 3.5 2.1 - - - +
453C ILE* 3.4 2.4 - - - -
454C VAL* 2.9 38.1 + - - +
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Residues in contact with CYS 439 (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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295C LEU* 4.0 17.9 - - + -
371C ILE 3.6 2.6 - - - +
373C ILE* 2.8 47.6 + - + +
375C PHE* 3.6 6.1 - - + -
388C LEU* 5.0 0.7 - - + -
390C PHE* 3.8 32.3 - - + -
438C THR* 1.3 74.3 - - - +
440C LEU* 1.3 59.8 + - - +
441C LEU* 3.9 23.3 + - - -
451C ILE* 4.5 1.1 - - - -
452C SER 3.3 3.8 - - - -
453C ILE* 4.1 14.8 - - + -
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Residues in contact with LEU 440 (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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370C ARG* 4.0 37.0 - - + +
371C ILE 3.3 18.4 - - - +
372C GLU* 3.8 19.7 - - + +
438C THR* 3.9 11.4 - - + +
439C CYS* 1.3 73.9 - - - +
441C LEU* 1.3 62.5 + - - +
442C ILE* 3.9 23.1 + - + +
450C ASP 3.6 3.5 - - - +
451C ILE* 3.6 0.5 - - - -
452C SER* 2.7 51.8 + - - +
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Residues in contact with LEU 441 (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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263C MET* 3.9 23.3 - - + -
265C PHE* 3.9 32.8 - - + -
293C VAL* 6.2 0.9 - - + -
370C ARG* 3.5 3.6 - - - -
371C ILE* 2.8 55.2 + - + +
373C ILE* 4.4 12.3 - - + -
390C PHE* 5.9 0.2 - - + -
439C CYS* 3.9 20.0 - - - +
440C LEU* 1.3 72.0 - - - +
442C ILE* 1.3 62.5 + - - +
449C TYR* 3.6 21.0 - - + -
450C ASP 3.7 2.5 - - - -
451C ILE* 3.6 31.2 - - + -
470C LEU* 6.1 0.4 - - + -
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Residues in contact with ILE 442 (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 HIS 3.7 6.7 - - - +
370C ARG* 4.9 8.5 - - + -
440C LEU* 4.1 31.4 - - + +
441C LEU* 1.3 76.3 - - - +
443C ALA* 1.3 74.4 + - - +
444C ASN 3.5 0.2 + - - -
449C TYR* 3.3 2.9 - - - -
450C ASP* 2.9 53.7 + - + +
452C SER* 5.3 5.8 - - - -
467C LEU* 6.5 0.9 - - + -
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Residues in contact with ALA 443 (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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268C ARG* 3.4 36.7 + - - +
368C LEU 3.9 5.4 - - - +
369C HIS* 2.9 20.0 + - + +
442C ILE* 1.3 82.4 - - - +
444C ASN* 1.3 60.1 + - - +
448C SER 3.4 2.0 - - - -
449C TYR* 3.2 25.7 - - + -
450C ASP* 5.1 0.2 - - - +
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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