Contacts of the strand formed by residues 424 - 432 (chain B) in PDB entry 1YGY
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 VAL 424 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416B ARG* 3.3 55.6 - - + +
417B ALA 3.6 3.6 - - - +
418B VAL* 4.3 8.3 - - + -
422B GLY 3.6 11.2 - - - +
423B SER* 1.3 79.1 - - - +
425B VAL* 1.3 71.7 + - - +
426B THR* 4.2 6.3 - - - +
444B ASN* 3.4 13.8 + - - +
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Residues in contact with VAL 425 (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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338B ALA* 4.0 23.7 - - - +
341B LEU* 3.8 35.7 - - + +
342B SER* 3.8 18.8 - - - +
343B ASP* 6.0 0.7 - - - +
415B VAL 3.6 1.0 - - - +
416B ARG* 3.2 3.5 - - - -
417B ALA* 2.8 41.9 + - + +
423B SER 5.8 0.4 - - - -
424B VAL* 1.3 79.9 - - - +
426B THR* 1.3 70.3 + - - +
427B VAL* 4.4 4.5 - - + -
444B ASN* 3.8 16.2 - - - +
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Residues in contact with THR 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B GLN* 5.0 1.3 - - - +
414B ASP* 3.9 24.9 - - + -
415B VAL 3.4 11.7 - - - +
416B ARG* 3.8 23.0 + - + -
424B VAL* 4.2 4.2 - - - +
425B VAL* 1.3 77.9 + - - +
427B VAL* 1.3 69.1 + - - +
428B SER* 4.5 0.2 - - - +
442B GLN* 4.1 20.1 - - - +
443B ILE* 3.4 3.8 - - - +
444B ASN* 2.8 39.7 + - - -
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Residues in contact with VAL 427 (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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334B LEU* 3.2 44.8 - - + +
337B LEU* 3.9 28.3 - - + -
338B ALA* 4.0 12.6 - - - +
341B LEU* 4.1 19.3 - - + -
413B VAL 3.9 0.2 - - - +
414B ASP* 3.4 1.7 - - - -
415B VAL* 2.8 34.0 + - - +
425B VAL* 4.4 2.5 - - + -
426B THR* 1.3 79.0 - - - +
428B SER* 1.3 62.6 + - - +
440B ILE* 5.1 2.9 - - + -
442B GLN 3.4 6.7 - - - +
443B ILE* 4.3 8.1 - - + -
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Residues in contact with SER 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 3.5 8.6 - - - +
412B VAL* 3.9 11.4 - - - -
413B VAL 3.0 5.2 - - - -
414B ASP* 2.8 30.3 + - - +
426B THR* 4.5 0.3 - - - +
427B VAL* 1.3 76.2 - - - +
429B GLY* 1.3 58.4 + - - +
440B ILE* 3.6 5.2 - - - +
441B VAL* 2.9 26.3 + - - -
442B GLN* 2.9 40.9 + - - +
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Residues in contact with GLY 429 (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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327B TRP* 3.9 3.6 - - - -
330B LEU* 3.7 13.0 - - - +
334B LEU* 3.5 14.7 - - - +
412B VAL* 3.3 6.9 - - - +
413B VAL* 2.9 32.7 + - - +
428B SER* 1.3 74.5 - - - +
430B THR* 1.3 59.6 + - - -
439B LYS 3.1 11.9 - - - -
441B VAL* 4.1 1.1 - - - -
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Residues in contact with THR 430 (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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327B TRP* 3.9 7.4 - - + -
330B LEU* 3.7 2.7 - - - +
409B HIS* 3.9 18.6 + - + +
411B SER* 2.6 33.4 - - - +
412B VAL* 4.9 0.4 - - - -
429B GLY* 1.3 72.2 - - - -
431B LEU* 1.3 81.1 + - - +
432B TYR* 4.2 14.2 - - + -
437B SER 3.8 0.2 - - - +
438B GLN* 3.6 3.6 - - - -
439B LYS* 2.8 33.5 + - - +
441B VAL* 3.4 22.8 - - - +
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Residues in contact with LEU 431 (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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326B PRO* 3.8 24.2 - - + +
327B TRP* 3.4 53.6 - - + +
330B LEU* 3.8 12.8 - - + -
411B SER* 6.0 0.3 - - - -
430B THR* 1.3 86.4 - - - +
432B TYR* 1.3 64.2 + - - +
436B LEU* 3.9 27.7 - - + +
437B SER 3.3 7.6 - - - +
438B GLN* 3.4 39.7 - - + -
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Residues in contact with TYR 432 (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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409B HIS* 5.8 4.9 - + - -
430B THR* 4.2 17.5 - - + -
431B LEU* 1.3 76.9 - - - +
433B GLY* 1.3 70.0 + - - +
436B LEU* 4.2 6.7 - - - +
437B SER* 3.3 30.5 + - - +
439B LYS* 2.8 45.0 + - + -
441B VAL* 5.6 1.1 - - + -
449B ASP* 2.7 28.9 + - - -
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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