Contacts of the strand formed by residues 411 - 419 (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 SER 411 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B ARG* 5.7 0.5 + - - -
327B TRP* 4.0 22.0 - - - -
354B ARG 3.3 11.2 - - - -
356B GLU* 3.2 8.8 + - - +
357B LEU* 3.1 29.9 + - - -
409B HIS* 3.1 4.8 - - - +
410B ARG* 1.3 83.0 + - - +
412B VAL* 1.3 58.7 + - - +
430B THR* 2.6 36.0 - - - +
431B LEU 6.0 0.2 - - - -
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Residues in contact with VAL 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B TRP* 4.7 1.6 - - - -
352B GLN 3.8 0.3 - - - +
353B VAL* 3.9 0.7 - - - +
354B ARG* 3.0 49.3 + - + +
357B LEU* 5.1 1.0 - - - +
406B SER* 3.7 19.5 - - - +
407B PRO* 5.4 2.7 - - + -
409B HIS* 4.1 15.7 - - + -
411B SER* 1.3 75.4 - - - +
413B VAL* 1.3 69.6 + - - +
414B ASP* 4.1 8.7 - - - +
428B SER* 3.9 22.4 - - - -
429B GLY 3.3 16.2 - - - +
430B THR* 4.5 0.7 - - - -
441B VAL* 3.9 14.8 - - + -
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Residues in contact with VAL 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B TRP* 3.8 14.4 - - + -
331B VAL* 4.1 18.8 - - + -
334B LEU* 3.7 14.6 - - + +
351B VAL* 3.6 27.4 - - + -
352B GLN 3.3 9.9 - - - +
353B VAL* 4.2 8.5 - - + -
357B LEU* 3.7 30.5 - - + -
365B LEU* 4.5 1.3 - - + -
412B VAL* 1.3 74.6 - - - +
414B ASP* 1.3 71.4 + - - +
415B VAL* 4.6 0.2 - - + -
428B SER* 3.0 4.9 - - - -
429B GLY 2.9 34.7 + - - +
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Residues in contact with ASP 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B SER 3.4 1.4 - - - +
351B VAL* 3.3 4.3 - - - -
352B GLN* 2.8 58.8 + - + +
354B ARG* 3.7 24.3 - - - -
412B VAL* 4.1 9.2 - - - +
413B VAL* 1.3 74.9 - - - +
415B VAL* 1.3 62.5 + - - +
416B ARG 4.0 0.2 - - - -
426B THR* 3.9 17.0 - - + -
427B VAL 3.4 3.8 - - - -
428B SER* 2.8 26.1 + - - +
442B GLN* 5.9 1.1 - - - -
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Residues in contact with VAL 415 (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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331B VAL* 4.1 10.5 - - + -
334B LEU* 3.8 34.1 - - + +
335B GLY* 4.4 5.6 - - - -
338B ALA* 3.8 16.6 - - + +
349B LEU* 3.8 30.5 - - + -
350B SER 3.4 2.7 - - - +
351B VAL* 4.3 7.2 - - + -
369B ALA* 4.1 20.0 - - + -
413B VAL 4.2 0.2 - - - -
414B ASP* 1.3 76.3 - - - +
416B ARG* 1.3 62.9 + - - +
425B VAL 3.6 1.6 - - - +
426B THR* 3.4 3.1 - - - -
427B VAL* 2.8 34.9 + - + +
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Residues in contact with ARG 416 (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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348B SER 3.8 0.5 - - - +
349B LEU* 3.2 6.4 - - - +
350B SER* 2.6 55.7 + - - +
352B GLN* 4.4 16.8 - - - +
414B ASP 4.0 0.2 - - - -
415B VAL* 1.3 73.6 - - - +
417B ALA* 1.3 61.4 + - - +
418B VAL* 4.2 19.0 + - + +
424B VAL* 3.3 41.3 - - + +
425B VAL 3.2 3.6 - - - +
426B THR* 3.8 18.3 + - + +
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Residues in contact with ALA 417 (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 18.6 - - + +
342B SER* 3.8 19.7 + - - +
346B PRO* 3.9 15.7 - - + -
348B SER 3.4 5.4 - - - -
349B LEU* 4.0 13.5 - - + -
373B LEU* 5.6 0.2 - - + -
415B VAL 4.2 0.4 - - - -
416B ARG* 1.3 73.9 - - - +
418B VAL* 1.3 62.6 + - - +
419B GLY 4.1 0.2 + - - -
423B SER 3.9 0.7 - - - +
424B VAL* 3.6 1.9 - - - -
425B VAL* 2.8 37.3 + - + +
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Residues in contact with VAL 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B PRO* 3.3 3.6 - - - +
347B VAL* 2.8 31.0 + - + +
348B SER* 3.0 25.9 + - - +
350B SER* 6.4 0.9 - - - -
416B ARG* 4.2 31.0 - - + +
417B ALA* 1.3 76.4 - - - +
419B GLY* 1.3 71.8 + - - +
422B GLY* 3.8 17.3 - - - +
423B SER 3.4 11.4 - - - +
424B VAL* 4.3 9.2 - - + -
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Residues in contact with GLY 419 (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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342B SER* 5.4 3.1 + - - -
344B GLU* 4.9 7.9 - - - -
345B LEU 4.4 2.5 - - - -
346B PRO* 4.1 11.0 - - - +
347B VAL* 4.1 4.5 - - - +
417B ALA 4.1 0.8 + - - -
418B VAL* 1.3 79.7 - - - +
420B ALA* 1.3 66.2 + - - +
421B ASP* 3.2 10.8 - - - -
422B GLY* 2.9 15.0 + - - -
423B SER* 2.9 17.5 + - - -
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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