Contacts of the strand formed by residues 349 - 354 (chain B) in PDB entry 5YL4
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 349 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B PHE* 4.7 2.2 - - + -
313B VAL* 3.5 19.3 - - + +
330B MET* 3.4 33.4 - - + -
334B GLN* 3.5 37.3 + - + +
341B PHE* 3.3 39.3 - - + -
347B ASN* 3.3 3.0 - - - +
348B ASN* 1.3 81.6 - - - +
350B LYS* 1.3 74.0 + - - +
351B THR* 4.6 1.8 + - - +
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Residues in contact with LYS 350 (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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175A PRO* 3.2 31.5 + - - +
178A SER 2.8 29.1 + - - +
179A THR* 3.8 27.1 - - + +
180A ALA 3.9 11.3 + - - -
181A VAL* 4.2 14.8 - - + +
313B VAL 3.1 8.8 + - - +
314B ALA* 3.3 5.7 - - - -
315B ALA* 3.1 23.2 + - - +
347B ASN* 3.4 21.2 + - - +
348B ASN 4.8 1.1 - - - +
349B VAL* 1.3 83.5 + - - +
351B THR* 1.3 64.5 + - - +
506B 8WR 3.9 25.5 - - + +
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Residues in contact with THR 351 (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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179A THR* 4.1 10.3 - - - +
315B ALA 3.3 7.4 + - - +
317B PHE* 3.6 36.3 - - + -
323B MET* 6.1 0.3 - - - +
326B VAL* 3.6 16.4 - - + -
327B ASP* 5.6 5.4 - - - +
330B MET* 3.7 24.3 - - - +
349B VAL* 4.6 1.7 + - - +
350B LYS* 1.3 81.2 + - - +
352B ALA* 1.3 67.9 + - - +
353B VAL* 5.0 1.1 - - + -
506B 8WR 3.7 8.9 - - - +
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Residues in contact with ALA 352 (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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179A THR* 6.0 0.2 - - + -
239B CYS* 5.3 5.2 - - + -
246B LEU* 5.1 11.2 - - + -
315B ALA 3.1 7.5 + - - +
316B ILE* 3.6 8.4 - - + -
317B PHE 2.9 23.8 + - - -
323B MET* 5.8 2.7 - - - -
351B THR* 1.3 78.8 - - - +
353B VAL* 1.3 72.8 + - - +
506B 8WR 3.9 26.7 - - + -
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Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLY* 5.2 11.1 + - - +
316B ILE* 5.4 0.9 - - - -
317B PHE* 3.3 18.4 - - + +
319B GLY 4.1 8.7 - - - +
321B MET* 4.1 26.5 - - + +
323B MET* 4.1 41.4 - - + +
326B VAL* 4.4 21.5 - - + -
351B THR* 5.0 1.1 - - + -
352B ALA* 1.3 83.1 - - - +
354B CYS* 1.3 65.9 + - - +
355B ASP* 5.0 6.6 - - - +
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Residues in contact with CYS 354 (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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238B THR* 3.6 33.4 - - + -
242B PHE* 4.0 27.4 - - - -
243B PRO 6.5 0.2 - - - -
244B GLY 6.2 2.0 - - - +
316B ILE* 4.4 2.9 - - + -
317B PHE 2.8 12.4 + - - +
318B ARG* 3.3 4.1 - - + -
319B GLY 2.8 34.3 + - - +
353B VAL* 1.3 76.2 - - - +
355B ASP* 1.3 58.3 + - - +
356B ILE* 3.6 22.1 + - - +
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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