Contacts of the strand formed by residues 349 - 354 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D PHE* 4.5 2.5 - - + -
313D VAL* 3.5 24.0 - - + -
315D ALA* 5.4 0.2 - - + -
330D MET* 3.5 32.3 - - + -
334D GLN* 3.5 33.3 + - + +
341D PHE* 3.5 31.6 - - + -
347D ASN* 3.4 3.2 - - - +
348D ASN* 1.3 88.6 - - - +
350D LYS* 1.3 73.0 + - - +
351D THR* 4.9 1.5 + - - +
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Residues in contact with LYS 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C PRO* 4.0 10.1 + - - +
178C SER* 2.9 39.4 + - - +
179C THR 5.1 0.7 - - - -
180C ALA 4.0 28.4 + - - +
181C VAL* 4.5 11.0 - - + +
246D LEU* 3.8 28.5 - - + +
247D ASN* 5.3 2.9 - - - +
256D ASN* 5.1 6.7 - - + +
313D VAL 3.1 11.0 + - - +
314D ALA* 3.5 4.1 - - + -
315D ALA* 3.0 26.7 + - - +
347D ASN* 3.4 34.7 + - - +
348D ASN 4.9 0.4 - - - -
349D VAL* 1.3 80.1 + - - +
351D THR* 1.3 64.2 + - - +
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Residues in contact with THR 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C ARG* 5.9 0.7 + - - -
246D LEU* 4.1 11.2 - - - +
315D ALA* 3.4 4.7 - - - +
317D PHE* 3.6 34.5 - - + -
326D VAL* 3.7 16.6 - - + -
327D ASP* 5.5 3.8 - - - +
330D MET* 3.5 27.8 - - + +
349D VAL* 4.9 1.6 + - - +
350D LYS* 1.3 78.8 + - - +
352D ALA* 1.3 64.9 + - - +
353D VAL* 4.6 2.6 - - + +
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Residues in contact with ALA 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D CYS* 4.2 19.7 - - - -
246D LEU* 4.1 27.0 - - + +
315D ALA 3.1 9.9 + - - +
316D ILE* 4.6 7.0 - - + -
317D PHE 3.1 23.4 + - - -
351D THR* 1.3 75.1 - - - +
353D VAL* 1.3 69.5 + - - +
354D CYS 4.4 0.2 - - - -
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Residues in contact with VAL 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D PHE* 3.5 21.8 - - + +
319D GLY 4.5 10.1 - - - +
321D MET* 4.7 13.9 - - + +
323D MET* 4.0 32.8 - - + +
326D VAL* 4.3 22.9 - - + -
351D THR* 4.6 2.7 - - + -
352D ALA* 1.3 81.5 - - - +
354D CYS* 1.3 69.1 + - - +
355D ASP* 4.3 4.0 + - - +
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Residues in contact with CYS 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D THR* 3.8 30.3 - - + -
242D PHE* 4.3 20.9 - - + -
243D PRO 6.2 0.4 - - - +
316D ILE* 5.4 2.0 - - + +
317D PHE 3.0 10.3 + - - +
318D ARG* 3.4 5.1 - - + -
319D GLY 3.0 28.2 + - - +
353D VAL* 1.3 74.7 - - - +
355D ASP* 1.3 64.4 + - - +
356D ILE* 3.4 31.4 + - - -
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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