Contacts of the strand formed by residues 308 - 312 (chain K) in PDB entry 6Y5D
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 308 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280K PHE* 4.0 5.6 - - + -
281K ARG* 3.5 34.5 - - + +
284K ILE* 3.9 15.5 - - + -
298K MET* 3.7 13.7 - - + -
299K LYS 5.9 0.4 - - - -
301K LYS* 6.1 0.4 - - - -
306K PRO* 4.5 2.3 - - - +
307K ALA* 1.3 86.1 + - - +
309K THR* 1.3 64.9 + - - +
310K LEU* 3.4 35.4 - - + -
318K VAL 3.5 1.0 - - - +
319K ASP* 3.6 2.3 - - - -
320K ILE* 2.8 46.9 + - + +
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Residues in contact with THR 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298K MET* 3.8 0.2 - - - -
299K LYS* 3.1 67.9 + - + +
306K PRO* 4.5 8.3 - - - +
308K VAL* 1.3 76.0 - - - +
310K LEU* 1.3 75.2 + - - +
311K LEU* 4.3 13.5 - - + -
317K SER* 4.7 6.3 - - - -
318K VAL 3.3 5.8 - - - +
319K ASP* 2.8 26.0 + - - +
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Residues in contact with LEU 310 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189K VAL* 3.7 30.3 - - + -
193K LEU* 3.9 8.1 - - + -
284K ILE* 4.1 3.6 - - + -
288K ILE* 4.1 7.0 - - + -
296K VAL* 4.0 18.8 - - + -
297K ILE 3.6 8.1 - - - +
298K MET* 3.9 16.4 - - + -
308K VAL* 3.4 26.5 - - + -
309K THR* 1.3 76.1 - - - +
311K LEU* 1.3 63.9 + - - +
312K ILE* 4.0 3.8 + - + -
316K ILE 3.9 0.3 - - - +
317K SER* 3.3 5.9 - - - -
318K VAL* 2.8 46.7 + - + +
320K ILE* 3.8 22.4 - - + -
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Residues in contact with LEU 311 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295K ASP 3.5 1.6 - - - +
296K VAL* 3.4 3.9 - - - -
297K ILE* 2.8 61.1 + - + +
298K MET 5.4 0.2 - - - +
299K LYS* 4.8 18.6 - - + +
309K THR* 4.3 14.1 - - + +
310K LEU* 1.3 79.5 - - - +
312K ILE* 1.3 61.8 + - - +
313K SER 3.9 6.8 + - - +
316K ILE 3.7 3.4 - - - +
317K SER* 4.2 16.6 - - - -
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Residues in contact with ILE 312 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185K MET* 4.0 26.4 - - + +
186K VAL* 4.1 15.0 - - + +
189K VAL* 4.2 19.5 - - + -
294K THR* 3.6 22.2 - - + -
295K ASP 3.5 2.9 - - - -
296K VAL* 4.3 16.8 - - + -
310K LEU* 4.9 3.1 - - + +
311K LEU* 1.3 73.9 - - - +
313K SER* 1.3 73.6 + - - +
314K GLU 3.3 0.2 + - - -
315K LYS* 3.5 0.3 + - - +
316K ILE* 2.8 46.3 + - + +
318K VAL* 3.8 28.3 - - + -
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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