Contacts of the strand formed by residues 329 - 337 (chain F) in PDB entry 5YUY
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 329 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249F MET* 4.6 1.8 - - + +
252F ASP* 3.4 4.0 - - - +
253F ILE* 3.0 46.9 + - + +
290F LEU* 4.5 9.0 - - + -
291F LYS 3.5 6.3 - - - +
292F PHE* 3.8 24.2 - - + -
320F TRP* 3.5 23.3 - - + -
324F ARG* 3.9 11.0 - - - -
328F GLY* 1.3 75.9 - - - -
330F ARG* 1.3 60.8 + - - +
331F LEU 3.3 29.6 - - - +
332F VAL* 4.1 13.9 - - + -
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Residues in contact with ARG 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F ARG* 3.4 45.5 - - - +
248F THR* 3.1 20.7 + - + +
249F MET* 2.8 32.9 + - - +
252F ASP* 3.5 7.5 + - - +
291F LYS* 2.9 32.4 + - + +
292F PHE 3.5 19.7 - - - +
293F ASP* 4.6 5.0 + - - +
295F PHE* 3.4 32.0 - - - -
328F GLY 4.1 1.4 + - - -
329F VAL* 1.3 72.6 - - - +
331F LEU* 1.3 61.5 + - + +
839G T 3.0 39.6 + - - +
840G A 2.9 24.7 + - - -
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Residues in contact with LEU 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F GLU* 3.9 21.3 - - + +
247F ARG 3.3 11.9 - - - +
248F THR* 3.6 8.1 - - - +
249F MET* 4.0 0.4 - - - -
289F LYS* 3.9 29.4 - - + +
290F LEU* 3.4 3.1 - - - -
291F LYS* 3.0 61.6 + - + +
329F VAL* 3.3 10.0 - - - +
330F ARG* 1.3 82.2 - - + +
332F VAL* 1.3 80.6 + - - +
333F GLY 3.8 3.8 - - - +
840G A 5.8 0.7 - - + -
841G G 3.5 22.2 - - - +
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Residues in contact with VAL 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F GLU* 3.3 1.2 - - - -
247F ARG 3.0 29.4 + - - +
249F MET* 4.1 12.1 - - + +
253F ILE* 4.3 5.8 - - + -
259F CYS* 3.9 25.1 - - - -
262F ILE* 4.0 16.4 - - + -
263F ILE* 3.7 30.5 - - + -
266F LEU* 3.4 11.5 - - + +
288F VAL* 6.2 1.3 - - + -
289F LYS 3.5 7.2 - - - +
290F LEU* 4.1 8.1 - - + -
316F ALA* 5.7 0.9 - - + -
329F VAL* 4.1 9.2 - - + -
331F LEU* 1.3 82.8 - - - +
333F GLY* 1.3 66.5 + - - +
334F LEU* 5.3 0.2 - - + -
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Residues in contact with GLY 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245F VAL 3.3 10.1 - - - -
246F GLU* 3.5 12.3 - - - -
266F LEU* 4.1 1.1 - - - -
288F VAL* 3.2 6.4 - - - +
289F LYS* 2.8 43.0 + - - +
331F LEU* 3.8 1.2 - - - +
332F VAL* 1.3 77.5 - - - +
334F LEU* 1.3 69.4 + - - +
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Residues in contact with LEU 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F GLY* 3.4 2.8 - - - -
245F VAL* 2.8 33.0 + - + +
246F GLU* 5.4 1.9 - - - +
263F ILE* 4.2 26.2 - - + +
266F LEU* 3.8 17.0 - - + +
267F TYR* 3.7 39.5 - - + +
270F LEU* 3.7 20.0 - - + -
287F GLY 3.5 3.4 - - - +
288F VAL* 4.1 18.8 - - + -
289F LYS* 6.2 0.2 - - - -
312F LEU* 4.2 24.5 - - + -
332F VAL* 5.3 0.2 - - + -
333F GLY* 1.3 83.7 - - - +
335F HIS* 1.3 64.2 + - - +
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Residues in contact with HIS 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242F SER* 3.7 21.7 + - - -
243F VAL 3.6 13.2 - - - -
244F GLY* 4.2 10.1 - - - -
270F LEU* 4.3 2.1 - - - +
286F GLN* 3.1 4.4 - - - +
287F GLY 2.8 38.2 + - - +
288F VAL* 4.9 2.7 - - - +
289F LYS* 6.3 1.6 - - + -
301F GLU* 3.6 32.5 + - - +
312F LEU* 4.6 1.2 - - - +
334F LEU* 1.3 77.1 - - - +
336F VAL* 1.3 86.1 + - - +
337F THR* 4.0 11.9 + - - -
844G T 5.7 4.4 - - - +
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Residues in contact with VAL 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242F SER* 3.3 8.3 - - - -
243F VAL* 2.9 56.3 + - + +
270F LEU* 4.0 9.9 - - + -
274F LEU* 4.3 6.3 - - + -
283F ILE* 3.9 25.4 - - + -
285F ARG 3.3 8.7 - - - +
286F GLN* 4.0 2.2 - - + +
307F LEU* 3.6 31.2 - - + -
335F HIS* 1.3 84.7 - - - +
337F THR* 1.3 60.8 + - - +
338F LEU* 4.1 17.9 - - + -
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Residues in contact with THR 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241F LYS* 3.8 12.1 - - + +
242F SER* 4.5 1.8 - - - +
283F ILE* 3.7 3.5 - - - +
284F ALA* 2.9 28.7 + - + -
285F ARG* 2.9 45.1 + - - +
301F GLU* 4.7 4.2 + - - -
335F HIS* 4.0 13.7 + - - -
336F VAL* 1.3 74.1 - - - +
338F LEU* 1.3 71.1 + - - +
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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