Contacts of the strand formed by residues 327 - 333 (chain F) 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 327 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93F TRP* 3.9 18.7 - - - +
283F ILE* 3.5 45.3 - - + +
286F GLN* 3.2 30.5 + - + +
287F ILE* 3.8 10.8 - - + -
290F ILE* 4.1 6.6 - - + +
319F PHE* 3.5 38.8 - - + -
320F MET 3.5 5.6 - - - +
321F VAL* 4.3 4.5 - - + +
326F LYS* 1.3 79.7 - - - +
328F TRP* 1.3 66.1 + - - +
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Residues in contact with TRP 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F THR 3.8 10.3 - - - -
93F TRP 3.3 9.9 - - - +
94F PHE 3.8 16.4 - - - -
95F PRO* 3.7 33.0 - - + -
96F GLU 5.4 0.7 - - - -
186F LEU* 3.7 38.7 - - + +
290F ILE* 4.9 0.2 - - - -
319F PHE* 3.2 11.6 - - - -
320F MET* 2.8 38.6 + - + +
322F ASP* 3.3 26.7 + - + -
326F LYS* 3.3 50.0 + - + +
327F VAL* 1.3 76.0 - - - +
329F LEU* 1.3 61.3 + - - +
330F ILE* 3.7 1.0 + - + -
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Residues in contact with LEU 329 (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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77F LEU* 4.7 9.0 - - + -
81F ILE* 4.8 0.4 - - + -
93F TRP* 2.9 42.5 + - + +
94F PHE* 3.4 19.6 - - + -
95F PRO* 3.2 24.3 - - - +
290F ILE* 4.1 8.3 - - + +
294F CYS* 3.9 17.9 - - - -
317F PHE* 3.9 21.1 - - + -
318F ASP 3.8 14.8 - - - +
319F PHE* 3.8 18.1 - - + -
328F TRP* 1.3 70.1 - - - +
330F ILE* 1.3 61.1 - - - +
331F GLU* 4.0 13.2 - - - +
332F VAL* 4.3 11.7 - - + -
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Residues in contact with ILE 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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74F LYS* 5.5 2.6 - - - +
77F LEU* 4.4 3.6 - - - +
94F PHE* 4.3 11.6 - - - -
95F PRO* 4.5 7.0 - - + -
150F LYS* 3.6 17.6 + - - +
183F GLN* 4.4 7.6 + - - +
186F LEU* 4.6 1.8 - - + -
200F ASP* 5.8 1.3 - - + -
318F ASP* 3.0 19.8 + - + +
319F PHE 4.3 1.8 - - - -
320F MET* 3.7 41.3 - - + +
328F TRP 4.5 1.6 - - - +
329F LEU* 1.3 81.7 - - - +
331F GLU* 1.3 62.7 + - - +
401F ACP 3.2 72.0 - - + +
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Residues in contact with GLU 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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72F CYS 4.0 11.8 - - - +
74F LYS* 2.8 43.2 + - + +
77F LEU* 4.4 7.9 - - + -
316F GLY 3.9 1.1 - - - +
317F PHE* 3.8 1.4 - - - -
318F ASP* 2.9 37.4 + - - +
329F LEU* 4.0 2.8 - - - +
330F ILE* 1.3 86.7 - - + +
332F VAL* 1.3 79.7 + - - +
333F ASN* 3.5 13.4 + - - -
401F ACP 2.9 39.5 + - - +
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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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71F LEU* 3.7 41.1 - - + +
72F CYS* 3.2 30.3 - - - +
77F LEU* 4.3 7.0 - - + +
294F CYS* 5.3 0.4 - - - -
315F PHE* 4.2 15.3 - - + -
316F GLY 3.5 4.5 - - - +
317F PHE* 3.6 46.7 - - + -
329F LEU* 4.3 15.7 - - + -
331F GLU* 1.3 82.8 - - - +
333F ASN* 1.3 61.0 + - - +
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Residues in contact with ASN 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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44F ARG* 5.6 2.6 + - - -
72F CYS* 3.9 2.7 - - - -
202F ARG* 4.2 11.4 - - - +
315F PHE* 3.4 8.4 - - - -
316F GLY* 2.8 44.1 + - - +
318F ASP* 5.4 0.4 - - - +
331F GLU* 3.5 9.0 + - - -
332F VAL* 1.3 72.0 - - - +
334F GLY* 1.3 59.7 + - - +
335F ALA* 3.3 29.1 + - - +
336F PRO* 3.6 8.9 - - + +
401F ACP 2.8 32.4 + - - +
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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