Contacts of the strand formed by residues 366 - 370 (chain A) in PDB entry 1YI1
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 LEU 366 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A LEU* 3.8 16.8 - - + +
296A ILE* 3.6 36.3 - - + +
299A SER* 3.9 11.4 - - - +
301A LYS 3.7 0.6 + - - -
302A PRO* 4.1 9.0 - - + -
303A VAL* 3.0 27.4 + - - +
364A SER* 3.6 3.5 - - - -
365A ASP* 1.3 91.1 + - - +
367A LEU* 1.3 58.8 + - - +
368A LEU* 3.6 24.1 + - + +
390A LYS* 3.3 36.1 - - + +
392A VAL* 4.1 14.4 - - + -
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Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A VAL* 3.8 17.7 - - + +
305A TYR* 3.7 34.8 - - + -
361A VAL* 4.0 21.5 - - + -
364A SER* 4.6 5.1 + - - +
366A LEU* 1.3 70.7 - - - +
368A LEU* 1.3 59.0 + - - +
369A ALA* 3.3 3.3 + - + +
374A PHE* 4.3 9.9 - - + -
385A PHE* 3.7 21.3 - - + -
386A ALA* 3.5 28.0 - - + -
389A ALA 4.9 1.5 - - - +
390A LYS 2.7 13.7 + - - +
391A ILE* 3.6 15.5 - - + +
392A VAL 2.9 31.0 + - - +
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Residues in contact with LEU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ILE* 4.5 8.5 - - + -
296A ILE* 4.3 6.3 - - + -
303A VAL 2.9 14.8 + - - +
304A LEU* 3.6 32.4 - - + +
305A TYR* 2.9 22.7 + - - -
320A PHE* 4.0 15.7 - - + -
326A ILE* 3.9 25.8 - - + -
366A LEU* 3.8 30.5 - - + +
367A LEU* 1.3 70.0 - - - +
369A ALA* 1.3 59.0 + - - +
370A PHE* 3.2 21.7 + - + -
392A VAL* 3.7 25.4 - - + -
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Residues in contact with ALA 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A TYR* 3.5 18.6 - - + -
367A LEU* 3.3 4.6 + - + +
368A LEU* 1.3 69.2 - - - +
370A PHE* 1.3 61.8 + - - +
372A VAL* 3.5 21.5 - - + -
374A PHE* 3.5 26.9 - - + -
391A ILE* 4.9 0.4 - - + -
392A VAL 2.8 15.3 + - - +
393A HIS* 3.4 9.2 - - + -
394A ILE 3.3 22.9 + - - -
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Residues in contact with PHE 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A ILE* 5.0 1.6 - - + -
304A LEU* 3.8 25.6 - - + -
305A TYR 3.2 8.4 + - - +
306A VAL* 3.6 4.8 - - + -
307A GLY 3.1 22.7 + - - -
310A CYS* 3.1 14.7 - - - -
317A LEU* 5.1 5.2 - - + -
320A PHE* 4.2 4.7 - + - -
368A LEU* 3.2 34.8 + - + +
369A ALA* 1.3 80.2 - - - +
371A GLY* 1.3 60.9 + - - +
372A VAL 3.4 0.2 - - - -
392A VAL* 4.4 9.9 - - + -
394A ILE* 3.6 29.4 - - + -
415A VAL* 3.7 18.2 - - + -
419A LEU* 4.1 19.5 - - + -
422A MET* 3.9 31.9 - - + -
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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