Contacts of the helix formed by residues 342 - 354 (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 LEU 342 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204F TRP* 3.8 31.0 - - + -
216F TYR* 3.6 22.2 - - + +
218F GLU* 3.7 30.5 - - + +
219F GLY 4.3 4.0 - - - +
263F PHE* 4.0 25.8 - - + -
338F CYS* 3.6 15.9 - - - -
339F ALA* 2.9 6.0 + - + +
341F LYS* 1.3 96.9 - - + +
343F TYR* 1.3 65.3 + - - +
344F ALA 3.3 2.9 - - - -
345F GLU* 3.3 8.8 + - + +
346F LEU* 3.0 23.0 + - - +
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Residues in contact with TYR 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F SER* 3.3 48.7 + - - -
13F VAL* 3.9 4.5 - - - -
16F GLU* 4.7 10.1 - - + -
337F ALA* 3.8 4.2 - - - +
338F CYS* 3.1 53.1 + - + -
339F ALA 3.4 19.8 + - - -
340F GLN* 3.7 30.7 - - - +
341F LYS 3.5 1.6 - - - -
342F LEU* 1.3 74.6 - - - +
344F ALA* 1.3 59.7 + - - +
347F CYS* 2.9 54.2 + - - +
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Residues in contact with ALA 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F GLU* 4.6 14.6 - - - +
20F LEU* 4.5 4.3 - - - +
341F LYS 4.5 6.8 + - - +
342F LEU 3.3 0.8 - - - -
343F TYR* 1.3 78.1 - - - +
345F GLU* 1.3 61.3 + - - +
348F GLN* 3.3 23.2 + - - +
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Residues in contact with GLU 345 (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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216F TYR* 2.7 30.9 + - - +
217F ARG* 2.8 31.3 + - - -
218F GLU* 4.2 8.7 - - - +
341F LYS 5.3 0.6 + - - +
342F LEU* 3.3 8.7 + - + +
343F TYR 3.3 0.6 - - - -
344F ALA* 1.3 77.9 - - - +
346F LEU* 1.3 60.7 + - - +
348F GLN* 3.5 5.5 + - - +
349F GLY 3.0 21.7 + - - -
374F ILE* 3.4 29.1 - - + +
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Residues in contact with LEU 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F VAL* 5.4 2.2 - - + -
204F TRP* 4.1 19.5 - - + -
216F TYR* 4.0 32.2 + - + -
314F LEU* 4.1 28.9 - - + -
338F CYS* 3.6 29.6 - - + -
342F LEU 3.0 17.2 + - - +
343F TYR* 4.1 1.6 - - - +
345F GLU* 1.3 76.3 - - - +
347F CYS* 1.3 53.6 + - - +
349F GLY* 2.8 6.2 + - - -
350F ILE* 2.8 44.2 + - + +
374F ILE* 4.3 4.5 - - - -
375F PHE* 4.1 20.0 - - + -
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Residues in contact with CYS 347 (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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13F VAL* 3.3 39.7 - - - -
16F GLU* 3.4 28.3 - - + -
17F VAL* 4.0 8.2 - - + +
20F LEU* 3.7 6.6 - - + +
343F TYR* 2.9 37.7 + - - +
346F LEU* 1.3 77.6 - - - +
348F GLN* 1.3 59.6 + - - +
350F ILE* 3.6 10.6 + - - +
351F VAL* 3.3 26.2 + - - +
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Residues in contact with GLN 348 (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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20F LEU* 3.6 29.1 - - + +
344F ALA 3.3 21.2 + - - +
345F GLU* 3.6 6.1 - - + +
346F LEU 3.2 0.6 - - - -
347F CYS* 1.3 75.0 - - - +
349F GLY* 1.3 58.0 + - - +
351F VAL* 3.2 12.3 + - - +
352F ASP* 2.6 66.7 + - - +
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Residues in contact with GLY 349 (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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345F GLU 3.0 7.7 + - - -
346F LEU 2.8 14.5 + - - -
348F GLN* 1.3 68.2 - - - +
350F ILE* 1.3 63.4 + - - -
352F ASP* 4.5 7.2 - - - -
353F VAL* 3.2 29.9 + - - +
374F ILE* 3.7 24.2 - - - -
375F PHE* 3.5 11.3 - - - -
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Residues in contact with ILE 350 (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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13F VAL* 3.9 28.7 - - + -
14F TYR* 4.3 12.3 - - + +
17F VAL* 4.4 8.7 - - + -
206F LEU* 4.0 23.6 - - + -
312F PHE* 4.1 25.1 - - + -
314F LEU* 4.1 18.8 - - + -
346F LEU* 2.8 36.5 + - + +
347F CYS* 3.9 11.2 - - - +
348F GLN 3.3 0.4 - - - -
349F GLY* 1.3 72.7 - - - +
351F VAL* 1.3 57.1 + - - +
354F ALA* 3.0 35.8 + - + +
355F ILE* 3.4 8.7 + - + +
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Residues in contact with VAL 351 (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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17F VAL* 4.1 22.9 - - + -
20F LEU* 4.5 21.3 - - + +
21F LEU* 4.3 21.3 - - + +
347F CYS 3.3 15.2 + - - +
348F GLN* 3.2 16.6 + - - +
350F ILE* 1.3 75.1 - - - +
352F ASP* 1.3 62.5 + - - +
355F ILE* 3.4 10.7 + - + -
356F SER* 2.7 46.1 + - - +
361F LEU* 5.6 5.2 - - + -
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Residues in contact with ASP 352 (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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348F GLN* 2.6 46.0 + - - +
349F GLY* 4.0 6.3 - - - +
350F ILE 3.5 0.2 - - - -
351F VAL* 1.3 80.0 - - - +
353F VAL* 1.3 68.8 - - + +
356F SER* 3.5 10.8 + - - -
357F SER* 3.5 17.0 + - - -
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Residues in contact with VAL 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F LEU* 4.1 11.2 - - + -
208F ASP* 4.2 10.4 - - + +
214F TYR* 3.3 48.7 - - + +
349F GLY* 3.2 15.7 + - - +
352F ASP* 1.3 87.3 - - + +
354F ALA* 1.3 56.4 + - - +
357F SER* 2.6 26.0 + - - -
373F SER* 5.7 2.9 - - - +
375F PHE* 4.0 18.4 - - + -
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Residues in contact with ALA 354 (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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61F LEU* 3.6 14.6 - - - +
206F LEU* 4.2 15.2 - - + +
208F ASP* 4.5 7.9 - - + -
209F HIS* 4.4 2.4 + - - -
312F PHE* 3.6 42.8 - - + +
350F ILE 3.0 16.9 + - - +
353F VAL* 1.3 79.8 - - - +
355F ILE* 1.3 58.2 + - - +
357F SER* 3.2 10.9 + - - -
358F VAL* 3.6 6.2 - - - +
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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