Contacts of the helix formed by residues 374 - 390 (chain B) 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 ILE 374 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B CYS* 4.0 15.5 - - + -
265B PHE 3.9 14.6 - - - +
266B PHE 4.5 5.4 - - - +
267B MET* 3.6 12.9 - - + +
301B ALA* 3.9 18.8 - - + -
303B CYS* 3.8 8.1 - - - -
371B SER 3.3 19.7 + - - +
372B THR 3.2 1.2 - - - -
373B ALA* 1.3 76.5 - - - +
375B GLN* 1.3 62.5 + - - +
376B GLU 3.1 0.4 - - - -
377B LEU* 3.0 43.6 + - + +
378B PHE* 3.4 18.4 + - + -
422B TYR* 3.4 36.6 - - + +
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Residues in contact with GLN 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B THR 3.3 13.2 + - - +
373B ALA* 3.0 4.2 + - - +
374B ILE* 1.3 82.2 - - - +
376B GLU* 1.3 56.7 + - + +
378B PHE* 3.2 12.2 + - - +
379B LYS* 2.7 61.4 + - - +
419B VAL* 3.8 25.9 - - + +
422B TYR* 4.0 15.2 - - + -
423B GLN* 3.4 36.8 + - - +
426B GLN* 2.8 30.7 + - - +
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Residues in contact with GLU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ALA 4.4 4.6 - - - +
303B CYS* 3.5 10.1 - - - -
304B ASP* 3.2 25.1 + - - +
307B HIS* 2.6 45.6 + - + +
373B ALA* 3.0 16.4 + - - +
375B GLN* 1.3 77.7 - - + +
377B LEU* 1.3 60.9 + - - +
379B LYS* 3.8 21.6 + - - +
380B ARG* 3.0 29.9 + - - +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B MET* 3.8 35.0 - - + -
201B CYS* 4.0 9.4 - - + -
203B ASP* 3.9 15.9 - - + +
301B ALA* 4.1 9.9 - - + -
302B ALA 5.5 1.3 - - - -
303B CYS* 3.8 11.5 - - - -
374B ILE* 3.0 32.1 + - + +
376B GLU* 1.3 79.4 - - - +
378B PHE* 1.3 70.3 + - + +
380B ARG* 3.3 21.8 + - - +
381B ILE* 3.2 44.7 + - + +
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Residues in contact with PHE 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B MET* 4.3 11.9 - - + -
189B VAL* 3.7 28.0 - - + -
201B CYS* 4.6 5.8 - - - -
265B PHE* 3.6 40.6 - + + -
374B ILE* 3.4 24.6 + - + -
375B GLN* 3.2 3.9 + - - +
377B LEU* 1.3 84.7 - - + +
379B LYS* 1.3 55.7 + - - +
381B ILE* 3.5 3.4 + - + +
382B SER* 2.9 30.5 + - - -
415B MET* 4.0 27.7 - - + +
418B LEU* 3.7 24.0 - - + -
419B VAL* 3.8 20.2 - - + -
422B TYR* 4.1 17.0 - + - -
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Residues in contact with LYS 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B GLN* 2.7 50.1 + - - +
376B GLU* 3.8 22.8 + - - +
378B PHE* 1.3 69.8 - - - +
380B ARG* 1.3 60.2 + - - +
382B SER* 3.4 6.8 + - - -
383B GLU* 3.0 43.2 + - - +
419B VAL* 3.7 21.5 - - + +
423B GLN* 5.1 3.0 + - - -
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Residues in contact with ARG 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B MET* 5.2 0.4 - - - +
171B PRO 3.4 20.6 + - - -
172B SER* 4.3 2.2 - - - +
203B ASP* 2.6 40.4 + - - -
205B GLU* 3.9 32.2 + - - +
302B ALA* 5.3 6.7 + - - +
376B GLU 3.0 18.8 + - - +
377B LEU* 3.3 22.4 + - - +
379B LYS* 1.3 76.6 - - - +
381B ILE* 1.3 70.6 + - - +
383B GLU* 3.4 10.5 + - - +
384B GLN* 3.2 47.3 + - - +
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B MET* 4.4 14.1 - - + -
171B PRO* 4.5 14.6 - - + +
182B PRO* 4.0 14.8 - - + +
185B ALA* 4.0 22.0 - - + -
186B THR* 3.6 19.1 - - - +
189B VAL* 5.6 2.5 - - + -
377B LEU* 3.2 37.5 + - + +
378B PHE* 4.0 8.1 - - + +
380B ARG* 1.3 90.4 - - - +
382B SER* 1.3 57.9 + - - +
384B GLN* 3.5 11.6 + - - +
385B PHE* 3.0 27.2 + - - +
415B MET* 3.9 9.2 - - + -
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Residues in contact with SER 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B PHE 2.9 19.6 + - - -
379B LYS* 3.7 8.5 - - - -
380B ARG 3.3 0.2 - - - -
381B ILE* 1.3 77.8 - - - +
383B GLU* 1.3 59.4 + - - +
385B PHE* 3.4 5.8 - - - +
386B THR* 3.1 32.1 + - - -
412B GLU* 4.9 6.2 + - - +
415B MET* 3.8 16.7 - - - +
416B ASN* 2.8 32.5 + - - -
419B VAL* 5.8 0.7 - - - -
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Residues in contact with GLU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B LYS* 3.0 33.1 + - + +
380B ARG* 3.7 7.6 - - - +
382B SER* 1.3 75.3 - - - +
384B GLN* 1.3 64.9 + - + +
386B THR* 3.4 5.7 + - - -
387B ALA* 3.1 24.6 + - - +
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Residues in contact with GLN 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PRO* 5.0 4.2 - - - +
172B SER* 5.4 0.2 - - - -
173B PRO* 3.5 38.6 - - + +
182B PRO* 3.6 26.7 - - + +
380B ARG* 3.2 43.0 + - - +
381B ILE* 3.8 12.9 - - - +
382B SER 3.4 0.2 - - - -
383B GLU* 1.3 79.4 - - + +
385B PHE* 1.3 61.8 + - - +
387B ALA* 3.6 15.7 + - - +
388B MET* 3.6 15.2 + - - +
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Residues in contact with PHE 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PRO* 3.7 11.3 - - + +
183B TYR* 3.6 26.3 - + - -
186B THR* 3.2 36.6 - - + +
187B LEU* 5.5 0.9 - - + -
381B ILE 3.0 19.1 + - - +
382B SER* 3.4 8.1 - - - +
384B GLN* 1.3 75.4 - - - +
386B THR* 1.3 54.5 + - - +
388B MET* 3.2 9.0 + - - +
389B PHE* 2.7 55.1 + + + +
408B PHE* 3.7 41.5 - + + -
411B ALA* 5.5 1.3 - - + -
412B GLU* 3.7 36.3 - - + -
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Residues in contact with THR 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B SER* 3.1 19.0 + - - -
383B GLU* 3.4 6.0 + - - -
385B PHE* 1.3 78.4 - - - +
387B ALA* 1.3 65.6 + - - +
389B PHE* 4.2 2.9 - - - +
390B ARG* 3.0 40.1 + - + +
412B GLU* 3.2 24.1 + - - +
416B ASN* 5.7 1.0 + - - -
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Residues in contact with ALA 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B GLU 3.1 17.1 + - - +
384B GLN* 3.6 10.3 - - - +
385B PHE 3.3 0.2 - - - -
386B THR* 1.3 75.7 - - - +
388B MET* 1.3 60.3 + - + +
390B ARG* 3.2 28.8 + - - +
345C ASP 4.7 6.3 - - - +
346C TRP* 3.2 29.0 - - - +
347C CYS 6.5 0.2 - - - -
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Residues in contact with MET 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B VAL* 3.2 33.4 - - - +
180B VAL* 4.9 0.2 - - - -
182B PRO* 3.8 25.8 - - + -
183B TYR* 3.3 34.3 - - + +
384B GLN 3.6 11.0 + - - +
385B PHE 3.2 3.6 + - - +
387B ALA* 1.3 78.6 - - + +
389B PHE* 1.3 64.8 + - - +
390B ARG 3.3 0.7 - - - -
391B ARG* 3.1 13.7 + - - +
393B ALA* 3.2 22.6 + - + +
394B PHE* 4.0 24.9 - - + -
346C TRP* 3.5 19.5 - - - +
348C PRO* 4.7 9.6 - - + -
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Residues in contact with PHE 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 3.3 10.3 + + + -
385B PHE* 2.7 43.2 + + + +
386B THR* 3.4 2.7 + - - -
388B MET* 1.3 74.3 - - - +
390B ARG* 1.3 60.0 + - - +
392B LYS* 2.9 24.0 + - + +
395B LEU* 3.7 28.9 - - + -
405B GLU* 3.8 13.2 - - + -
408B PHE* 3.3 40.8 - + + -
409B THR* 3.7 28.9 - - + -
412B GLU* 4.1 13.0 - - - -
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Residues in contact with ARG 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B THR* 3.0 28.3 + - + +
387B ALA* 3.2 28.3 + - - +
389B PHE* 1.3 78.8 - - - +
391B ARG* 1.3 70.5 + - + +
392B LYS* 5.2 3.1 - - - +
345C ASP* 3.2 41.8 + - - +
439C SER* 3.6 29.1 + - - +
440C VAL 5.7 3.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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