Contacts of the helix formed by residues 374 - 390 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201D CYS* 4.1 26.9 - - + -
265D PHE* 4.1 18.4 - - + +
266D PHE 4.4 7.2 - - - +
267D MET* 4.3 10.1 - - + +
301D ALA* 4.2 18.4 - - + -
303D CYS* 4.0 8.1 - - - -
371D SER 3.1 16.4 + - - +
372D THR 3.1 1.8 - - - -
373D ALA* 1.3 76.0 - - - +
375D GLN* 1.3 64.3 + - - +
377D LEU* 3.0 23.4 + - + +
378D PHE* 3.4 19.6 + - + -
422D TYR* 3.4 43.3 - - + +
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Residues in contact with GLN 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D HIS 5.0 2.8 + - - -
372D THR 3.3 13.5 + - - +
373D ALA* 4.4 4.6 - - - +
374D ILE* 1.3 81.4 - - - +
376D GLU* 1.3 60.5 + - + +
378D PHE* 3.2 11.1 + - - +
379D LYS* 2.7 66.4 + - + +
419D VAL* 3.6 36.9 - - + +
422D TYR* 4.5 4.7 - - + -
423D GLN* 3.0 33.3 + - - +
426D GLN* 3.2 22.0 + - - +
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Residues in contact with GLU 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D ALA 4.5 5.8 - - - +
303D CYS* 3.4 10.4 - - + +
304D ASP* 3.0 29.3 + - - +
307D HIS* 2.8 38.4 + - + +
373D ALA* 3.2 13.0 + - - +
374D ILE 3.1 1.0 + - - -
375D GLN* 1.3 84.0 - - + +
377D LEU* 1.3 59.8 + - - +
379D LYS* 4.2 9.8 - - + +
380D ARG* 3.4 22.3 + - - +
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Residues in contact with LEU 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D MET* 3.6 42.0 - - + -
201D CYS* 4.3 11.0 - - + -
203D ASP* 3.5 37.0 - - + +
301D ALA* 4.1 15.5 - - + -
302D ALA 4.7 3.1 - - - +
303D CYS* 3.8 12.9 - - - -
374D ILE* 3.0 13.0 + - + +
376D GLU* 1.3 77.3 - - - +
378D PHE* 1.3 85.8 + - + +
380D ARG* 3.5 14.7 + - - +
381D ILE* 3.2 26.3 + - - +
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Residues in contact with PHE 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D MET* 4.9 3.4 - - + -
189D VAL* 3.9 25.4 - - + -
201D CYS* 4.8 2.7 - - - -
265D PHE* 3.7 31.4 - + + -
374D ILE* 3.4 30.2 + - + -
375D GLN* 3.2 5.6 + - - +
377D LEU* 1.3 92.9 - - + +
379D LYS* 1.3 61.1 + - - +
381D ILE* 3.4 4.5 + - + +
382D SER* 2.8 30.3 + - - -
415D MET* 3.9 29.5 - - + +
418D LEU* 3.4 26.0 - - + -
419D VAL* 3.7 21.1 - - + -
422D TYR* 4.1 14.4 - + - -
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Residues in contact with LYS 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375D GLN* 2.7 50.9 + - + +
376D GLU* 4.2 9.6 - - + +
378D PHE* 1.3 73.7 - - - +
380D ARG* 1.3 58.0 + - - +
382D SER* 3.4 8.5 + - - -
383D GLU* 2.9 29.1 + - - +
419D VAL* 3.9 22.0 - - + -
423D GLN* 5.2 1.6 + - - -
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Residues in contact with ARG 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D MET* 4.4 4.4 - - - +
171D PRO 3.4 22.4 + - - -
172D SER* 5.7 0.2 - - - +
203D ASP* 2.8 42.0 + - - -
205D GLU* 3.2 42.8 + - - +
302D ALA* 3.8 9.3 + - - +
376D GLU 3.4 17.1 + - - +
377D LEU* 3.6 14.4 + - - +
379D LYS* 1.3 75.9 - - - +
381D ILE* 1.3 76.1 + - - +
383D GLU* 3.3 9.2 + - - +
384D GLN* 3.2 45.2 + - - +
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Residues in contact with ILE 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D MET* 4.1 17.9 - - + -
171D PRO* 4.0 42.2 - - + +
182D PRO* 4.1 9.5 - - + +
185D ALA* 4.0 16.4 - - + -
186D THR* 3.4 22.2 - - - +
189D VAL* 6.0 0.4 - - + -
377D LEU 3.2 15.1 + - - +
378D PHE* 3.8 8.7 - - + +
380D ARG* 1.3 85.2 - - - +
382D SER* 1.3 56.4 + - - +
384D GLN* 3.3 14.8 + - - +
385D PHE* 2.8 27.2 + - - +
415D MET* 4.1 8.7 - - + -
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Residues in contact with SER 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378D PHE 2.8 19.3 + - - -
379D LYS* 3.4 11.0 - - - -
381D ILE* 1.3 77.4 - - - +
383D GLU* 1.3 56.0 + - - +
385D PHE* 3.5 5.4 - - - +
386D THR* 2.9 33.6 + - - +
412D GLU* 5.1 6.6 - - - +
415D MET* 3.8 17.1 - - - +
416D ASN* 3.3 22.5 + - - -
419D VAL* 6.2 1.6 - - - -
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Residues in contact with GLU 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D LYS 2.9 16.5 + - - +
380D ARG* 3.8 7.2 - - - +
381D ILE 3.3 0.4 - - - -
382D SER* 1.3 73.0 - - - +
384D GLN* 1.3 62.6 + - + +
386D THR* 3.5 11.5 - - + +
387D ALA* 3.2 28.1 + - - +
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Residues in contact with GLN 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D PRO* 4.8 3.1 - - - +
173D PRO* 3.6 37.6 - - - +
182D PRO* 3.5 30.1 - - + +
205D GLU* 5.3 0.8 + - - -
380D ARG* 3.2 36.6 + - + +
381D ILE* 3.8 15.1 - - - +
383D GLU* 1.3 74.5 - - + +
385D PHE* 1.3 64.6 + - - +
387D ALA* 3.8 8.4 - - - +
388D MET* 3.6 18.9 - - - +
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Residues in contact with PHE 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D PRO* 3.5 15.9 - - - +
183D TYR* 3.5 26.9 - + - -
186D THR* 3.4 38.1 - - + +
187D LEU* 5.6 0.9 - - + -
381D ILE 2.8 17.9 + - - +
382D SER* 3.5 7.4 - - - +
384D GLN* 1.3 75.6 - - - +
386D THR* 1.3 57.5 + - - +
388D MET* 3.0 21.6 + - - +
389D PHE* 3.0 30.3 + + + +
408D PHE* 3.7 38.6 - + - -
411D ALA* 5.7 0.7 - - + -
412D GLU* 3.3 44.9 - - + -
415D MET* 5.7 0.2 - - + -
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Residues in contact with THR 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D SER* 2.9 26.2 + - - +
383D GLU* 3.5 16.6 - - + +
385D PHE* 1.3 71.6 - - - +
387D ALA* 1.3 65.6 + - - +
389D PHE* 4.0 4.0 - - - +
390D ARG* 3.2 45.9 + - - +
412D GLU* 3.5 21.7 + - - -
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Residues in contact with ALA 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D GLU 3.2 19.0 + - - +
384D GLN* 3.8 10.5 - - - +
385D PHE 3.2 0.2 - - - -
386D THR* 1.3 79.5 - - - +
388D MET* 1.3 62.4 + - + +
390D ARG* 4.3 21.9 + - - +
391D ARG* 3.2 21.7 + - - +
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Residues in contact with MET 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D VAL* 3.3 47.1 - - + +
180D VAL* 4.4 6.1 - - + -
182D PRO* 5.1 6.3 - - - -
183D TYR* 3.3 28.0 - - + +
384D GLN 3.6 15.5 - - - +
385D PHE 3.0 6.3 + - - +
387D ALA* 1.3 80.1 - - + +
389D PHE* 1.3 65.0 + - - +
390D ARG 3.4 1.0 + - - -
391D ARG* 3.5 21.7 + - - +
393D ALA* 3.2 30.0 + - + +
394D PHE* 3.9 29.4 - - + -
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Residues in contact with PHE 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D TYR* 3.3 9.1 + + + +
385D PHE* 3.0 34.5 + + + +
386D THR* 3.9 3.3 + - - -
387D ALA 3.7 0.2 - - - -
388D MET* 1.3 78.1 - - - +
390D ARG* 1.3 60.6 + - - +
392D LYS* 3.0 24.1 + - + +
395D LEU* 4.1 24.0 - - + -
405D GLU* 4.2 16.8 - - + -
408D PHE* 3.3 43.3 - + + -
409D THR* 3.8 28.5 - - + -
412D GLU* 4.6 11.2 - - - -
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Residues in contact with ARG 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D THR* 3.2 39.7 + - - +
387D ALA* 4.3 18.9 + - - +
389D PHE* 1.3 81.8 - - + +
391D ARG* 1.3 61.5 + - + +
392D LYS* 3.5 4.7 + - - +
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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
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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