Contacts of the helix formed by residues 393 - 408 (chain A) in PDB entry 1YY4
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 GLN 393 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A TRP* 3.8 1.3 - - - -
391A LYS* 2.7 31.1 + - - +
392A LEU* 1.3 78.2 + - - +
394A HIS* 1.3 60.7 + - - +
395A LYS* 4.4 3.8 - - + +
396A GLU* 2.7 52.9 + - + +
397A TYR* 2.9 11.6 + - - +
440A VAL* 5.3 3.6 - - + -
444A SER* 6.4 2.7 - - - -
454A ARG* 4.6 2.7 - - - +
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Residues in contact with HIS 394 (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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273A LEU* 3.5 31.2 - - + +
276A GLU* 4.3 7.8 + - + +
345A TRP* 3.2 47.0 + + + -
393A GLN* 1.3 72.2 + - - +
395A LYS* 1.3 60.3 + - + +
397A TYR* 2.9 29.4 + + - +
398A LEU* 2.9 41.9 + - + +
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Residues in contact with LYS 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLU* 5.3 4.4 + - - -
269A VAL* 4.0 18.9 - - + +
270A LEU* 5.5 10.6 - - - +
273A LEU* 6.5 0.9 - - - -
393A GLN* 3.3 3.7 - - + +
394A HIS* 1.3 80.9 - - + +
396A GLU* 1.3 62.1 + - + +
398A LEU* 3.6 15.1 + - + +
399A CYS* 3.3 27.7 + - - -
439A TRP* 4.9 17.1 - - + -
440A VAL* 4.0 26.0 - - + +
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Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LEU* 3.4 14.0 - - + +
393A GLN* 2.7 43.3 + - + +
395A LYS* 1.3 73.5 - - - +
397A TYR* 1.3 61.9 + - - +
399A CYS* 3.1 3.8 + - - +
400A VAL* 2.9 34.9 + - + +
437A LEU* 4.1 16.8 - - + +
440A VAL* 3.6 20.3 - - + +
441A ILE* 4.2 9.4 - - + +
444A SER* 6.1 0.9 - - - -
454A ARG* 2.8 42.4 + - - -
458A LEU* 3.9 13.1 - - + +
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Residues in contact with TYR 397 (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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276A GLU* 3.4 21.0 + - - -
341A MET* 3.8 30.5 - - + -
342A GLY* 3.7 13.2 - - - -
345A TRP* 3.5 53.4 - + + -
346A ARG* 5.0 2.8 + - - +
392A LEU* 4.1 10.0 - - + +
393A GLN 2.9 10.4 + - - +
394A HIS* 3.1 30.3 - + - +
396A GLU* 1.3 77.9 - - - +
398A LEU* 1.3 68.7 + - + +
400A VAL* 3.8 5.6 - - - +
401A LYS* 2.9 56.9 + - - +
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Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A VAL* 4.1 11.4 - - + +
272A LEU* 3.7 23.4 - - + +
273A LEU* 3.9 36.1 - - + +
276A GLU* 3.7 37.9 - - + +
312A TRP* 5.4 1.0 + - - -
394A HIS* 2.9 33.3 + - + +
395A LYS* 3.7 19.1 - - + +
396A GLU 3.1 0.2 - - - -
397A TYR* 1.3 83.3 - - + +
399A CYS* 1.3 62.4 + - - +
401A LYS* 3.9 5.4 - - - +
402A ALA* 3.1 22.3 + - - +
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Residues in contact with CYS 399 (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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269A VAL* 3.9 24.9 - - - -
272A LEU* 4.1 7.2 - - - -
395A LYS 3.3 15.0 - - - -
396A GLU 3.1 6.8 + - - +
398A LEU* 1.3 76.6 - - - +
400A VAL* 1.3 54.5 + - - +
402A ALA* 3.0 4.3 + - - +
403A MET* 2.8 39.1 + - - +
433A VAL* 4.0 11.9 - - + +
436A ALA* 4.0 6.1 - - - -
437A LEU* 3.8 43.3 - - + -
440A VAL* 4.2 2.0 - - - -
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Residues in contact with VAL 400 (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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341A MET* 4.0 23.1 - - + -
387A PHE* 5.4 4.5 - - + -
392A LEU* 5.2 8.1 - - + -
396A GLU* 2.9 23.3 + - + +
397A TYR* 3.8 7.0 - - - +
399A CYS* 1.3 74.8 - - - +
401A LYS* 1.3 58.4 + - - +
403A MET* 3.0 12.6 + - - +
404A ILE* 2.8 32.6 + - + +
437A LEU* 4.3 18.8 - - + -
458A LEU* 5.1 14.8 - - + +
459A LEU* 5.6 2.5 - - + -
462A LEU* 3.4 30.7 - - + -
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Residues in contact with LYS 401 (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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276A GLU* 2.5 31.2 + - - -
277A PRO* 4.1 12.1 - - - +
312A TRP* 3.4 31.5 - - + +
338A VAL* 3.6 29.2 - - + +
341A MET* 4.3 14.8 - - + -
342A GLY* 5.1 3.1 - - - -
397A TYR* 2.9 52.3 + - - +
398A LEU* 3.9 5.4 - - - +
400A VAL* 1.3 76.8 - - - +
402A ALA* 1.3 62.6 + - - +
404A ILE* 3.3 20.7 + - - +
405A LEU 3.3 8.1 + - - -
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Residues in contact with ALA 402 (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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272A LEU* 4.0 21.8 - - + -
312A TRP* 4.0 11.8 - - + -
316A ILE* 4.7 8.1 - - + -
398A LEU 3.1 14.8 + - - +
399A CYS 3.0 9.5 + - - +
401A LYS* 1.3 76.0 - - - +
403A MET* 1.3 62.8 - - - +
405A LEU* 3.1 7.6 + - - +
406A LEU* 3.1 25.8 + - + +
433A VAL* 3.6 20.2 - - + -
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Residues in contact with MET 403 (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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399A CYS 2.8 17.3 + - - +
400A VAL* 3.0 9.8 + - - +
402A ALA* 1.3 74.7 - - - +
404A ILE* 1.3 59.4 + - - +
406A LEU* 3.7 1.3 - - - +
407A ASN* 2.8 36.4 + - + +
430A LEU* 4.5 10.3 - - + -
433A VAL* 3.4 20.0 - - + +
434A THR* 4.0 19.3 - - + +
437A LEU* 3.6 29.4 - - + -
459A LEU* 3.4 28.9 - - + -
462A LEU* 4.7 9.4 - - + -
460B MET* 3.4 34.3 - - + -
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Residues in contact with ILE 404 (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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334A CYS* 3.8 2.6 - - + +
337A GLU* 3.6 41.6 - - + +
338A VAL* 3.9 13.2 - - + +
341A MET* 3.7 39.0 - - + -
400A VAL* 2.8 23.6 + - + +
401A LYS* 3.5 9.6 - - - +
402A ALA 3.2 0.2 - - - -
403A MET* 1.3 75.5 - - - +
405A LEU* 1.3 64.4 + - - +
407A ASN* 4.0 2.6 - - - -
408A SER* 3.2 22.3 + - - -
462A LEU* 4.1 23.1 - - + -
465A VAL* 4.6 9.6 - - + -
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Residues in contact with LEU 405 (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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312A TRP* 3.9 17.3 - - + -
313A ALA* 3.7 17.5 - - + -
316A ILE* 3.4 31.4 - - + -
319A PHE* 4.0 15.9 - - + -
330A LEU* 3.8 21.4 - - + +
331A LEU* 3.6 20.9 - - + -
334A CYS* 3.5 27.1 - - - -
338A VAL* 4.7 0.2 - - - +
401A LYS 3.3 1.6 + - - -
402A ALA 3.1 8.7 + - - +
403A MET 3.1 0.6 - - - -
404A ILE* 1.3 79.8 - - - +
406A LEU* 1.3 66.8 + - + +
407A ASN 3.2 0.2 + - - -
408A SER* 2.7 23.2 + - - -
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Residues in contact with LEU 406 (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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316A ILE* 5.0 5.6 - - + -
319A PHE* 4.7 7.6 - - + -
322A LEU* 5.1 0.2 - - + -
330A LEU* 4.4 9.6 - - + -
402A ALA 3.1 13.8 + - - +
405A LEU* 1.3 87.7 - - + +
407A ASN* 1.3 57.9 + - - +
408A SER 3.6 0.4 - - - -
409A SER* 4.6 2.6 - - - -
426A LEU* 3.6 41.2 - - + +
429A LEU* 3.4 44.2 - - + -
430A LEU* 3.7 37.7 - - + +
433A VAL* 3.5 23.1 - - + -
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Residues in contact with ASN 407 (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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403A MET* 2.8 18.6 + - + +
404A ILE* 4.0 2.7 - - - +
406A LEU* 1.3 78.2 + - - +
408A SER* 1.3 57.2 + - - +
409A SER* 2.9 9.8 + - - -
410A MET* 4.1 0.7 - - - +
430A LEU* 4.2 20.4 - - + +
462A LEU* 5.6 5.0 - - + +
466A ARG* 4.2 2.7 + - - -
386B ARG* 5.7 2.4 - - - +
460B MET* 2.9 43.3 + - - +
461B LEU* 5.6 1.8 - - - +
463B SER* 4.9 4.1 + - - -
464B HIS* 2.7 38.5 + - - -
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Residues in contact with SER 408 (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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330A LEU* 3.0 21.2 + - - -
333A SER* 3.4 24.6 + - - -
334A CYS* 3.4 26.8 - - - +
337A GLU* 4.7 4.0 - - - -
404A ILE 3.2 6.8 + - - -
405A LEU 2.7 19.9 + - - -
407A ASN* 1.3 75.6 - - - +
409A SER* 1.3 61.7 + - - +
410A MET* 3.5 14.1 + - - +
466A ARG* 4.3 12.0 + - - +
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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