Contacts of the helix formed by residues 393 - 408 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345B TRP* 3.6 2.7 - - - -
391B LYS* 3.5 32.0 + - - +
392B LEU* 1.3 78.2 + - - +
394B HIS* 1.3 56.5 + - - +
395B LYS* 4.3 6.3 - - + +
396B GLU* 2.7 34.0 + - + +
397B TYR* 2.8 34.5 + - - +
440B VAL* 5.5 1.8 - - + -
454B ARG* 5.2 1.8 - - - +
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Residues in contact with HIS 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 4.3 19.2 - - + +
276B GLU* 4.5 10.0 - - + +
345B TRP* 3.3 40.6 + - + -
393B GLN* 1.3 73.6 + - - +
395B LYS* 1.3 73.5 + - + +
397B TYR* 3.2 4.9 + + - +
398B LEU* 3.1 56.1 + - + +
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Residues in contact with LYS 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B VAL* 3.4 29.6 - - + +
270B LEU* 4.7 11.0 - - - +
273B LEU* 4.4 20.4 - - - -
393B GLN* 3.2 3.2 - - + +
394B HIS* 1.3 88.8 - - + +
396B GLU* 1.3 66.9 + - - +
398B LEU* 3.5 10.9 + - + +
399B CYS* 3.4 24.8 + - - -
439B TRP* 5.2 9.3 - - + -
440B VAL* 3.5 25.8 - - + -
443B LYS* 5.3 7.3 - - - +
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 3.6 12.3 - - + +
393B GLN* 2.7 46.6 + - + +
395B LYS* 1.3 74.8 - - - +
397B TYR* 1.3 52.4 + - - +
399B CYS* 3.0 5.7 + - - +
400B VAL* 2.8 39.0 + - + +
437B LEU* 3.9 19.2 - - + +
440B VAL* 3.8 16.8 - - + -
441B ILE* 3.4 13.7 - - + +
444B SER* 6.0 0.9 - - - -
454B ARG* 2.8 47.2 + - - -
458B LEU* 3.8 6.2 - - + +
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Residues in contact with TYR 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLU* 3.4 20.2 + - - -
341B MET* 3.7 26.5 - - + -
342B GLY* 3.7 12.0 + - - -
345B TRP* 3.4 57.6 - + + -
392B LEU* 4.0 17.4 - - + +
393B GLN 2.8 12.0 + - - +
394B HIS* 3.3 15.9 - + - +
396B GLU* 1.3 76.6 - - - +
398B LEU* 1.3 71.5 + - + +
400B VAL* 3.3 4.5 + - - +
401B LYS* 2.9 68.4 + - + +
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B VAL* 3.9 12.1 - - + +
272B LEU* 3.6 22.0 - - + +
273B LEU* 3.4 39.9 - - + +
276B GLU* 3.4 40.8 - - + +
312B TRP* 5.3 1.7 - - - -
394B HIS* 3.1 30.5 + - + +
395B LYS* 3.7 13.5 - - + +
396B GLU 3.3 0.2 - - - -
397B TYR* 1.3 87.9 - - + +
399B CYS* 1.3 57.2 + - - +
401B LYS* 3.8 5.3 + - - +
402B ALA* 3.2 27.4 + - - +
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Residues in contact with CYS 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B VAL* 4.0 12.8 - - - -
272B LEU* 4.3 6.5 - - - -
395B LYS 3.4 13.9 + - - -
396B GLU 3.0 8.1 + - - +
398B LEU* 1.3 78.5 - - - +
400B VAL* 1.3 55.9 + - - +
402B ALA 3.2 0.7 + - - -
403B MET* 2.8 41.4 + - - +
433B VAL* 3.6 15.0 - - + +
436B ALA* 3.8 17.5 - - - -
437B LEU* 3.7 43.3 - - + -
440B VAL* 4.5 1.6 - - - -
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Residues in contact with VAL 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B MET* 4.1 20.6 - - + -
387B PHE* 5.2 7.4 - - + -
392B LEU* 4.7 12.1 - - + -
396B GLU 2.8 24.5 + - - +
397B TYR* 3.7 7.2 - - - +
399B CYS* 1.3 75.1 - - - +
401B LYS* 1.3 57.9 + - - +
403B MET* 3.3 9.8 + - - +
404B ILE* 3.0 32.4 + - + +
437B LEU* 4.4 17.7 - - + -
458B LEU* 5.0 15.5 - - + +
459B LEU* 5.3 4.3 - - + -
462B LEU* 3.6 27.9 - - + +
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Residues in contact with LYS 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLU* 2.6 32.1 + - - -
277B PRO* 4.0 14.3 - - - +
312B TRP* 3.8 30.2 - - + +
338B VAL* 4.0 34.1 - - + +
341B MET* 4.1 16.4 - - + +
342B GLY* 4.6 2.4 - - - +
397B TYR* 2.9 48.3 + - + +
398B LEU* 4.0 5.2 - - - +
400B VAL* 1.3 75.8 - - - +
402B ALA* 1.3 63.9 + - - +
404B ILE* 3.3 22.4 + - - +
405B LEU* 3.5 4.7 + - - +
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Residues in contact with ALA 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 3.9 27.4 - - + -
312B TRP* 4.0 15.0 - - + -
316B ILE* 4.5 7.8 - - + +
398B LEU 3.2 17.8 + - - +
399B CYS 3.6 3.1 - - - +
401B LYS* 1.3 79.1 - - - +
403B MET* 1.3 60.6 + - - +
405B LEU* 3.4 5.7 + - - +
406B LEU* 3.2 27.5 + - - +
433B VAL* 4.1 13.0 - - + -
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Residues in contact with MET 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A MET* 3.8 20.4 - - + -
399B CYS 2.8 22.4 + - - +
400B VAL* 3.5 7.6 - - - +
402B ALA* 1.3 75.3 - - - +
404B ILE* 1.3 57.0 + - - +
406B LEU* 4.0 0.8 - - - +
407B ASN* 2.7 39.5 + - - +
430B LEU* 3.9 19.5 - - + +
433B VAL* 3.6 18.8 - - + -
434B THR* 3.5 25.6 - - + +
437B LEU* 3.8 29.2 - - + -
459B LEU* 3.7 29.2 - - + -
462B LEU* 5.2 7.0 - - + -
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Residues in contact with ILE 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B CYS* 4.2 2.0 - - + -
337B GLU* 3.7 39.4 - - + +
338B VAL* 4.0 12.1 - - + -
341B MET* 3.8 39.0 - - + -
400B VAL 3.0 20.7 + - - +
401B LYS* 3.4 9.9 - - + +
402B ALA 3.3 0.4 - - - -
403B MET* 1.3 75.8 - - - +
405B LEU* 1.3 62.4 + - - +
407B ASN* 3.5 3.5 + - - +
408B SER* 3.2 23.6 + - - -
462B LEU* 3.6 28.0 - - + -
465B VAL* 4.4 9.4 - - + -
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TRP* 4.1 14.8 - - + -
313B ALA* 4.3 5.4 - - + -
316B ILE* 3.2 32.8 - - + -
319B PHE* 4.0 23.8 - - + -
330B LEU* 3.7 22.3 - - + +
331B LEU* 3.5 28.7 - - + -
334B CYS* 3.5 23.3 - - - -
338B VAL* 4.6 1.3 - - + +
401B LYS 3.5 6.5 + - - +
402B ALA 3.4 7.5 + - - +
403B MET 3.2 0.6 - - - -
404B ILE* 1.3 80.5 - - - +
406B LEU* 1.3 64.4 + - + +
408B SER* 2.8 21.5 + - - -
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Residues in contact with LEU 406 (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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316B ILE* 4.6 19.1 - - + -
319B PHE* 4.7 9.2 - - + -
330B LEU* 4.5 2.9 - - + +
402B ALA 3.2 16.6 + - - +
405B LEU* 1.3 86.9 - - + +
407B ASN* 1.3 60.3 + - - +
408B SER 3.6 0.3 + - - -
409B SER* 4.1 2.8 + - - -
426B LEU* 4.0 43.1 - - + +
429B LEU* 3.8 32.5 - - + +
430B LEU* 3.8 28.7 - - + +
433B VAL* 3.6 31.9 - - + -
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Residues in contact with ASN 407 (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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386A ARG* 4.8 7.9 - - - +
460A MET* 2.9 48.7 + - + +
461A LEU* 5.1 0.2 - - - +
463A SER* 3.8 10.9 + - - -
464A HIS* 2.5 50.9 + - - -
403B MET 2.7 23.6 + - - +
404B ILE* 3.9 4.0 - - - +
406B LEU* 1.3 70.8 - - - +
408B SER* 1.3 54.6 + - - +
409B SER* 2.9 7.8 + - - -
430B LEU* 4.0 18.1 - - + +
462B LEU* 4.8 5.8 - - + +
466B ARG* 4.3 2.0 + - - -
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Residues in contact with SER 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ARG* 4.7 1.2 + - - +
330B LEU* 3.3 24.3 + - - +
333B SER* 2.9 25.6 + - - -
334B CYS* 3.6 14.1 - - - +
337B GLU* 4.5 5.6 - - - -
404B ILE 3.2 13.6 + - - -
405B LEU 2.8 19.8 + - - -
406B LEU 3.3 1.0 - - - -
407B ASN* 1.3 75.1 - - - +
409B SER* 1.3 48.6 + - - +
410B MET* 2.4 32.6 + - - +
466B ARG* 4.3 3.6 - - - +
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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