Contacts of the strand formed by residues 284 - 296 (chain G) in PDB entry 1YYL
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 284 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272G ILE* 4.1 25.4 - - + -
273G ARG 3.5 9.0 - - - +
274G SER* 4.3 11.7 - - - -
277G PHE* 4.2 19.1 - - + -
282G LYS 4.3 5.6 - - - +
283G THR* 1.3 74.5 - - - +
285G ILE* 1.3 63.0 + - - +
286G VAL* 3.6 13.1 + - + -
349G LEU* 4.3 9.6 - - + -
353G PHE* 4.5 4.9 - - + -
452G LEU 3.7 0.2 - - - +
453G LEU* 3.6 3.3 - - - -
454G LEU* 2.9 42.8 + - + +
455G THR* 5.2 0.4 - - - -
456G ARG* 4.7 10.1 - - + +
468G PHE* 4.1 31.6 - - + -
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Residues in contact with ILE 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G MET* 4.1 7.6 - - + -
96G TRP* 3.7 33.2 - - + -
260G LEU* 4.3 5.6 - - + -
271G VAL 4.0 0.7 - - - +
272G ILE* 3.6 1.4 - - - -
273G ARG* 2.7 39.5 + - + +
283G THR* 4.8 2.9 - - + +
284G ILE* 1.3 73.4 - - - +
286G VAL* 1.3 64.2 + - - +
287G GLN* 3.8 4.6 + - + +
452G LEU 3.7 2.7 - - - -
453G LEU* 3.8 20.6 - - + -
477G ASP* 3.7 29.4 - - + +
480G ARG* 4.1 11.9 - - + -
481G SER* 3.6 27.1 - - - +
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Residues in contact with VAL 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260G LEU* 4.8 1.6 - - - +
270G ILE* 4.1 15.0 - - + -
271G VAL 3.9 2.7 - - - -
272G ILE* 4.4 9.2 - - + +
284G ILE* 4.3 12.6 - - + +
285G ILE* 1.3 77.8 - - - +
287G GLN* 1.3 60.0 + - - +
288G LEU* 4.1 8.1 - - + -
345G ILE* 3.9 37.0 - - + -
349G LEU* 6.4 0.2 - - + -
451G GLY* 3.0 25.5 - - - -
452G LEU* 2.9 26.4 + - + +
454G LEU* 3.7 31.9 - - + -
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Residues in contact with GLN 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264G SER* 3.6 24.4 + - - +
265G LEU 3.6 9.1 + - - -
266G ALA* 3.6 21.7 - - + +
270G ILE* 3.4 6.7 - - - +
271G VAL* 2.9 40.2 + - - +
273G ARG* 2.6 31.2 + - - +
285G ILE* 3.8 4.2 + - + +
286G VAL* 1.3 73.1 - - - +
288G LEU* 1.3 71.9 + - - +
450G THR 3.9 2.9 - - - +
451G GLY* 4.5 0.2 - - - -
481G SER* 4.6 6.5 + - - +
484G TYR* 3.3 29.0 + - - -
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Residues in contact with LEU 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265G LEU* 3.3 14.7 - - + +
266G ALA 2.8 18.6 + - - -
270G ILE* 4.3 10.5 - - + -
286G VAL* 4.1 6.1 - - + -
287G GLN* 1.3 73.8 - - - +
289G ASN* 1.3 59.8 + - - +
290G GLU 3.3 19.5 - - - +
292G VAL* 4.2 13.2 - - + -
341G THR* 3.8 25.4 - - + -
345G ILE* 4.0 13.5 - - + -
449G ILE* 3.5 28.7 - - + +
450G THR 2.8 22.9 + - - +
451G GLY 3.9 2.5 - - - +
452G LEU* 3.9 21.8 - - + -
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Residues in contact with ASN 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G LEU* 4.0 11.4 - - - +
266G ALA* 3.4 22.2 - - + +
267G GLU 5.4 0.2 - - - +
268G GLU 3.2 19.5 + - - +
269G GLU* 3.4 10.1 - - - +
270G ILE* 3.4 15.4 - - - +
287G GLN 3.9 0.6 + - - -
288G LEU* 1.3 73.7 - - - +
290G GLU* 1.3 66.9 + - - +
789G NAG 1.5 74.5 + - - +
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Residues in contact with GLU 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G LEU* 3.8 8.4 - - - +
288G LEU* 3.3 19.6 - - - +
289G ASN* 1.3 90.4 + - - +
291G SER* 1.3 70.4 + - - +
292G VAL* 3.7 4.9 + - - +
337G GLN* 3.8 19.4 + - - +
341G THR* 5.4 0.5 + - - -
789G NAG 3.9 21.3 + - - +
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Residues in contact with SER 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G LEU* 3.3 27.9 - - - +
290G GLU* 1.3 78.7 - - - +
292G VAL* 1.3 60.0 + - - +
293G VAL* 4.1 3.1 + - - +
337G GLN* 3.4 17.2 - - - +
448G ASN* 3.3 37.7 + - - +
449G ILE 3.5 7.4 - - - -
450G THR* 3.8 3.5 - - - +
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Residues in contact with VAL 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G LEU* 4.2 11.4 - - + -
290G GLU 3.9 8.7 - - - +
291G SER* 1.3 75.5 - - - +
293G VAL* 1.3 66.9 + - - +
333G LEU* 3.3 28.3 - - + -
334G SER* 5.2 1.1 - - - +
337G GLN* 3.5 34.1 - - + +
338G TRP* 4.1 16.4 - - + +
341G THR* 3.5 23.1 - - - +
448G ASN* 4.4 0.7 - - - -
449G ILE* 3.0 39.8 + - + +
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Residues in contact with VAL 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291G SER* 5.4 2.2 - - - +
292G VAL* 1.3 73.8 - - - +
294G ILE* 1.3 61.8 + - - +
295G ASN* 3.7 22.9 - - - +
332G ASN 4.0 0.7 - - - +
333G LEU* 3.6 20.7 - - - +
334G SER* 4.4 3.1 + - - -
337G GLN* 5.7 1.2 - - - +
446G SER* 4.6 4.5 - - - +
447G SER 3.6 10.3 - - - +
448G ASN* 3.3 20.9 - - - +
795G NAG 4.0 30.0 - - + +
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Residues in contact with ILE 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259G LEU* 4.7 3.4 - - + -
261G LEU* 4.8 5.2 - - + -
293G VAL* 1.3 74.4 - - - +
295G ASN* 1.3 61.5 + - - +
296G CYS* 4.1 5.3 + - - -
331G CYS* 3.8 25.6 - - + -
332G ASN 3.2 16.2 - - - +
333G LEU* 4.5 7.0 - - + -
374G HIS* 4.5 24.2 - - + +
376G PHE* 5.9 0.9 - - + -
385G CYS* 5.8 0.2 - - - -
416G LEU* 4.7 14.1 - - + -
445G CYS 3.9 2.3 - - - +
447G SER* 3.1 43.5 + - - +
449G ILE* 3.9 31.4 - - + -
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Residues in contact with ASN 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293G VAL* 3.7 5.3 - - - +
294G ILE* 1.3 74.4 - - - +
296G CYS* 1.3 61.9 + - - +
331G CYS* 3.1 1.7 - - - -
332G ASN* 2.6 49.6 + - + +
445G CYS 3.5 2.0 - - - +
446G SER* 2.8 26.1 + - - -
795G NAG 1.4 71.9 + - + +
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Residues in contact with CYS 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294G ILE* 4.8 8.1 - - - -
295G ASN* 1.3 78.5 - - - +
297G THR* 1.3 69.5 + - - +
331G CYS* 2.0 49.8 - - - +
376G PHE* 4.0 21.3 - - - -
383G PHE* 4.1 11.2 - - + -
444G ARG* 4.0 8.8 - - - +
445G CYS* 2.7 42.9 + - + +
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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