Contacts of the strand formed by residues 445 - 456 (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 CYS 445 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294G ILE 3.9 1.4 - - - +
295G ASN* 3.5 3.1 - - - +
296G CYS* 2.7 50.4 + - + +
376G PHE* 4.0 9.9 - - - -
378G CYS* 2.0 51.6 - - + -
383G PHE* 4.3 5.6 - - + -
444G ARG* 1.3 83.7 - - - +
446G SER* 1.3 59.4 + - - +
447G SER* 3.5 20.0 - - - -
762G NAG 3.8 2.5 - - - -
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Residues in contact with SER 446 (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* 4.6 4.5 - - - +
295G ASN* 2.8 22.3 + - - -
444G ARG* 5.4 1.3 - - - +
445G CYS* 1.3 74.4 - - - +
447G SER* 1.3 64.1 + - - +
762G NAG 3.1 38.6 + - - +
795G NAG 3.8 26.1 + - - -
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Residues in contact with SER 447 (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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261G LEU* 4.0 25.2 - - - +
262G ASN* 3.4 10.8 - - - -
293G VAL* 3.6 5.7 - - - +
294G ILE* 3.1 43.4 + - - +
376G PHE* 5.2 0.3 - - - -
445G CYS* 3.5 14.7 - - - -
446G SER* 1.3 80.5 + - - +
448G ASN* 1.3 63.2 + - - +
449G ILE 4.0 0.2 - - - -
762G NAG 3.3 19.3 + - - -
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Residues in contact with ASN 448 (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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252G ARG* 5.6 6.9 - - - +
261G LEU* 3.6 2.5 - - - -
262G ASN* 2.8 44.9 + - - +
291G SER* 3.3 33.9 + - - +
292G VAL 4.0 1.3 - - - -
293G VAL* 3.3 25.4 - - - +
447G SER* 1.3 73.2 - - - +
449G ILE* 1.3 64.5 + - - +
450G THR* 3.2 6.9 + - + +
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Residues in contact with ILE 449 (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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259G LEU* 4.0 27.1 - - + -
260G LEU 3.6 7.2 - - - +
261G LEU* 4.1 9.4 - - + -
288G LEU* 3.5 12.0 - - + +
291G SER* 3.5 6.8 - - - -
292G VAL* 3.0 44.5 + - + +
294G ILE* 3.9 22.4 - - + -
333G LEU* 3.9 24.7 - - + -
338G TRP* 3.9 24.7 - - + -
448G ASN* 1.3 68.5 - - - +
450G THR* 1.3 61.2 + - - +
451G GLY 3.8 17.9 - - - +
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Residues in contact with THR 450 (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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260G LEU* 3.1 14.2 + - - +
261G LEU 4.1 0.3 - - - -
262G ASN 4.4 0.9 - - - -
263G GLY* 2.9 53.0 + - - +
264G SER 4.4 5.7 - - - +
265G LEU* 3.5 26.9 - - + +
287G GLN* 3.8 3.1 - - - +
288G LEU* 2.8 31.7 + - - +
291G SER* 3.8 10.8 - - - +
448G ASN* 3.2 11.9 + - + +
449G ILE* 1.3 73.3 - - - +
451G GLY* 1.3 58.6 + - - +
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Residues in contact with GLY 451 (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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259G LEU* 3.7 2.1 - - - -
260G LEU* 2.8 36.6 + - - +
286G VAL 3.0 14.6 - - - -
287G GLN* 4.5 0.2 - - - -
288G LEU* 3.9 2.1 - - - +
449G ILE* 3.7 4.6 - - - +
450G THR* 1.3 81.7 + - - +
452G LEU* 1.3 78.4 + - - +
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Residues in contact with LEU 452 (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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258G GLN 3.2 9.6 - - - +
259G LEU* 3.8 12.1 - - + -
260G LEU* 4.2 4.5 - - - +
284G ILE 3.7 0.5 - - - +
285G ILE* 3.7 0.9 - - - +
286G VAL* 2.9 40.4 + - + +
288G LEU* 3.9 28.7 - - + -
338G TRP* 3.5 30.5 - - + -
342G LEU* 5.2 2.0 - - + -
345G ILE* 4.1 18.2 - - + -
361G PHE* 6.3 0.4 - - + -
391G PHE* 4.0 19.5 - - + -
451G GLY* 1.3 97.0 - - - +
453G LEU* 1.3 70.6 + - - +
454G LEU* 4.0 11.4 - - + -
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Residues in contact with LEU 453 (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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256G SER 5.3 1.6 - - - +
257G THR* 5.4 0.4 - - - -
258G GLN 2.8 19.3 + - - +
260G LEU* 4.2 18.2 - - + -
283G THR* 4.0 11.4 - - + -
284G ILE 3.6 1.1 - - - -
285G ILE* 3.8 33.2 - - + -
452G LEU* 1.3 81.6 - - - +
454G LEU* 1.3 57.6 + - - +
470G PRO* 3.4 5.7 - - - +
471G GLY* 2.5 31.8 + - - +
472G GLY* 3.5 36.1 - - - +
474G ASP 5.3 0.2 - - - +
477G ASP* 4.3 16.8 - - + +
478G ASN* 3.9 22.7 - - - +
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Residues in contact with LEU 454 (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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283G THR* 3.4 5.0 - - - +
284G ILE* 2.9 45.0 + - + +
286G VAL* 3.7 27.4 - - + -
345G ILE* 4.5 7.6 - - + -
349G LEU* 4.8 6.7 - - + -
361G PHE* 3.9 29.2 - - + -
391G PHE* 4.0 28.9 - - + -
452G LEU* 4.5 10.3 - - + -
453G LEU* 1.3 81.7 - - - +
455G THR* 1.3 67.8 + - - +
468G PHE* 4.6 11.0 - - + -
469G ARG 3.2 19.1 - - - +
470G PRO* 4.3 0.2 - - + -
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Residues in contact with THR 455 (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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280G ASN 4.7 10.3 - - - +
281G ALA 6.5 0.4 - - - -
282G LYS 5.0 4.7 - - - -
283G THR* 4.8 13.9 - - + +
284G ILE* 5.0 1.6 - - - -
454G LEU* 1.3 78.8 - - - +
456G ARG* 1.3 60.9 + - - +
457G ASP* 4.1 0.9 + - - -
468G PHE* 3.0 10.0 - - - +
469G ARG* 2.9 48.5 + - - +
470G PRO 5.0 1.3 + - - +
471G GLY* 4.3 17.9 - - - -
27M VLM 6.4 2.5 - - + -
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Residues in contact with ARG 456 (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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277G PHE 2.8 24.0 + - - -
278G THR* 3.2 19.6 + - - +
280G ASN* 3.1 44.6 + - + +
282G LYS 5.4 0.8 + - - -
284G ILE* 4.7 7.8 - - + +
353G PHE* 3.1 36.1 - - - -
455G THR* 1.3 75.0 - - - +
457G ASP* 1.3 80.8 + - - +
458G GLY* 3.3 2.5 + - - -
459G GLY 5.3 2.2 - - - +
466G GLU* 3.1 33.8 + - + +
467G ILE 3.2 13.5 - - - +
468G PHE* 3.8 19.3 - - + -
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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