Contacts of the helix formed by residues 280 - 288 (chain H) in PDB entry 6GYS
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 GLY 280 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202H GLY 4.0 11.3 + - - -
203H GLN* 5.1 5.6 - - - -
278H VAL* 4.5 2.1 - - - +
279H ARG* 1.3 79.5 - - - +
281H GLU* 1.3 55.5 + - - -
282H LYS* 3.3 3.1 - - - -
283H LEU* 3.1 14.8 + - - +
284H TYR* 2.5 35.8 + - - +
316H ARG 4.3 1.1 - - - -
317H MET* 4.5 1.8 - - - -
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Residues in contact with GLU 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H GLY* 1.3 68.3 - - - -
282H LYS* 1.3 73.7 + - + +
284H TYR* 3.1 4.4 + - + +
285H GLU* 2.6 60.9 + - - +
316H ARG 3.9 6.7 + - - -
317H MET* 3.6 35.0 - - + -
318H ASN* 3.7 14.0 - - + +
319H GLN 3.1 27.1 - - - +
322H ARG* 4.2 12.5 - - - +
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Residues in contact with LYS 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203H GLN* 3.3 28.3 - - - +
253H ASN* 5.0 17.3 - - - +
280H GLY* 3.3 0.6 - - - -
281H GLU* 1.3 87.6 - - + +
283H LEU* 1.3 62.8 + - - +
285H GLU* 3.4 9.7 + - + +
286H LEU* 3.3 32.7 + - + +
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Residues in contact with LEU 283 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201H PHE* 3.7 23.8 - - + -
202H GLY 3.6 41.3 - - - +
203H GLN* 2.8 22.9 + - + +
260H VAL* 4.5 17.5 - - + -
278H VAL* 4.0 7.9 - - + -
280H GLY* 3.1 14.6 + - - +
282H LYS* 1.3 73.4 - - - +
284H TYR* 1.3 65.2 + - - +
286H LEU* 3.1 11.0 + - + +
287H LEU* 3.0 51.4 + - + +
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Residues in contact with TYR 284 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278H VAL* 4.4 6.1 - - + -
280H GLY 2.5 19.7 + - - +
281H GLU* 3.1 8.5 + - - +
283H LEU* 1.3 72.8 - - - +
285H GLU* 1.3 65.1 + - - +
287H LEU* 3.7 7.6 - - - +
288H ILE* 3.4 38.5 + - + -
289H ASN* 3.0 58.5 + - + +
314H LEU* 4.3 14.9 - - + +
317H MET* 3.5 28.3 - - - -
319H GLN 4.7 0.4 - - - -
320H ILE* 3.9 21.9 - - + +
326H ALA* 3.3 32.4 - - - +
328H PHE* 4.0 13.9 - + - -
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Residues in contact with GLU 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281H GLU* 2.6 45.8 + - - +
282H LYS* 3.5 13.5 - - + +
284H TYR* 1.3 80.2 - - - +
286H LEU* 1.3 67.0 + - + +
287H LEU 3.5 0.2 + - - -
289H ASN* 2.9 53.4 + - - +
291H HIS* 5.7 0.5 - - - +
320H ILE 4.1 3.6 - - - +
322H ARG* 4.5 7.1 - - - +
323H THR* 4.0 15.1 - - - +
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Residues in contact with LEU 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203H GLN* 5.6 5.8 - - - +
253H ASN 3.4 21.5 - - - +
254H GLN* 4.4 7.6 - - + -
255H LEU 3.6 27.8 - - - +
256H THR* 3.6 33.3 - - + +
282H LYS* 3.3 24.9 - - + +
283H LEU* 3.1 12.4 + - + +
285H GLU* 1.3 86.5 - - + +
287H LEU* 1.3 61.7 + - + +
299H LYS* 3.3 35.4 - - + +
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Residues in contact with LEU 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201H PHE* 4.0 19.7 - - + -
256H THR* 6.3 1.6 - - + -
260H VAL* 5.1 7.2 - - + -
264H ILE* 5.8 5.4 - - + -
276H ILE* 5.3 0.2 - - + -
278H VAL* 3.7 26.5 - - + -
283H LEU* 3.0 45.7 + - + +
284H TYR* 3.7 6.3 - - - -
285H GLU 3.4 0.6 - - - -
286H LEU* 1.3 84.2 - - + +
288H ILE* 1.3 89.0 + - + +
289H ASN 5.4 0.4 - - - -
299H LYS* 4.1 8.7 - - - +
301H ILE* 3.4 43.6 - - + +
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Residues in contact with ILE 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276H ILE* 5.8 2.2 - - + -
278H VAL* 4.8 7.0 - - + -
284H TYR* 3.5 31.0 - - + -
287H LEU* 1.3 99.4 - - + +
289H ASN* 1.3 65.9 + - - +
290H PHE* 2.9 13.2 + - - +
301H ILE* 3.8 5.6 - - + -
312H ILE* 4.5 12.6 - - + -
314H LEU* 4.2 15.9 - - + -
327H ASP 3.0 13.2 - - - +
328H PHE* 3.3 26.4 - - + -
331H TRP* 3.6 36.3 + - + +
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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