Contacts of the helix formed by residues 244 - 249 (chain B) 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 THR 244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172B TYR* 3.2 33.6 - - + +
206B LEU* 3.7 22.5 - - - +
209B CYS* 5.3 1.1 - - - -
243B THR* 1.3 73.2 - - - +
245B PHE* 1.3 51.6 + - - +
246B PRO 3.2 2.2 - - - -
247B TYR* 2.8 32.7 + - + -
248B ASP* 2.5 39.3 + - - -
457B PRO* 4.7 2.2 - - + -
460B MET* 6.5 0.2 - - + -
499B ILE* 5.2 3.1 + - + +
500B PHE* 4.7 20.9 - - + -
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Residues in contact with PHE 245 (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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213B ALA* 4.8 9.4 - - + -
217B LEU* 4.8 11.0 - - + -
237B TYR* 3.5 28.5 - + - -
240B LEU* 3.7 40.2 - - + +
243B THR* 3.1 18.9 + - - +
244B THR* 1.3 75.2 - - - +
246B PRO* 1.3 69.0 - - + +
248B ASP* 3.0 31.9 + - + +
249B GLU 3.3 12.4 + - - +
252B LEU* 3.9 27.4 - - + -
253B ALA* 3.6 29.2 - - + -
256B LEU* 4.7 7.2 - - + -
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Residues in contact with PRO 246 (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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78B TYR 4.9 0.3 - - - +
240B LEU 4.3 4.7 - - - +
241B ALA* 5.1 8.5 - - - +
243B THR 3.5 14.1 - - - +
244B THR* 3.5 2.5 - - - -
245B PHE* 1.3 93.2 - - + +
247B TYR* 1.3 77.2 + - + +
250B PRO* 3.1 36.4 - - + +
253B ALA* 4.2 10.3 - - + -
299B CYS* 5.6 5.4 - - - -
302B LEU 6.0 0.4 - - - +
303B GLN* 3.3 34.1 - - + +
457B PRO* 6.3 0.2 - - + -
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Residues in contact with TYR 247 (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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78B TYR* 3.5 34.8 - + + -
210B GLN* 5.6 0.2 + - - -
244B THR* 2.8 37.5 + - + +
246B PRO* 1.3 89.1 - - + +
248B ASP* 1.3 65.9 + - - +
250B PRO* 4.9 2.5 - - - +
302B LEU* 5.4 5.2 + - - +
457B PRO* 3.6 30.8 - - + +
460B MET* 5.8 4.5 - - + -
461B GLN* 3.0 44.8 + - + +
503B LYS* 3.3 34.2 + - + +
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Residues in contact with ASP 248 (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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81B LYS* 5.8 1.4 - - - +
206B LEU* 4.1 2.8 - - - +
209B CYS* 5.2 5.7 - - - -
210B GLN* 3.1 50.3 + - + +
213B ALA* 5.1 3.3 - - - +
244B THR* 2.5 30.0 + - - +
245B PHE* 3.0 34.2 + - + +
246B PRO 3.2 0.2 - - - -
247B TYR* 1.3 79.7 - - - +
249B GLU* 1.3 81.1 + - + +
250B PRO* 4.1 2.3 - - - +
503B LYS* 5.3 0.7 + - - -
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Residues in contact with GLU 249 (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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81B LYS* 4.2 30.8 + - - +
83B ARG* 5.4 2.8 - - - -
214B ARG* 5.8 5.6 - - - +
245B PHE* 3.3 6.1 + - + +
246B PRO 3.6 1.3 - - - -
248B ASP* 1.3 90.3 - - + +
250B PRO* 1.3 65.2 - - - +
251B LEU* 3.2 5.6 + - + +
252B LEU* 3.1 28.1 + - + +
253B ALA* 2.9 25.8 + - - +
227C ALA* 6.0 3.4 - - + +
228C HIS* 5.7 2.9 + - - -
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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