Contacts of the strand formed by residues 242 - 248 (chain G) in PDB entry 6S7T
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 LEU 242 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201G GLY* 3.7 7.8 - - - -
202G MET* 2.8 50.2 + - + +
203G VAL* 4.3 2.0 - - - -
204G ALA* 3.7 35.9 - - + +
212G LEU 4.7 0.7 - - - +
213G ASP* 3.5 33.2 - - + +
215G LEU 4.2 3.1 - - - +
216G THR* 3.6 22.7 - - + -
240G ASN* 4.1 9.4 - - - +
241G THR* 1.3 73.9 - - - +
243G LEU* 1.3 62.8 + - - +
244G ILE 4.9 0.7 - - - +
245G ALA* 4.0 22.2 - - + -
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Residues in contact with LEU 243 (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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156G VAL* 3.8 26.9 - - + -
173G ILE* 4.5 7.9 - - + -
175G ALA* 4.1 16.2 - - + -
197G PHE* 3.7 41.9 - - + -
202G MET* 3.9 10.6 - - - +
215G LEU* 2.8 40.4 + - + +
216G THR 3.9 17.0 - - - +
217G GLY* 4.2 6.3 - - - -
241G THR* 4.1 5.6 - - + -
242G LEU* 1.3 81.5 - - - +
244G ILE* 1.3 56.7 + - - +
258G SER 2.7 30.0 - - - +
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Residues in contact with ILE 244 (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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197G PHE* 4.1 11.2 - - + -
213G ASP* 3.7 1.9 - - - +
214G ILE* 2.9 41.8 + - + -
215G LEU* 3.1 33.6 + - + +
242G LEU* 4.9 0.7 - - - +
243G LEU* 1.3 79.1 + - - +
245G ALA* 1.3 64.1 + - - +
256G ILE* 4.2 9.2 - - + -
257G PHE 3.6 6.5 - - - +
258G SER* 3.3 33.4 - - - +
263G PHE* 4.7 22.2 - - + -
291G LEU* 5.8 2.0 - - + -
295G LEU* 3.6 28.3 - - + -
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Residues in contact with ALA 245 (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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147G ILE* 3.6 25.2 - - + +
202G MET* 4.1 15.9 - - + -
212G LEU 3.8 12.3 - - - +
214G ILE 4.3 0.4 - - - +
242G LEU* 4.0 20.0 - - + -
243G LEU 4.2 0.2 - - - -
244G ILE* 1.3 76.0 - - - +
246G GLY* 1.3 59.6 + - - +
255G VAL 4.2 0.2 - - - +
256G ILE* 4.1 3.6 - - - -
257G PHE* 2.9 37.8 + - - +
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Residues in contact with GLY 246 (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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147G ILE* 4.9 1.3 - - - -
211G VAL* 3.6 6.5 - - - +
212G LEU* 2.7 46.9 + - - +
214G ILE* 3.9 9.6 - - - +
245G ALA* 1.3 75.4 - - - +
247G LEU* 1.3 57.5 + - - -
255G VAL 3.2 10.5 - - - -
256G ILE* 3.6 12.8 - - - -
298G TRP* 4.8 3.8 - - - -
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Residues in contact with LEU 247 (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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778A ARG* 4.7 15.7 - - + -
779A GLU 5.9 0.4 - - - +
120G ILE* 5.3 2.2 - - + -
145G CYS* 3.2 42.8 - - + +
147G ILE* 5.4 4.5 - - + -
208G ASN* 6.3 0.9 - - - +
210G LEU* 4.4 17.3 - - + -
211G VAL* 4.7 11.7 - - + +
212G LEU* 5.3 0.4 - - - -
246G GLY* 1.3 75.0 - - - +
248G GLN* 1.3 63.0 + - - +
249G ALA* 3.8 27.4 - - + +
253G ALA 3.2 8.7 - - - +
254G ARG* 3.5 3.1 - - - -
255G VAL* 2.8 51.0 + - + +
257G PHE* 6.3 0.2 - - + -
298G TRP* 4.1 5.7 - - - -
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Residues in contact with GLN 248 (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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210G LEU* 3.8 27.9 + - - +
212G LEU* 4.7 9.6 - - + +
247G LEU* 1.3 75.4 - - - +
249G ALA* 1.3 65.3 + - - +
252G ASN* 2.9 43.0 + - - +
253G ALA 3.7 1.8 - - - -
254G ARG* 2.9 38.5 + - - +
298G TRP* 3.8 11.9 + - + -
395G ASN* 6.2 1.6 - - - +
398G GLY 4.8 1.0 - - - +
399G TYR 4.4 11.7 - - - +
400G THR* 4.0 10.7 - - - +
401G HIS* 4.4 2.4 - - + +
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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