Contacts of the strand formed by residues 235 - 242 (chain L) in PDB entry 6G2T
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 235 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193L LYS* 5.5 3.8 - - - -
233L PHE 3.5 3.2 + - - -
234L THR* 1.3 78.5 - - - +
236L SER* 1.3 60.3 + - - -
237L TYR* 4.9 5.4 - - - -
253L ASN* 3.5 10.4 - - - +
254L LEU 3.1 30.0 + - - +
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Residues in contact with SER 236 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193L LYS* 4.3 1.5 - - - +
194L GLY* 2.9 30.5 + - - -
235L GLY* 1.3 72.5 - - - -
237L TYR* 1.3 72.4 + - - +
251L ASN* 5.1 8.5 + - - +
252L PHE 4.1 1.6 + - - -
253L ASN* 3.2 18.4 + - - -
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Residues in contact with TYR 237 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174L PHE* 4.8 0.2 - + - -
192L PHE 3.2 7.4 - - - +
193L LYS* 3.4 38.5 - - + +
199L LEU* 4.7 12.7 - - + +
224L LEU* 4.4 9.2 - - + -
226L ILE* 3.9 14.6 - - + +
233L PHE* 3.0 38.9 + - - +
235L GLY 4.4 1.1 + - - -
236L SER* 1.3 88.4 + - - +
238L ARG* 1.3 60.6 + - - +
251L ASN* 3.7 4.0 - - - +
252L PHE* 2.8 75.0 + + + +
254L LEU* 3.6 33.0 - - + +
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Residues in contact with ARG 238 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190L LYS 4.1 0.2 - - - +
191L TRP* 3.7 2.6 - - - -
192L PHE* 2.8 66.2 + - + +
194L GLY 4.6 10.8 + - - +
195L LYS* 4.4 27.8 - - - +
236L SER 4.4 0.4 + - - -
237L TYR* 1.3 74.1 - - - +
239L CYS* 1.3 63.8 + - - +
240L GLU* 4.0 6.8 + - + +
249L CYS* 3.9 34.8 - - + -
250L SER 3.5 5.4 - - - +
251L ASN* 3.4 34.9 + - - +
252L PHE* 4.5 2.5 - - - -
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Residues in contact with CYS 239 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157L PHE* 3.5 12.1 - - + -
161L PRO* 3.7 27.8 - - + -
176L ALA* 4.1 11.9 - - - -
189L VAL* 4.1 10.3 - - - -
190L LYS 3.9 2.2 - - - -
191L TRP* 3.6 43.5 - - + -
237L TYR 4.2 0.6 + - - -
238L ARG* 1.3 72.4 - - - +
240L GLU* 1.3 61.2 + - - +
241L VAL* 4.5 1.3 - - - -
249L CYS* 3.2 4.5 - - - -
250L SER 2.9 37.6 + - - +
252L PHE* 4.0 2.8 - - + -
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Residues in contact with GLU 240 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188L VAL 4.0 0.5 - - - +
189L VAL* 3.4 2.1 - - - +
190L LYS* 2.7 61.1 + - + +
192L PHE* 3.8 25.0 - - + -
238L ARG* 4.0 8.3 + - + -
239L CYS* 1.3 74.4 - - - +
241L VAL* 1.3 69.4 + - - +
242L SER* 5.1 7.3 - - - +
247L PHE* 5.4 10.0 - - + +
248L ASP 3.6 14.6 - - - +
249L CYS* 4.3 9.2 - - + -
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Residues in contact with VAL 241 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156L LEU* 3.8 8.8 - - + +
157L PHE* 3.3 28.6 - - + -
176L ALA* 5.0 2.7 - - + -
178L VAL* 3.8 31.0 - - + -
187L PRO* 3.9 20.2 - - + -
188L VAL 3.4 8.1 - - - +
189L VAL* 3.7 20.4 - - + -
222L PHE* 4.2 6.5 - - + -
239L CYS* 4.5 4.3 - - - -
240L GLU* 1.3 80.1 - - - +
242L SER* 1.3 65.3 + - - +
243L THR* 4.7 2.2 - - + -
247L PHE* 4.2 0.2 - - - -
248L ASP* 3.2 29.7 + - - +
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Residues in contact with SER 242 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187L PRO* 3.4 4.5 - - - +
188L VAL* 2.8 53.5 + - - +
190L LYS* 5.8 4.3 - - - +
240L GLU* 5.3 7.9 - - - -
241L VAL* 1.3 75.6 - - - +
243L THR* 1.3 63.2 + - - +
246L LYS 4.0 2.7 - - - -
247L PHE* 3.7 25.1 - - - -
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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