Contacts of the strand formed by residues 252 - 262 (chain F) in PDB entry 6GL7
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 GLU 252 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160F LEU 5.6 0.3 - - - +
161F LYS* 5.4 6.6 + - - +
162F PRO* 3.3 35.0 - - + +
243F CYS 3.9 0.7 - - - +
244F THR* 3.4 3.9 - - - -
245F VAL* 3.1 44.9 + - + +
246F HIS* 5.1 3.5 + - - -
250F ARG 3.8 9.8 - - - +
251F GLU* 1.3 79.9 - - - +
253F VAL* 1.3 63.5 + - - +
254F VAL 4.2 0.3 + - - -
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Residues in contact with VAL 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F PRO* 5.6 0.3 - - - +
205F ARG* 5.6 5.4 - - - +
242F VAL* 3.5 26.5 - - + -
243F CYS 3.4 5.2 - - - +
244F THR* 3.6 23.6 - - + +
251F GLU* 5.6 2.5 - - + -
252F GLU* 1.3 76.1 - - - +
254F VAL* 1.3 64.3 + - - +
255F MET* 4.8 9.6 - - + -
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Residues in contact with VAL 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162F PRO* 3.7 34.3 - - + +
163F ARG* 4.2 25.6 - - + +
167F PHE* 3.5 9.1 - - + -
242F VAL* 3.5 3.1 - - - +
243F CYS* 3.0 50.7 + - - -
253F VAL* 1.3 75.9 - - - +
255F MET* 1.3 71.8 + - - +
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Residues in contact with MET 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F PHE* 4.1 0.7 - - - -
207F LEU* 4.4 12.3 - - + -
240F VAL* 3.7 23.3 - - + -
241F ALA 3.0 15.5 - - - +
242F VAL* 3.9 22.2 - - + -
253F VAL* 4.8 8.7 - - + -
254F VAL* 1.3 80.0 - - - +
256F VAL* 1.3 66.4 + - - +
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Residues in contact with VAL 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F ARG* 3.8 33.0 - - - +
167F PHE* 3.5 48.2 - - + -
171F ARG* 5.9 1.3 - - + -
172F PRO* 4.9 12.3 - - + -
240F VAL* 3.8 5.8 - - - +
241F ALA* 2.8 35.9 + - + +
254F VAL* 5.1 0.4 - - + -
255F MET* 1.3 80.8 - - - +
257F PRO* 1.3 81.7 - - + +
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Residues in contact with PRO 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F ARG* 4.0 40.6 - - + +
172F PRO* 4.1 10.7 - - - +
238F GLU* 4.1 19.5 - - + +
239F LEU 3.7 5.2 - - - +
240F VAL* 4.9 2.5 - - + -
256F VAL* 1.3 101.1 - - + +
258F PHE* 1.3 58.3 + - - +
259F PRO* 3.3 17.6 - - + +
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Residues in contact with PHE 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F PRO* 5.0 4.5 - - + -
174F PHE* 3.1 38.6 - + - -
185F PHE* 3.6 28.0 - + - -
188F PHE* 3.4 39.3 - + - -
206F LEU* 4.3 10.5 - - + -
214F PHE* 4.2 9.6 - + - -
223F VAL* 4.2 3.4 - - + -
237F TYR 4.4 0.2 - - - -
238F GLU* 3.6 1.8 - - - +
239F LEU* 2.7 53.5 + - + +
241F ALA* 3.9 13.7 - - + +
257F PRO* 1.3 74.1 - - - +
259F PRO* 1.3 64.3 - - - +
260F VAL* 3.8 15.3 + - + +
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Residues in contact with PRO 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C GLU* 4.7 12.3 - - - +
171F ARG* 5.9 3.1 - - + -
172F PRO 3.4 20.4 - - - +
173F SER* 3.9 6.5 - - - -
174F PHE* 3.2 28.1 + - - -
237F TYR 3.4 10.5 - - - +
238F GLU* 4.1 12.8 - - + -
257F PRO* 3.3 18.8 - - + +
258F PHE* 1.3 90.0 - - - +
260F VAL* 1.3 59.0 + - - +
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Residues in contact with VAL 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C GLU* 4.6 4.5 - - - +
174F PHE* 3.6 31.9 - - + +
176F ILE* 3.5 35.4 - - + -
214F PHE* 3.8 29.4 - - + -
236F LYS* 3.9 4.9 - - - +
237F TYR* 2.9 41.1 + - + +
239F LEU* 5.6 0.2 - - + -
258F PHE* 3.9 14.4 - - + +
259F PRO* 1.3 80.5 - - - +
261F THR* 1.3 63.7 + - - +
262F VAL* 3.6 1.7 + - - +
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Residues in contact with THR 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C GLY 5.7 1.3 - - - +
330C ASN 4.3 13.9 - - - +
332C GLU* 6.2 0.7 - - + +
333C GLU* 2.8 38.5 + - + +
334C GLU* 6.0 0.4 - - - +
173F SER* 4.2 1.9 + - - -
174F PHE 2.6 19.6 + - - -
175F ARG* 3.5 10.6 + - - +
176F ILE* 2.8 31.0 + - - +
236F LYS* 5.6 1.3 - - - +
259F PRO 4.4 0.2 - - - -
260F VAL* 1.3 69.7 - - - +
262F VAL* 1.3 67.5 - - - +
263F TYR* 3.6 27.4 - - + +
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Residues in contact with VAL 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C GLY 5.3 2.8 - - - +
330C ASN* 4.5 5.5 - - - +
176F ILE* 3.5 10.8 - - + -
178F GLU* 3.5 14.4 - - - +
229F LEU* 3.7 13.2 - - + -
234F ARG 3.9 10.1 - - - +
235F GLU* 3.3 21.1 + - - +
236F LYS* 3.6 15.6 - - - +
237F TYR* 3.5 36.8 - - + -
260F VAL 3.6 1.1 + - - +
261F THR* 1.3 81.3 - - - +
263F TYR* 1.3 77.2 + - - +
264F ASP* 5.5 0.9 - - - +
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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