Contacts of the helix formed by residues 268 - 277 (chain B) in PDB entry 7A62
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 SER 268 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 3.6 35.1 - - - +
126B TYR* 5.2 0.2 - - - -
131B LEU* 6.0 1.2 - - - +
171B GLU* 4.6 1.2 + - - -
266B GLN 4.4 0.7 + - - -
267B SER* 1.3 74.0 + - - +
269B VAL* 1.3 58.8 + - - +
270B PHE 3.6 0.9 - - - -
271B GLN* 3.9 3.3 - - - +
272B CYS* 2.9 30.9 + - - +
299B MET* 3.2 30.8 - - - +
300B PRO* 5.2 1.0 - - - +
303B HIS* 4.0 16.6 + - - +
307B LEU* 4.3 8.0 - - - +
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Residues in contact with VAL 269 (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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23B PHE* 4.0 15.3 - - + -
170B VAL* 5.7 6.3 - - + +
171B GLU* 3.2 36.1 - - - +
174B ALA* 3.8 30.5 - - + -
178B ILE* 4.8 0.7 - - + -
207B LEU* 5.4 4.9 - - + -
267B SER* 3.1 8.0 + - - +
268B SER* 1.3 75.8 - - - +
270B PHE* 1.3 87.0 + - + +
272B CYS* 3.3 6.5 + - - +
273B PHE* 3.2 33.4 - - + -
342B LEU* 5.7 1.3 - - + -
503B HEM 5.7 3.8 - - + -
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Residues in contact with PHE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B VAL* 6.1 2.2 - - + -
214B PHE* 5.1 4.5 - + - -
267B SER* 4.8 2.0 + - - -
268B SER 3.6 0.2 - - - -
269B VAL* 1.3 89.4 - - + +
271B GLN* 1.3 59.3 + - - +
273B PHE* 3.3 2.9 + - - +
274B ASP* 2.8 31.4 + - - -
339B LEU* 4.1 18.2 - - + +
342B LEU* 3.9 43.3 - - + -
343B ARG* 3.4 34.7 + - + +
346B HIS* 4.7 13.7 - + + -
503B HEM 3.1 71.7 - + + +
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Residues in contact with GLN 271 (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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267B SER 5.1 3.0 + - - +
268B SER 3.7 6.3 + - - +
269B VAL 3.3 0.6 - - - -
270B PHE* 1.3 77.1 - - + +
272B CYS* 1.3 66.5 + - - +
274B ASP* 3.4 15.8 - - + +
275B VAL* 3.0 28.1 + - - +
281B GLN* 6.4 1.3 - - + -
282B THR* 4.1 4.7 - - - +
292B LEU* 3.0 50.4 + - + +
295B MET* 4.7 3.0 - - - +
296B ARG* 2.7 42.5 + - - +
299B MET* 4.0 20.7 - - + +
307B LEU* 4.0 13.2 - - + -
343B ARG* 5.4 0.9 - - - +
503B HEM 5.7 3.5 - - + +
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Residues in contact with CYS 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 4.2 12.8 - - + -
178B ILE* 4.5 4.9 - - - -
181B ILE* 3.7 28.0 - - - -
268B SER 2.9 20.5 + - - +
269B VAL* 3.4 6.7 - - - +
271B GLN* 1.3 77.9 - - - +
273B PHE* 1.3 71.6 + - + +
275B VAL* 3.2 5.2 - - - +
276B LEU* 3.2 23.7 + - - +
306B PHE* 3.8 18.6 - - - -
307B LEU* 3.5 16.3 - - + +
310B LEU* 3.9 1.9 - - - +
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Residues in contact with PHE 273 (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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174B ALA* 4.7 2.2 - - + -
177B ALA* 3.7 24.5 - - + -
178B ILE* 3.8 30.3 - - + -
181B ILE* 4.2 7.4 - - + -
203B ILE* 3.8 26.9 - - + -
207B LEU* 4.2 25.1 - - + -
269B VAL* 3.2 28.9 - - + +
270B PHE 3.3 3.2 + - - +
271B GLN 3.2 0.2 - - - -
272B CYS* 1.3 80.4 - - + +
274B ASP* 1.3 67.9 + - - +
275B VAL 3.3 0.2 - - - -
276B LEU* 3.8 24.5 - - + -
277B LEU* 3.1 33.7 + - + +
339B LEU* 4.0 21.5 - - + -
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Residues in contact with ASP 274 (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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270B PHE 2.8 15.0 + - - +
271B GLN* 3.4 19.9 - - + +
273B PHE* 1.3 77.2 - - - +
275B VAL* 1.3 65.0 + - + +
277B LEU 3.2 0.2 + - - -
278B GLY 3.1 3.3 + - - -
279B ILE* 2.9 54.4 + - + +
281B GLN* 3.3 26.2 + - + +
292B LEU* 5.5 1.0 - - - +
339B LEU* 3.7 5.0 - - - +
343B ARG* 2.8 39.5 + - - -
395B THR* 4.3 0.2 + - - -
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Residues in contact with VAL 275 (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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271B GLN* 3.0 18.2 + - - +
272B CYS* 3.2 15.0 - - - +
274B ASP* 1.3 76.2 - - + +
276B LEU* 1.3 71.3 + - - +
278B GLY* 3.0 13.4 + - - +
279B ILE 4.8 5.8 - - - +
282B THR* 5.7 1.8 - - - +
296B ARG* 3.7 25.6 - - - +
307B LEU* 4.2 10.1 - - + +
310B LEU* 3.7 32.1 - - + +
311B GLU* 4.1 24.0 - - + +
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Residues in contact with LEU 276 (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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181B ILE* 4.0 25.8 - - + -
184B VAL* 4.8 7.9 - - + -
185B PHE* 3.7 34.2 - - + -
200B LEU* 6.0 2.2 - - + -
203B ILE* 4.2 15.3 - - + -
272B CYS 3.2 14.2 + - - +
273B PHE* 3.8 28.9 - - + +
274B ASP 3.3 0.2 - - - -
275B VAL* 1.3 85.1 - - - +
277B LEU* 1.3 70.6 + - + +
278B GLY 3.5 0.5 + - - -
310B LEU* 4.7 8.3 - - + -
316B VAL* 3.5 34.2 + - + +
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Residues in contact with LEU 277 (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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200B LEU* 5.2 4.9 - - + -
203B ILE* 6.4 0.4 - - + -
207B LEU* 6.0 0.9 - - + -
273B PHE* 3.1 25.2 + - + +
276B LEU* 1.3 92.8 - - + +
278B GLY* 1.3 61.8 + - - +
279B ILE* 3.2 13.0 + - + +
316B VAL* 5.0 4.9 - - + -
317B ARG* 3.7 7.7 - - - +
332B TYR* 2.6 55.3 + - + +
335B CYS* 3.8 40.8 - - + +
336B VAL* 4.0 16.2 - - + -
339B LEU* 4.5 12.3 - - + -
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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