Contacts of the helix formed by residues 276 - 287 (chain B) in PDB entry 5FQD
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 ASN 276 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B MET* 4.5 0.2 - - - -
274B PRO* 3.6 2.4 - - + +
275B SER* 1.4 80.1 + - - +
277B PRO* 1.4 73.8 - - - +
278B ILE* 3.0 45.3 + - - +
279B ASP* 3.2 25.2 + - - +
280B PHE* 2.9 23.4 + - - +
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Residues in contact with PRO 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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250B ALA* 3.7 24.5 - - + -
254B MET* 3.7 28.9 - - + -
275B SER 3.5 7.3 - - - +
276B ASN* 1.4 88.2 - - - +
278B ILE* 1.4 52.1 + - + +
280B PHE* 3.7 0.2 - - - +
281B SER* 2.8 37.8 + - - -
304B ALA* 3.9 16.8 - - + +
305B ILE* 5.6 0.7 - - + -
308B LEU* 4.3 6.4 - - + +
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Residues in contact with ILE 278 (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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187B GLU* 3.7 29.8 - - + +
188B CYS 5.6 0.7 - - - +
189B VAL* 3.8 30.1 - - + -
276B ASN* 3.0 21.0 + - - +
277B PRO* 1.4 75.8 - - + +
279B ASP* 1.3 61.8 + - - +
281B SER* 2.8 22.2 + - - -
282B TYR* 3.1 44.5 + - + -
304B ALA* 3.9 11.0 - - + +
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Residues in contact with ASP 279 (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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274B PRO* 3.9 20.0 - - + +
276B ASN* 3.2 29.0 + - - +
278B ILE* 1.3 78.5 - - - +
280B PHE* 1.3 60.5 + - - +
282B TYR* 3.3 8.0 + - - +
283B ARG* 2.8 31.0 + - - +
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Residues in contact with PHE 280 (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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254B MET* 3.5 42.6 - - + -
257B ILE* 3.6 33.9 - - + -
258B LYS* 3.9 25.6 - - + -
261B LEU* 4.1 8.3 - - + -
273B LEU* 4.2 14.8 - - + -
274B PRO* 3.4 38.7 - - + +
276B ASN 2.9 16.8 + - - +
277B PRO 3.7 2.9 - - - +
279B ASP* 1.3 75.2 - - - +
281B SER* 1.3 61.5 + - - +
283B ARG* 3.1 4.6 + - + +
284B VAL* 3.0 32.5 + - + +
308B LEU* 3.5 19.7 - - + -
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Residues in contact with SER 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B PRO 2.8 18.8 + - - -
278B ILE* 2.8 19.1 + - - -
280B PHE* 1.3 71.9 - - - +
282B TYR* 1.3 55.2 + - - +
285B ALA* 3.1 12.1 + - - +
304B ALA* 4.1 2.6 - - - +
307B ARG* 2.8 41.3 + - - -
308B LEU* 3.8 22.9 - - - -
311B GLU* 2.6 33.3 - - - +
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Residues in contact with TYR 282 (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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92B ILE* 3.4 15.5 - - + +
93B PRO* 3.4 56.9 - - + +
94B GLY* 5.6 0.4 - - - -
164B ARG* 2.9 28.1 + - - +
187B GLU* 2.6 30.1 + - - -
278B ILE* 3.1 35.0 + - + +
279B ASP* 3.8 7.4 - - - +
280B PHE 3.2 0.4 - - - -
281B SER* 1.3 77.6 + - - +
283B ARG* 1.3 65.8 + - - +
285B ALA* 3.3 2.8 + - + -
286B ALA* 3.1 21.3 + - - +
298B LEU 6.0 0.2 - - - -
299B LEU* 5.6 2.5 - - + -
307B ARG* 3.2 30.3 + - - -
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Residues in contact with ARG 283 (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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272B SER* 2.9 37.7 + - - +
273B LEU* 4.6 16.1 - - + +
274B PRO* 3.8 22.8 - - + +
279B ASP 2.8 18.0 + - - +
280B PHE* 3.4 8.5 - - + +
282B TYR* 1.3 77.0 - - - +
284B VAL* 1.4 63.2 + - + +
286B ALA* 3.6 13.1 + - - +
287B CYS* 3.6 14.4 - - - +
342B LEU* 2.8 28.5 + - - +
343B CYS* 3.7 24.5 + - - +
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Residues in contact with VAL 284 (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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257B ILE* 3.7 9.4 - - + -
261B LEU* 4.1 20.2 - - + -
273B LEU* 6.0 0.4 - - + -
280B PHE* 3.0 41.7 + - + +
283B ARG* 1.4 78.9 - - + +
285B ALA* 1.3 61.8 + - - +
287B CYS* 3.2 19.3 + - - -
288B LEU* 3.4 19.3 + - + +
311B GLU* 3.4 24.7 - - + +
315B MET* 3.8 27.6 - - + -
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Residues in contact with ALA 285 (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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92B ILE* 3.7 25.3 - - + +
281B SER 3.1 12.3 + - - +
282B TYR* 3.3 8.0 + - + +
284B VAL* 1.3 74.5 - - - +
286B ALA* 1.3 61.8 + - - +
287B CYS 3.5 0.3 + - - -
288B LEU* 3.6 13.4 + - - +
290B ILE* 5.8 0.5 - - - +
295B ARG* 3.8 6.8 + - - -
298B LEU* 3.9 26.7 - - + +
307B ARG* 4.8 5.4 - - - -
311B GLU* 3.3 20.1 + - - +
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Residues in contact with ALA 286 (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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92B ILE* 3.8 13.8 - - + +
93B PRO 5.8 0.2 - - - +
94B GLY 6.0 0.4 - - - -
95B GLN* 3.8 35.1 + - + +
282B TYR 3.1 16.2 + - - +
283B ARG* 3.7 9.0 - - - +
284B VAL 3.2 0.4 - - - -
285B ALA* 1.3 76.7 - - - +
287B CYS* 1.3 59.0 + - + +
288B LEU 3.6 0.2 - - - -
295B ARG* 3.2 17.0 + - - -
346B MET* 3.4 11.0 - - - +
358B GLU* 3.7 5.2 - - - +
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Residues in contact with CYS 287 (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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261B LEU* 5.1 7.4 - - - -
264B TRP* 4.7 8.8 - - - -
283B ARG* 3.6 12.3 - - - +
284B VAL* 3.2 16.8 + - - -
286B ALA* 1.3 78.8 - - + +
288B LEU* 1.3 61.1 + - - +
289B PRO* 3.6 8.3 - - - +
343B CYS 3.9 15.5 - - - +
344B GLY* 4.5 0.9 - - - -
345B PRO* 3.8 37.2 - - + +
346B MET* 3.5 30.9 - - - +
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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