Contacts of the helix formed by residues 251 - 260 (chain D) in PDB entry 5FLZ
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 251 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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486B SER* 3.8 25.2 + - - -
487B ASP* 5.0 2.3 + - - +
241D SER* 4.3 6.7 - - - -
245D PRO* 4.2 12.8 + - - +
247D TYR 4.1 2.8 + - - -
249D TYR 4.0 1.4 - - - -
250D SER* 1.3 77.8 + - - +
252D MET* 1.3 61.9 + - - +
253D SER* 3.5 3.4 - - - -
254D SER* 3.8 12.3 + - - -
255D ILE* 3.1 28.9 + - - +
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Residues in contact with MET 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 5.7 9.9 - - + -
134D GLU* 5.9 4.5 - - + +
137D GLN* 6.1 0.7 - - - +
170D TYR* 5.5 4.0 - - - +
238D VAL* 4.2 25.6 - - + +
239D THR* 5.4 6.3 - - + -
241D SER* 4.1 19.2 + - - -
242D ILE* 3.9 42.1 - - + +
251D SER* 1.3 72.2 - - - +
253D SER* 1.4 58.7 + - - +
255D ILE* 3.3 12.5 + - - +
256D TYR* 2.8 48.6 + - + +
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Residues in contact with SER 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B ASP* 5.9 2.5 - - - -
605B LEU* 6.2 1.6 - - - -
2D GLY 4.2 11.1 + - - -
134D GLU* 3.0 40.1 + - - +
166D ILE* 5.6 1.2 - - - +
251D SER* 3.5 1.9 - - - -
252D MET* 1.4 76.8 - - - +
254D SER* 1.4 59.4 + - - +
256D TYR* 3.4 6.1 + - - +
257D SER* 2.8 30.4 + - - -
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Residues in contact with SER 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B ASP* 4.3 12.8 + - - -
597B ASN* 5.1 4.5 + - - -
601B GLN* 3.8 28.2 - - - +
251D SER* 3.8 14.7 + - - -
252D MET 3.4 0.4 - - - -
253D SER* 1.4 77.5 - - - +
255D ILE* 1.4 62.8 + - - +
257D SER* 3.3 14.8 + - - -
258D THR* 2.9 24.0 + - - -
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Residues in contact with ILE 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D SER* 4.8 4.5 - - - +
249D TYR 4.4 5.6 - - - +
250D SER* 3.9 12.6 - - - -
251D SER 3.1 35.2 + - - +
252D MET* 3.3 15.0 + - - +
253D SER 3.3 0.2 - - - -
254D SER* 1.4 76.2 - - - +
256D TYR* 1.4 65.5 - - - +
258D THR* 3.6 5.2 + - - -
259D LEU* 3.1 49.0 + - + +
356D ILE* 5.9 8.3 - - + -
358D ARG* 4.0 27.6 - - + +
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Residues in contact with TYR 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B LEU* 6.4 0.4 - - + -
134D GLU* 5.4 0.7 - - - +
166D ILE* 3.8 41.6 - - + +
168D THR* 3.5 18.5 + - + -
199D ASP* 3.6 7.8 + - + +
200D ALA* 2.9 39.8 + - + +
252D MET* 2.8 34.8 + - + +
253D SER* 3.6 8.3 - - - +
255D ILE* 1.4 76.8 - - - +
257D SER* 1.4 64.2 + - - +
259D LEU* 3.5 12.0 + - - +
260D ILE* 3.3 37.8 + - + +
268D LEU* 6.3 0.7 - - + -
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Residues in contact with SER 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601B GLN* 3.2 23.7 + - - +
604B MET* 5.6 5.7 - - - +
605B LEU* 3.7 37.6 - - - +
608B ASN* 5.1 5.3 + - - +
639B THR* 5.2 0.7 - - - +
642B GLN* 3.9 8.5 - - - +
166D ILE* 6.1 0.2 - - - +
253D SER 2.8 21.8 + - - -
254D SER* 3.5 4.3 - - - -
255D ILE 3.3 0.6 - - - -
256D TYR* 1.4 77.7 - - - +
258D THR* 1.4 55.1 + - - +
260D ILE* 3.2 23.8 - - - +
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Residues in contact with THR 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601B GLN* 3.6 16.3 + - - -
639B THR* 3.6 19.8 - - - +
642B GLN* 3.5 15.2 + - + +
643B GLN* 4.6 21.5 - - + +
646B SER* 4.2 24.3 + - - +
254D SER 2.9 16.4 + - - -
255D ILE* 3.7 7.0 - - - -
256D TYR 3.5 0.2 - - - -
257D SER* 1.4 73.1 - - - +
259D LEU* 1.4 70.5 + - + +
260D ILE 3.3 0.4 + - - -
356D ILE* 5.5 9.2 - - + -
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Residues in contact with LEU 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639B THR* 5.1 0.5 - - - +
255D ILE* 3.1 38.5 + - + +
256D TYR* 3.5 5.7 + - - +
258D THR* 1.4 81.3 - - + +
260D ILE* 1.3 62.3 + - + +
261D PRO* 3.5 2.8 - - - +
318D VAL* 3.4 46.8 - - + +
320D ASN* 3.8 28.0 - - + +
354D VAL* 5.8 0.3 - - - +
356D ILE* 3.6 36.1 - - + -
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Residues in contact with ILE 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608B ASN* 5.0 13.9 - - - +
638B ARG* 5.7 0.7 + - - -
639B THR* 3.1 18.9 + - - +
199D ASP* 3.5 30.5 - - + +
200D ALA* 5.5 0.9 - - + -
256D TYR* 3.3 36.0 + - + +
257D SER* 3.2 22.0 - - - +
258D THR 3.7 1.2 - - - +
259D LEU* 1.3 75.1 - - - +
261D PRO* 1.3 68.6 - - + +
262D SER* 3.2 15.0 - - - +
263D PRO* 4.4 15.5 - - + -
265D LEU 4.9 2.2 - - - +
266D HIS* 5.4 1.6 - - + -
318D VAL* 5.6 0.2 - - - -
379D ASN* 5.5 0.2 - - - +
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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