Contacts of the helix formed by residues 251 - 260 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436A LEU* 5.9 4.7 - - - -
242C ILE* 5.4 4.3 - - - -
248C MET* 3.0 26.7 + - - +
249C TYR 3.5 4.7 - - - +
250C SER* 1.4 74.2 + - - +
252C MET* 1.4 62.4 + - - +
253C SER* 3.4 3.1 - - - -
254C SER* 3.1 28.7 + - - -
255C ILE* 2.9 29.8 + - - +
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Residues in contact with MET 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 5.4 6.3 - - + -
134C GLU* 3.5 36.4 + - + +
137C GLN* 5.1 10.8 - - + +
166C ILE* 3.7 32.1 - - + -
168C THR* 4.1 24.0 - - + +
170C TYR* 5.0 9.0 - - - +
242C ILE* 5.2 18.9 - - + +
250C SER 3.8 1.7 + - - -
251C SER* 1.4 70.2 - - - +
253C SER* 1.3 61.2 + - - +
255C ILE* 3.5 7.8 + - - +
256C TYR* 2.9 31.9 + - - +
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Residues in contact with SER 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A ASP* 3.9 22.6 + - - +
601A GLU* 5.6 0.9 - - - -
604A MET* 5.1 8.8 - - - +
134C GLU* 5.1 0.4 + - - -
166C ILE* 5.3 3.8 - - - -
251C SER* 3.4 3.1 - - - -
252C MET* 1.3 78.9 - - - +
254C SER* 1.4 64.1 + - - +
256C TYR* 3.2 7.2 + - - +
257C SER* 2.8 31.7 + - - -
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Residues in contact with SER 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A SER* 4.2 9.4 + - - -
600A ASP* 3.1 25.1 + - - -
637A ASN* 4.2 3.6 + - - -
641A LYS* 5.9 8.0 - - - +
248C MET 4.8 1.2 + - - -
249C TYR* 4.7 12.9 - - - -
251C SER* 3.1 25.4 + - - -
252C MET 3.6 0.4 - - - -
253C SER* 1.4 77.6 - - - +
255C ILE* 1.4 59.8 + - - +
257C SER* 3.6 1.9 + - - -
258C THR* 3.3 25.0 + - - +
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Residues in contact with ILE 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A LYS* 6.2 2.7 - - - -
242C ILE* 5.9 0.4 - - + -
249C TYR 3.8 10.5 - - - +
250C SER* 2.7 22.4 - - - +
251C SER 2.9 10.7 + - - +
252C MET* 3.6 7.9 - - - +
253C SER 3.2 0.2 - - - -
254C SER* 1.4 75.1 - - - +
256C TYR* 1.4 62.7 + - - +
258C THR* 3.4 10.8 - - + +
259C LEU* 3.1 39.2 + - + +
320C ASN* 4.7 11.0 - - - +
322C ILE* 5.7 0.2 - - + -
358C ARG* 2.5 39.7 - - - +
377C LEU* 4.7 14.1 - - + -
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Residues in contact with TYR 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604A MET* 4.0 29.3 + - + +
607A ASN* 3.4 39.9 + - - +
166C ILE* 4.3 20.4 - - + -
199C ASP* 3.6 40.9 + - + +
200C ALA* 4.2 7.2 - - + -
252C MET* 2.9 19.9 + - - +
253C SER* 3.5 8.3 - - - +
255C ILE* 1.4 74.5 - - - +
257C SER* 1.4 66.5 - - - +
259C LEU* 3.4 2.9 + - - +
260C ILE* 2.9 77.5 + - + +
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Residues in contact with SER 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A ASP* 3.3 46.8 + - - +
603A TRP* 4.4 15.5 - - - +
604A MET* 5.0 0.5 + - - +
633A HIS* 5.1 1.9 - - - -
634A ALA* 5.9 1.4 - - - -
637A ASN* 3.8 17.6 - - - +
253C SER* 2.8 17.8 + - - -
254C SER 3.9 1.6 - - - -
255C ILE 3.4 0.2 - - - -
256C TYR* 1.4 83.7 - - - +
258C THR* 1.3 60.4 + - - +
260C ILE 3.4 16.4 + - - +
261C PRO* 4.9 3.8 - - - +
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Residues in contact with THR 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A ALA 5.7 1.2 - - - +
637A ASN* 3.2 32.9 + - - +
638A HIS* 4.2 7.8 + - - +
641A LYS* 4.4 10.5 - - + +
254C SER 3.3 12.7 + - - +
255C ILE* 3.4 15.7 - - + +
257C SER* 1.3 79.0 - - - +
259C LEU* 1.4 65.0 + - + +
260C ILE 5.3 0.2 - - - -
261C PRO* 5.7 2.3 - - - +
318C VAL* 4.1 12.1 - - - +
320C ASN* 6.1 1.6 - - - +
354C VAL* 5.9 0.2 - - - +
356C ILE* 2.8 43.3 - - + +
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ILE* 3.1 28.0 + - + +
256C TYR* 4.1 2.7 - - - +
258C THR* 1.4 90.4 - - + +
260C ILE* 1.4 67.2 - - + +
261C PRO* 3.9 8.0 - - - +
268C LEU* 3.9 25.8 - - + -
317C ASN* 4.1 4.7 + - - -
318C VAL* 3.3 39.8 - - + +
320C ASN* 3.7 28.0 - - + +
356C ILE* 4.2 5.8 - - + -
377C LEU* 3.9 28.0 - - + +
379C ASN* 4.5 4.9 + - - +
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Residues in contact with ILE 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A TRP* 5.7 0.7 - - - +
607A ASN* 4.1 12.9 - - - +
633A HIS* 4.8 1.0 - - - -
199C ASP 4.1 5.2 - - - +
200C ALA* 3.7 18.8 - - + -
256C TYR* 2.9 57.9 + - + +
257C SER* 3.4 14.8 - - - +
258C THR 3.7 0.4 - - - -
259C LEU* 1.4 80.8 - - + +
261C PRO* 1.4 60.3 - - - +
262C SER 3.5 24.2 - - - +
263C PRO* 5.2 1.6 - - + -
265C LEU 3.6 9.4 - - - +
266C HIS* 4.3 17.5 - - + -
268C LEU* 4.5 11.7 - - + -
379C ASN* 5.1 2.2 - - - +
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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