Contacts of the strand formed by residues 267 - 273 (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 PHE 267 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C LEU* 5.4 7.6 - - + -
194C LEU* 6.1 0.7 - - + -
195C ILE* 3.7 22.9 - - + -
201C THR* 3.4 19.3 - - + -
203C VAL* 4.6 12.6 - - + -
264C GLU 3.5 18.6 - - - -
265C LEU* 4.4 5.8 - - + -
266C HIS* 1.4 112.5 - + - +
268C LEU* 1.4 61.0 + - - +
269C SER 4.2 0.2 + - - -
379C ASN* 3.2 25.0 + - - +
380C MET 4.4 4.0 + - - +
383C VAL* 4.5 16.4 - - + -
387C PHE* 3.9 32.3 - + + -
430C VAL* 4.4 11.7 - - + -
434C MET* 4.4 20.0 - - + -
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Residues in contact with LEU 268 (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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200C ALA* 4.9 3.4 - - + -
201C THR 2.9 20.4 + - - +
202C VAL* 4.3 18.4 - - + +
203C VAL* 3.2 30.3 + - - +
259C LEU* 3.9 29.2 - - + -
260C ILE* 4.5 16.8 - - + -
266C HIS* 3.2 30.1 - - - +
267C PHE* 1.4 74.1 - - - +
269C SER* 1.3 65.0 + - - +
270C PRO* 4.3 0.4 - - - -
377C LEU* 5.4 8.5 - - + -
378C SER 3.5 24.7 - - - +
379C ASN* 4.0 14.6 - - + +
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Residues in contact with SER 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C PHE 4.2 0.4 + - - -
268C LEU* 1.3 74.4 - - - +
270C PRO* 1.3 69.0 - - - +
271C SER* 5.9 0.4 - - - -
304C SER* 3.8 18.0 + - - -
306C VAL* 3.8 14.2 - - - +
376C MET* 3.8 3.9 - - - +
377C LEU* 3.8 2.3 - - - -
378C SER* 2.9 34.8 + - - -
380C MET* 3.7 33.4 + - - +
382C THR* 5.5 0.2 - - - +
383C VAL* 5.2 5.5 - - - +
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Residues in contact with PRO 270 (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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202C VAL* 4.6 5.6 - - + -
203C VAL 3.6 17.9 - - - +
204C PHE* 3.7 30.5 - - + -
234C ILE* 4.8 7.6 - - + -
268C LEU 4.1 1.8 - - - +
269C SER* 1.3 88.8 - - - +
271C SER* 1.4 66.8 + - - +
302C SER* 4.3 0.2 - - - -
303C ASN* 3.9 26.4 + - + +
304C SER* 3.5 19.0 + - - +
375C MET* 6.1 1.8 - - + -
376C MET* 3.2 11.2 - - - +
377C LEU* 4.3 12.6 - - + -
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Residues in contact with SER 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C SER* 5.9 0.2 - - - -
270C PRO* 1.4 76.5 + - - +
272C PHE* 1.4 65.2 - - - +
296C LEU* 3.0 48.2 + - - -
302C SER* 3.6 11.6 - - - -
303C ASN* 4.5 2.5 - - - -
304C SER* 5.2 0.7 + - - -
312C ASN* 5.7 0.7 + - - -
375C MET* 3.4 6.9 - - - +
376C MET* 3.0 48.6 + - - +
380C MET* 5.8 1.7 - - - +
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Residues in contact with PHE 272 (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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230C LEU* 6.2 1.8 - - + -
233C THR* 4.8 11.7 - - + -
234C ILE* 4.5 27.1 - - + -
237C SER* 4.0 24.5 - - - -
271C SER* 1.4 76.3 - - - +
273C THR* 1.3 85.3 + - - +
274C PRO* 3.3 28.3 - - + -
275C PHE* 3.3 38.1 - + + -
295C MET* 5.1 2.4 - - - +
296C LEU* 3.5 11.4 - - - +
301C PRO 4.7 1.0 - - - +
302C SER* 5.0 2.3 - - - +
303C ASN* 3.7 16.6 + - - +
373C SER* 5.9 2.0 - - - -
374C GLY 3.7 11.4 - - - -
375C MET* 3.8 32.8 - - + -
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Residues in contact with THR 273 (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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272C PHE* 1.3 87.8 + - - +
274C PRO* 1.4 75.4 - - + +
275C PHE* 4.6 2.3 - - - -
287C LYS* 4.2 12.3 - - + -
292C TYR* 3.6 29.9 - - + -
295C MET* 3.4 38.2 - - - +
296C LEU* 4.0 0.9 - - - +
372C VAL 4.1 16.8 - - - +
373C SER* 3.6 2.1 - - - -
374C GLY 2.9 26.9 + - - +
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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
------------------------------------------------------------
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