Contacts of the strand formed by residues 267 - 273 (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 PHE 267 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D PHE* 3.9 23.6 - + - -
191D LEU* 3.8 14.4 - - + -
194D LEU* 5.6 0.9 - - + -
195D ILE* 3.8 10.8 - - + -
201D THR* 3.3 21.5 - - + -
203D VAL* 3.8 22.9 - - + -
264D GLU 5.4 1.1 - - - -
265D LEU* 5.9 0.4 - - - +
266D HIS* 1.4 102.1 - + - +
268D LEU* 1.3 59.2 + - - +
306D VAL* 5.9 0.4 - - + -
379D ASN* 3.3 19.0 + - - +
380D MET 4.2 1.0 + - - -
383D VAL* 3.7 44.8 - - + +
386D VAL* 6.0 3.8 - - + -
387D PHE* 3.7 35.9 - + - -
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Residues in contact with LEU 268 (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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200D ALA* 4.1 18.4 - - + -
201D THR 2.8 9.9 + - - +
202D VAL* 3.8 23.5 - - + -
203D VAL* 2.9 31.9 + - - +
256D TYR* 6.3 0.2 - - + -
266D HIS* 3.8 15.0 - - - +
267D PHE* 1.3 75.7 - - - +
269D SER* 1.4 59.7 + - - +
270D PRO* 4.5 0.7 - - - -
306D VAL* 4.7 2.6 - - - +
318D VAL* 5.3 3.8 - - + -
320D ASN* 5.2 3.6 - - - +
377D LEU* 4.0 32.1 - - + -
378D SER* 3.1 20.0 - - - +
379D ASN* 3.8 22.4 - - + +
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Residues in contact with SER 269 (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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203D VAL 4.2 2.0 - - - -
267D PHE 4.5 0.2 + - - -
268D LEU* 1.4 73.1 - - - +
270D PRO* 1.3 74.4 + - - +
304D SER* 3.7 15.0 + - - -
306D VAL* 3.9 23.8 - - - -
308D THR* 3.7 18.7 - - - +
376D MET* 2.9 25.5 - - - +
377D LEU* 3.6 4.1 - - - -
378D SER* 2.9 20.6 + - - -
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Residues in contact with PRO 270 (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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202D VAL* 4.3 5.8 - - + -
203D VAL 3.2 18.6 - - - +
204D PHE* 3.9 29.4 - - + -
234D ILE* 4.2 9.4 - - + -
268D LEU 4.2 1.1 - - - +
269D SER* 1.3 94.5 + - - +
271D SER* 1.3 59.3 - - - +
303D ASN* 3.9 18.0 + - + +
304D SER* 3.8 13.5 + - - +
375D MET* 3.8 22.2 - - + -
376D MET* 3.1 14.6 - - - +
377D LEU* 4.1 2.7 - - + -
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Residues in contact with SER 271 (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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270D PRO* 1.3 73.4 - - - +
272D PHE* 1.3 66.2 + - - +
273D THR* 5.6 0.9 - - - +
296D LEU 6.0 1.6 - - - -
298D LEU 4.2 6.3 + - - -
299D LEU* 4.1 19.8 - - - -
301D PRO* 3.3 21.6 + - - +
302D SER* 6.2 0.2 - - - -
303D ASN* 4.3 8.5 - - - -
375D MET* 3.5 4.0 - - - +
376D MET* 2.8 52.0 + - - +
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Residues in contact with PHE 272 (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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233D THR* 4.6 18.8 - - + -
234D ILE* 4.8 22.0 - - + -
237D SER* 3.9 21.5 - - - -
271D SER* 1.3 78.8 + - - +
273D THR* 1.3 70.2 + - - +
274D PRO* 3.0 35.0 - - + +
275D PHE* 4.2 27.8 - + + -
276D THR* 5.0 5.2 - - + -
296D LEU* 6.5 0.2 - - - -
301D PRO* 3.8 11.4 - - - +
303D ASN* 4.0 11.3 + - - +
373D SER* 4.2 19.7 - - - -
374D GLY* 3.0 33.0 - - - -
375D MET* 3.6 19.3 - - + +
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Residues in contact with THR 273 (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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271D SER* 5.6 0.9 - - - +
272D PHE* 1.3 83.3 - - - +
274D PRO* 1.3 73.1 - - + +
275D PHE* 5.5 1.1 - - + -
292D TYR* 4.7 5.5 - - - -
295D MET* 3.6 52.5 - - + +
296D LEU* 4.0 14.3 + - - +
298D LEU 5.0 1.3 - - - +
301D PRO* 3.9 19.3 - - + -
373D SER* 3.5 1.7 - - - -
374D GLY 3.1 29.2 + - - +
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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