Contacts of the strand formed by residues 373 - 380 (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 373 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272D PHE* 4.2 16.9 - - - -
273D THR 3.5 6.1 - - - -
274D PRO* 3.5 17.3 - - - -
276D THR* 5.9 4.9 - - - +
292D TYR* 3.0 20.0 + - - -
324D GLY* 3.0 26.7 + - - +
362D TYR* 3.1 20.1 + - - -
372D VAL* 1.3 76.8 - - - +
374D GLY* 1.4 58.2 + - - +
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Residues in contact with GLY 374 (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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272D PHE* 3.0 20.8 - - - -
273D THR 3.1 22.4 + - - -
292D TYR* 3.4 9.7 - - - -
296D LEU* 4.2 10.2 - - - +
322D ILE* 3.0 15.3 - - - -
323D ILE* 4.5 0.2 - - - -
324D GLY 4.6 0.7 - - - -
373D SER* 1.4 74.7 + - - +
375D MET* 1.3 61.7 + - - -
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Residues in contact with MET 375 (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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234D ILE* 3.4 36.3 - - + +
237D SER* 4.0 11.4 - - - -
238D VAL* 3.4 26.5 - - + -
270D PRO* 3.8 22.9 - - + -
271D SER 3.5 13.5 - - - +
272D PHE* 3.6 14.1 - - + -
296D LEU* 4.5 4.5 - - - +
321D THR* 3.8 2.4 - - - +
322D ILE* 2.9 49.4 + - + +
374D GLY* 1.3 76.3 - - - -
376D MET* 1.3 63.8 + - - +
377D LEU* 3.9 23.6 - - + -
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Residues in contact with MET 376 (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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269D SER* 2.9 42.0 - - - +
270D PRO* 3.1 5.2 - - - +
271D SER* 2.8 44.2 + - - +
296D LEU* 5.0 7.8 - - + +
299D LEU* 4.1 33.2 - - + -
308D THR* 4.9 3.1 - - + -
316D PHE* 5.4 4.3 - - + -
319D TYR* 3.6 26.2 - - + +
320D ASN 3.5 5.4 - - - -
321D THR* 4.7 0.9 - - + +
375D MET* 1.3 78.6 - - - +
377D LEU* 1.3 59.7 + - - +
378D SER* 3.5 28.9 - - - +
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Residues in contact with LEU 377 (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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170D TYR* 5.5 0.9 - - + +
202D VAL* 3.8 33.4 - - + -
238D VAL* 4.4 19.5 - - + -
259D LEU* 6.4 0.2 - - + -
268D LEU* 4.0 32.3 - - + -
269D SER 3.6 13.9 - - - +
270D PRO* 4.1 1.3 - - + -
320D ASN* 2.9 62.0 + - - +
322D ILE* 5.2 1.1 - - + +
375D MET* 3.9 22.8 - - + -
376D MET* 1.3 69.8 - - - +
378D SER* 1.4 62.3 + - - +
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Residues in contact with SER 378 (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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268D LEU* 3.1 9.9 - - - -
269D SER* 2.9 33.6 + - - +
308D THR* 6.1 0.2 - - - -
316D PHE* 4.5 11.2 - - - -
318D VAL* 3.5 12.3 - - - -
319D TYR* 3.1 36.6 - - - -
320D ASN* 5.0 0.2 - - - -
376D MET* 3.5 22.4 - - - +
377D LEU* 1.4 73.0 + - - +
379D ASN* 1.4 58.7 + - - +
380D MET* 4.2 2.4 + - - -
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Residues in contact with ASN 379 (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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260D ILE* 5.5 0.2 - - - +
261D PRO* 3.5 24.9 - - - +
265D LEU* 3.2 31.6 + - - +
266D HIS* 3.3 19.5 + - - +
267D PHE 3.3 19.1 + - - +
268D LEU* 3.8 10.8 - - + +
316D PHE* 3.8 2.1 - - - +
317D ASN* 2.9 32.8 + - - -
318D VAL* 3.0 30.6 + - + +
378D SER* 1.4 70.6 - - - +
380D MET* 1.3 59.4 + - - +
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Residues in contact with MET 380 (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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265D LEU* 4.7 2.2 - - - +
267D PHE 4.2 3.7 + - - +
306D VAL* 5.9 1.1 - - + +
308D THR* 3.1 21.8 - - + +
311D ASN 4.4 0.2 - - - +
312D ASN* 3.0 40.8 - - - +
313D PRO* 4.5 0.2 - - + -
314D THR* 3.2 23.1 - - - +
315D TYR 3.4 14.8 - - - +
316D PHE* 3.8 15.3 - - + -
317D ASN* 3.4 5.8 - - - +
346D SER* 3.6 23.6 - - - +
378D SER* 4.2 2.7 + - - -
379D ASN* 1.3 76.3 + - - +
381D SER* 1.3 57.3 + - - +
382D THR* 3.2 25.8 + - + +
383D VAL* 3.1 29.4 + - + +
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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