Contacts of the strand formed by residues 349 - 357 (chain C) in PDB entry 3F7F
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 LEU 349 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C TYR* 3.5 35.0 - - + -
286C THR* 3.9 32.8 - - + +
336C LEU* 4.2 18.2 - - + -
337C THR 3.6 13.9 - - - +
338C ARG* 4.7 0.9 - - - -
339C PRO* 4.5 4.0 - - + -
348C TYR* 1.3 112.5 - - + +
350C ASN* 1.3 71.5 - - - +
366C LEU 4.5 0.2 - - - -
367C ASN* 3.7 2.1 - - - +
368C VAL* 3.2 35.5 + - + +
373C PHE* 4.3 6.1 - - + -
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Residues in contact with ASN 350 (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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335C VAL 3.7 1.4 - - - +
336C LEU* 3.5 5.2 - - - +
337C THR* 2.8 47.7 + - + +
338C ARG 3.8 8.5 - - - +
339C PRO* 3.8 0.7 - - - -
340C LEU* 3.2 40.0 - - + +
342C LEU* 3.6 8.1 - - - +
347C SER* 3.7 3.3 + - - -
349C LEU* 1.3 91.3 - - - +
351C LEU* 1.3 60.7 + - - +
352C ILE* 4.0 3.1 - - + +
365C ILE* 3.4 26.0 - - + +
366C LEU 3.4 2.7 - - - -
367C ASN* 3.2 20.3 - - - +
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Residues in contact with LEU 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C VAL* 3.9 20.9 - - + -
298C PHE* 3.6 36.6 - - + -
300C MET* 4.7 2.5 - - + -
334C LEU* 4.3 9.4 - - + -
335C VAL 3.7 4.7 - - - +
336C LEU* 3.7 38.1 - - + +
350C ASN* 1.3 76.3 - - - +
352C ILE* 1.3 60.7 + - - +
353C VAL* 3.6 15.0 + - + +
365C ILE* 3.2 4.0 - - - -
366C LEU* 2.6 64.1 + - + +
368C VAL* 6.3 0.9 - - + -
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Residues in contact with ILE 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C LEU* 3.2 6.1 - - - -
335C VAL* 2.8 47.6 + - + +
337C THR* 4.5 12.6 - - + -
340C LEU* 6.1 2.9 - - + -
350C ASN* 5.2 2.2 - - + +
351C LEU* 1.3 74.1 - - - +
353C VAL* 1.3 61.4 + - - +
363C LEU* 4.0 20.0 - - + -
364C GLN 3.6 6.5 - - - +
365C ILE* 4.2 11.9 - - + +
463C ILE* 3.9 18.5 - - + +
465C LEU* 3.8 21.8 - - + -
469C GLU 5.4 0.4 - - - +
471C ILE* 3.3 41.7 - - + -
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Residues in contact with VAL 353 (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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298C PHE* 3.9 13.5 - - + -
331C ILE* 3.3 27.1 - - + -
333C ASP 4.0 1.8 - - - -
334C LEU* 4.5 2.5 - - + +
351C LEU* 3.7 33.9 - - + +
352C ILE* 1.3 78.0 - - - +
354C LEU* 1.3 62.2 + - - +
355C TRP* 3.6 27.7 - - + +
362C LYS 3.6 1.4 - - - +
363C LEU* 3.3 6.5 - - - +
364C GLN* 2.8 42.6 + - + +
378C TRP* 4.1 14.6 - - + -
463C ILE* 4.7 1.1 - - - -
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Residues in contact with LEU 354 (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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331C ILE* 3.6 5.2 - - - +
332C VAL* 2.7 61.6 + - + -
333C ASP 2.9 19.2 + - - +
353C VAL* 1.3 74.0 - - - +
355C TRP* 1.3 59.2 + - - +
361C SER* 4.5 6.5 - - - +
362C LYS 3.5 13.9 - - - +
363C LEU* 4.2 20.9 - - + -
460C ALA* 3.9 19.7 - - + -
462C SER 4.2 11.0 - - - +
463C ILE* 3.9 15.9 - - + -
473C VAL* 4.0 22.2 - - + -
484C TYR* 5.4 2.0 - - - +
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Residues in contact with TRP 355 (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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290C LEU* 4.0 11.7 - - + -
295C ASN* 3.1 35.2 - - - -
298C PHE* 3.6 34.1 - + - -
321C THR* 4.1 10.5 - - + -
323C LEU* 3.7 26.2 - - + +
329C TRP* 3.7 22.2 - - + -
330C SER 3.1 8.5 - - - +
331C ILE* 3.5 35.7 - - + -
332C VAL* 3.6 3.6 - - - +
353C VAL* 3.6 19.0 - - + +
354C LEU* 1.3 75.0 - - - +
356C LYS* 1.3 63.7 + - - +
361C SER* 3.6 6.4 - - - -
362C LYS* 2.8 41.4 + - + +
364C GLN* 2.7 31.4 + - - -
378C TRP* 5.5 1.3 - + - -
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Residues in contact with LYS 356 (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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329C TRP* 3.4 6.1 - - - -
330C SER* 2.8 40.3 + - - +
332C VAL* 3.3 19.5 - - + +
355C TRP* 1.3 77.2 - - - +
357C SER* 1.3 64.6 + - - +
358C GLY 3.0 26.2 - - - +
359C THR* 5.1 0.7 - - - -
360C ALA 3.5 8.7 - - - +
361C SER* 5.0 0.9 - - - -
459C GLU* 2.8 31.4 + - + +
460C ALA* 3.2 29.6 + - + +
476C PHE* 3.3 13.1 - - - -
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Residues in contact with SER 357 (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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328C ILE* 3.2 29.0 + - - +
329C TRP* 3.3 28.7 - - - -
330C SER* 5.4 0.7 - - - -
356C LYS* 1.3 76.5 - - - +
358C GLY* 1.3 61.9 + - - +
359C THR 3.6 0.2 + - - -
360C ALA* 3.0 22.5 + - - +
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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