Contacts of the strand formed by residues 297 - 304 (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 297 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C SER* 4.4 8.7 - - - +
289C THR 3.2 0.2 - - - +
290C LEU* 3.2 10.1 - - - +
291C LEU* 2.7 51.1 + - + +
293C LEU* 3.1 44.4 - - + -
295C ASN 4.1 0.2 - - - -
296C GLY* 1.3 87.0 - - - +
298C PHE* 1.3 62.1 + - - +
299C GLN 3.8 0.7 - - - -
318C ASN* 2.9 37.9 - - + +
320C PRO* 4.0 18.8 - - + -
321C THR* 4.0 1.0 - - - +
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Residues in contact with PHE 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C VAL* 4.9 5.8 - - + -
289C THR 3.2 11.7 - - - -
290C LEU* 3.5 28.5 - - + -
297C LEU* 1.3 71.7 - - - +
299C GLN* 1.3 60.9 + - - +
300C MET* 3.2 26.8 + - + +
318C ASN* 4.7 0.4 - - - -
319C ILE* 2.9 34.2 + - + +
321C THR* 3.5 30.1 - - + -
331C ILE* 4.5 2.9 - - + -
334C LEU* 4.0 20.6 - - + -
351C LEU* 3.6 26.7 - - + -
353C VAL* 3.9 24.9 - - + -
355C TRP* 3.6 12.1 - + - -
366C LEU* 5.1 0.7 - - + -
378C TRP* 4.2 19.3 - + - -
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Residues in contact with GLN 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C MET* 3.4 38.1 + - - +
262C GLN* 2.7 27.4 + - - +
287C LEU 3.7 0.3 - - - +
288C VAL* 3.0 2.1 - - - -
289C THR* 2.5 48.6 + - - +
291C LEU* 4.4 10.5 - - + +
297C LEU 3.8 1.6 - - - -
298C PHE* 1.3 71.6 - - - +
300C MET* 1.3 63.0 + - - +
301C GLY 4.3 0.2 - - - -
313C TYR* 2.9 23.6 + - - +
315C PHE* 3.1 24.9 - - + -
317C ASN 3.8 5.4 - - - +
318C ASN* 3.1 26.9 + - - +
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Residues in contact with MET 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C THR* 4.8 0.2 - - + -
287C LEU 3.0 6.3 - - - +
288C VAL* 3.3 38.6 - - + -
298C PHE* 3.2 29.6 - - + +
299C GLN* 1.3 74.8 - - - +
301C GLY* 1.3 60.6 + - - +
313C TYR* 4.3 0.7 - - - -
316C GLN* 2.9 26.0 + - - +
317C ASN 3.4 8.1 + - - +
319C ILE* 3.7 26.5 - - + -
336C LEU* 6.4 0.2 - - - -
351C LEU* 4.7 1.8 - - + -
366C LEU* 3.9 15.7 - - + -
368C VAL* 4.4 8.5 - - - -
373C PHE* 3.2 38.9 - - + -
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Residues in contact with GLY 301 (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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286C THR* 3.6 5.4 - - - +
287C LEU 3.1 22.1 + - - -
300C MET* 1.3 75.3 - - - +
302C THR* 1.3 70.4 + - - +
313C TYR* 3.5 22.7 + - - -
314C THR 3.1 17.3 - - - -
315C PHE 4.0 2.0 - - - -
316C GLN* 3.5 6.0 - - - +
373C PHE* 4.6 0.2 - - - -
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Residues in contact with THR 302 (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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285C ASN* 3.3 20.4 - - - +
286C THR* 4.4 6.1 - - - +
287C LEU 4.7 0.7 - - - +
301C GLY* 1.3 81.1 - - - +
303C LEU* 1.3 67.3 + - - +
304C LEU* 4.9 6.9 - - - +
312C THR 3.4 0.9 - - - +
313C TYR* 3.9 4.9 - - - -
314C THR* 3.0 40.7 + - - -
316C GLN* 3.8 24.9 + - + +
373C PHE* 4.3 12.6 - - + -
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Residues in contact with LEU 303 (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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229C PHE* 3.6 54.1 - - + -
235C ILE* 4.2 19.7 - - + -
243C LEU* 5.6 0.2 - - + -
245C ILE* 4.5 13.9 - - + -
282C LEU* 4.5 8.1 - - + -
285C ASN* 2.8 36.9 + - - +
287C LEU* 4.9 16.4 - - + -
302C THR* 1.3 73.0 - - - +
304C LEU* 1.3 66.9 + - - +
311C LEU* 4.4 6.7 - - + -
312C THR 3.2 3.6 - - - +
313C TYR* 3.9 31.4 - - + -
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Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C PHE* 6.2 0.7 - - - -
285C ASN* 5.9 2.9 - - - +
302C THR* 4.8 9.4 - - - +
303C LEU* 1.3 78.9 - - - +
305C VAL* 1.3 89.1 + - - +
311C LEU* 4.4 3.8 - - - +
312C THR* 2.8 31.6 + - - +
314C THR* 5.1 5.4 - - - +
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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