Contacts of the strand formed by residues 297 - 304 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A SER* 4.1 10.1 - - - +
289A THR 3.2 0.3 - - - +
290A LEU* 3.2 11.6 - - - +
291A LEU* 2.7 51.1 + - + +
293A LEU* 3.1 44.9 - - + -
296A GLY* 1.3 88.4 - - - +
298A PHE* 1.3 61.7 + - - +
299A GLN 3.8 0.7 - - - -
318A ASN* 2.9 38.1 - - + +
320A PRO* 4.0 18.6 - - + -
321A THR* 4.0 0.8 - - - +
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Residues in contact with PHE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A VAL* 4.9 5.8 - - + -
289A THR 3.2 12.6 - - - -
290A LEU* 3.5 28.3 - - + -
297A LEU* 1.3 70.9 - - - +
299A GLN* 1.3 60.2 + - - +
300A MET* 3.2 27.0 + - + +
318A ASN* 4.7 0.4 - - - -
319A ILE* 2.9 34.3 + - + +
321A THR* 3.5 29.2 - - + -
331A ILE* 4.5 3.1 - - + -
334A LEU* 4.0 20.2 - - + -
351A LEU* 3.6 26.5 - - + -
353A VAL* 3.9 25.6 - - + -
355A TRP* 3.7 11.9 - + - -
366A LEU* 5.1 0.7 - - + -
378A TRP* 4.2 19.5 - + - -
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Residues in contact with GLN 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A MET* 3.4 39.0 + - - +
262A GLN* 3.4 18.1 - - - +
287A LEU 3.7 0.7 - - - +
288A VAL* 3.0 1.9 - - - -
289A THR* 2.5 48.4 + - - +
291A LEU* 4.4 9.9 - - + -
297A LEU 3.8 1.4 - - - -
298A PHE* 1.3 73.9 - - - +
300A MET* 1.3 63.1 + - - +
313A TYR* 2.9 22.4 + - - +
315A PHE* 3.1 34.7 - - + -
317A ASN 3.8 4.3 - - - +
318A ASN* 3.1 27.1 + - - +
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Residues in contact with MET 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A LEU 3.0 7.4 - - - +
288A VAL* 3.3 35.7 - - + -
298A PHE* 3.2 30.1 - - + +
299A GLN* 1.3 77.4 - - - +
301A GLY* 1.3 61.0 + - - +
313A TYR* 4.3 0.7 - - - -
316A GLN* 2.9 25.8 + - - +
317A ASN 3.4 8.2 + - - +
319A ILE* 3.7 26.0 - - + -
336A LEU* 6.4 0.2 - - - -
351A LEU* 4.7 2.2 - - + -
366A LEU* 3.9 16.2 - - + -
368A VAL* 4.4 7.6 - - - -
373A PHE* 3.2 39.7 - - + -
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Residues in contact with GLY 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A THR* 3.6 5.5 - - - +
287A LEU 3.1 21.5 + - - -
300A MET* 1.3 76.9 - - - +
302A THR* 1.3 70.3 + - - +
313A TYR* 3.5 22.9 + - - -
314A THR 3.1 17.9 - - - -
315A PHE 4.0 2.0 - - - -
316A GLN* 3.5 6.3 - - - -
373A PHE* 4.6 0.3 - - - -
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Residues in contact with THR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ASN* 3.3 20.9 - - - +
286A THR* 4.4 6.3 - - - +
287A LEU* 4.7 0.9 - - - +
301A GLY* 1.3 81.6 - - - +
303A LEU* 1.3 67.4 + - - +
304A LEU* 4.9 6.4 - - - +
312A THR 3.4 0.7 - - - +
313A TYR* 3.5 4.8 - - - -
314A THR* 3.0 40.6 + - - -
316A GLN* 3.8 24.9 + - + +
373A PHE* 4.3 12.1 - - + -
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A PHE* 3.6 54.1 - - + -
235A ILE* 4.2 19.3 - - + -
243A LEU* 5.6 0.7 - - + -
245A ILE* 4.5 13.9 - - + -
282A LEU* 4.5 8.5 - - + -
285A ASN* 2.8 36.6 + - - +
287A LEU* 4.9 15.5 - - + -
302A THR* 1.3 73.9 - - - +
304A LEU* 1.3 67.7 + - - +
311A LEU* 4.4 6.5 - - + -
312A THR 3.2 3.6 - - - +
313A TYR* 3.9 31.2 - - + -
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PHE* 5.6 1.3 - - - -
285A ASN* 5.8 3.8 - - - +
302A THR* 4.8 9.0 - - - +
303A LEU* 1.3 79.5 - - - +
305A VAL* 1.3 89.5 + - - +
311A LEU* 4.4 3.1 - - - +
312A THR* 2.8 32.2 + - - +
314A 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