Contacts of the strand formed by residues 297 - 304 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D SER* 4.1 9.2 - - - +
264D ASP* 5.4 0.2 - - - +
289D THR 3.2 0.2 - - - +
290D LEU* 3.2 9.9 - - - +
291D LEU* 2.7 50.9 + - + +
293D LEU* 3.1 44.9 - - + -
295D ASN 4.1 0.2 - - - -
296D GLY* 1.3 87.0 - - - +
298D PHE* 1.3 62.5 + - - +
299D GLN 3.8 0.7 - - - -
318D ASN* 2.9 38.1 - - + +
320D PRO* 4.0 18.8 - - + -
321D THR* 4.0 1.0 - - - +
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Residues in contact with PHE 298 (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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288D VAL* 4.9 6.1 - - + -
289D THR 3.2 11.7 - - - -
290D LEU* 3.5 28.7 - - + -
297D LEU* 1.3 71.7 - - - +
299D GLN* 1.3 60.3 + - - +
300D MET* 3.2 24.9 + - + +
318D ASN* 4.7 0.4 - - - -
319D ILE* 2.9 36.2 + - + +
321D THR* 3.5 30.3 - - + -
331D ILE* 4.5 2.9 - - + -
334D LEU* 4.0 20.4 - - + -
351D LEU* 3.6 26.5 - - + -
353D VAL* 3.9 25.4 - - + -
355D TRP* 3.7 12.3 - + - -
366D LEU* 5.1 0.7 - - + -
378D TRP* 4.2 19.3 - + - -
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Residues in contact with GLN 299 (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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259D MET* 3.4 32.2 + - - +
262D GLN* 3.1 25.8 - - - +
287D LEU 3.7 0.3 - - - +
288D VAL* 3.0 2.1 - - - -
289D THR* 2.5 48.4 + - - +
291D LEU* 4.4 10.1 - - + +
297D LEU 3.8 1.6 - - - -
298D PHE* 1.3 72.0 - - - +
300D MET* 1.3 63.0 + - - +
301D GLY 4.3 0.2 - - - -
313D TYR* 2.9 23.8 + - - +
315D PHE* 3.1 32.7 - - + -
317D ASN 3.8 5.2 - - - +
318D ASN* 3.1 26.8 + - - +
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Residues in contact with MET 300 (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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286D THR* 4.8 0.2 - - + -
287D LEU 3.0 6.3 - - - +
288D VAL* 3.2 38.6 - - + -
298D PHE* 3.2 29.4 - - + +
299D GLN* 1.3 74.4 - - - +
301D GLY* 1.3 61.4 + - - +
313D TYR* 4.3 0.7 - - - -
316D GLN* 2.9 25.9 + - - +
317D ASN 3.4 8.1 + - - +
319D ILE* 3.7 26.2 - - + -
336D LEU* 6.4 0.2 - - - -
351D LEU* 4.8 1.8 - - + -
366D LEU* 3.9 16.2 - - + -
368D VAL* 4.4 8.5 - - - -
373D PHE* 3.2 38.9 - - + -
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Residues in contact with GLY 301 (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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286D THR* 3.6 5.4 - - - +
287D LEU 3.1 22.1 + - - -
300D MET* 1.3 75.7 - - - +
302D THR* 1.3 70.0 + - - +
313D TYR* 3.5 22.7 + - - -
314D THR 3.1 17.7 - - - -
315D PHE 4.0 1.8 - - - -
316D GLN* 3.5 5.8 - - - +
373D PHE* 4.6 0.2 - - - -
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Residues in contact with THR 302 (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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285D ASN* 3.3 20.6 - - - +
286D THR* 4.4 6.1 - - - +
287D LEU 4.7 0.7 - - - +
301D GLY* 1.3 82.0 - - - +
303D LEU* 1.3 67.1 + - - +
304D LEU* 4.9 6.8 - - - +
312D THR 3.4 0.9 - - - +
313D TYR* 3.9 5.1 - - - -
314D THR* 3.0 40.5 + - - -
316D GLN* 3.8 24.9 + - + +
373D PHE* 4.3 13.2 - - + -
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Residues in contact with LEU 303 (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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229D PHE* 3.6 57.0 - - + -
235D ILE* 4.2 16.8 - - + -
243D LEU* 5.6 0.2 - - + -
245D ILE* 4.6 13.5 - - + -
282D LEU* 4.6 8.3 - - + -
285D ASN* 2.8 36.7 + - - +
287D LEU* 4.9 17.3 - - + -
302D THR* 1.3 73.0 - - - +
304D LEU* 1.3 66.9 + - - +
311D LEU* 4.4 7.0 - - + -
312D THR 3.2 3.4 - - - +
313D TYR* 3.9 31.4 - - + -
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Residues in contact with LEU 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D PHE* 5.6 0.6 - - - -
285D ASN* 5.9 3.6 - - - +
302D THR* 4.8 9.2 - - - +
303D LEU* 1.3 78.7 - - - +
305D VAL* 1.3 89.6 + - - +
311D LEU* 4.4 3.1 - - - +
312D THR* 2.8 32.4 + - - +
314D THR* 5.1 5.6 - - - +
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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