Contacts of the strand formed by residues 300 - 309 (chain D) in PDB entry 4JF7
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 TRP 300 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295D VAL 3.7 0.2 - - - +
296D TYR* 3.5 4.2 - - - -
297D TYR* 2.8 34.8 + - - +
298D LEU 3.4 15.9 - - - -
299D GLY* 1.3 82.2 - - - +
301D VAL* 1.3 63.4 + - - +
302D LEU* 4.0 15.2 + - + -
364D ALA* 3.6 23.6 - - + -
365D CYS 3.3 7.9 - - - -
366D PRO* 3.4 46.4 - - + +
374D GLU 3.9 3.8 - - - -
376D LEU* 3.8 27.1 - - + -
422D PHE* 4.2 14.6 - + + -
425D GLY 3.6 23.9 + - - -
426D GLN* 4.1 15.3 - - + -
427D PRO* 3.7 14.4 - - + -
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Residues in contact with VAL 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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230D SER* 3.6 26.2 - - - +
232D VAL* 3.8 24.0 - - + -
237D MET* 3.8 27.4 - - + -
295D VAL 3.3 4.3 - - - +
296D TYR* 4.0 11.0 - - + -
300D TRP* 1.3 76.8 - - - +
302D LEU* 1.3 63.0 + - - +
303D PHE* 3.6 28.9 + - + -
363D LEU 3.3 3.8 - - - +
364D ALA* 3.5 0.3 - - - -
365D CYS* 2.6 44.3 + - + +
367D LEU* 4.6 4.7 - - + -
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Residues in contact with LEU 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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294D GLY* 2.9 5.1 - - - -
295D VAL* 2.8 51.3 + - + +
297D TYR* 4.0 25.6 - - + -
300D TRP* 4.1 15.3 - - + +
301D VAL* 1.3 76.9 - - - +
303D PHE* 1.3 60.6 + - - +
362D ILE* 4.0 11.4 - - + -
363D LEU 3.2 2.9 - - - -
364D ALA* 3.8 24.5 - - + -
378D LEU* 6.2 0.4 - - + -
393D LEU* 3.2 17.3 - - + +
400D VAL* 4.4 9.0 - - + -
420D ILE* 3.6 30.7 - - + -
422D PHE* 6.4 0.7 - - + -
427D PRO* 5.3 5.2 - - + -
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Residues in contact with PHE 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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228D SER* 3.6 38.6 - - - -
229D ILE 4.1 0.2 - - - -
230D SER* 4.0 13.0 - - - -
237D MET* 3.5 40.4 - - + -
239D TYR* 3.8 39.5 - + + -
261D ILE* 4.0 5.2 - - + -
294D GLY* 3.8 8.3 - - - -
301D VAL* 3.6 30.3 - - + -
302D LEU* 1.3 72.4 - - - +
304D PRO* 1.3 69.4 - - + +
362D ILE* 3.4 5.4 - - - +
363D LEU* 2.8 46.2 + - + +
365D CYS* 4.9 1.8 - - - -
393D LEU* 3.4 5.2 - - - -
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Residues in contact with PRO 304 (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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228D SER* 4.0 4.9 - - - +
289D PRO* 3.4 3.6 - - - +
290D GLY* 2.8 24.1 + - - +
292D GLY 3.7 13.7 - - - +
293D SER 3.5 19.1 - - - +
303D PHE* 1.3 90.0 - - + +
305D ILE* 1.3 64.5 + - - +
361D GLY 3.8 6.1 - - - +
362D ILE* 4.8 0.2 - - - -
391D GLY* 3.3 37.2 - - - +
392D ARG* 3.9 6.3 - - - +
393D LEU* 3.5 11.9 - - + -
402D TYR* 4.0 15.3 - - + +
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Residues in contact with ILE 305 (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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239D TYR* 3.4 31.9 - - + +
284D TRP* 4.4 6.7 - - + -
287D LEU* 3.7 22.7 - - + -
288D ASN 3.1 10.8 - - - +
290D GLY* 4.1 1.6 - - - +
304D PRO* 1.3 79.9 - - - +
306D TYR* 1.3 68.6 + - - +
360D SER* 3.6 4.0 + - - -
361D GLY* 3.0 43.6 + - - +
362D ILE 3.6 13.2 - - - +
363D LEU* 3.7 16.2 - - + -
377D VAL* 3.7 29.8 - - + -
389D ALA 4.2 2.6 - - - +
402D TYR* 4.4 2.3 + - - -
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Residues in contact with TYR 306 (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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226D SER* 4.7 2.7 + - - -
247D GLU* 4.2 11.2 + - - -
251D TYR* 4.0 17.9 - - - -
284D TRP* 4.0 6.1 - - - -
287D LEU* 3.6 2.4 - - - +
288D ASN* 2.8 67.3 + - + +
289D PRO 3.6 11.4 - - - -
290D GLY* 4.2 1.1 - - - -
305D ILE* 1.3 78.6 - - - +
307D GLY* 1.3 61.5 + - - +
358D ILE* 4.9 3.1 - - + -
359D GLN 2.9 16.2 - - - +
360D SER* 4.3 0.4 - - - -
388D GLY 4.2 4.5 - - - -
389D ALA* 3.3 39.5 - - - +
390D GLU* 3.6 37.6 + - + +
407D ASN* 6.2 2.0 - - - -
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Residues in contact with GLY 307 (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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251D TYR* 3.9 21.3 - - - -
284D TRP* 3.6 7.7 - - - -
286D THR* 3.4 15.0 - - - -
288D ASN* 5.7 0.7 - - - -
306D TYR* 1.3 79.1 - - - +
308D GLY* 1.3 56.7 + - - -
358D ILE* 3.3 8.5 - - - +
359D GLN 2.8 31.6 + - - -
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Residues in contact with GLY 308 (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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251D TYR* 3.8 15.7 - - - -
284D TRP* 3.4 3.8 - - - -
285D ALA* 2.6 34.7 + - - -
286D THR* 3.1 15.8 + - - +
307D GLY* 1.3 73.2 - - - -
309D VAL* 1.3 58.2 + - - -
356D ARG* 3.9 11.9 - - - -
357D MET 3.3 7.2 - - - -
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Residues in contact with VAL 309 (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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283D VAL* 3.5 9.6 - - + +
284D TRP* 4.0 14.1 - - + +
308D GLY* 1.3 76.1 - - - -
310D ILE* 1.3 67.7 + - - +
313D THR* 3.5 22.0 - - - +
315D LEU* 3.6 27.4 - - + -
316D TRP* 3.8 9.2 - - + +
356D ARG* 3.4 8.4 - - - -
357D MET* 2.8 53.7 + - + +
359D GLN* 3.8 24.9 - - + -
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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