Contacts of the strand formed by residues 287 - 295 (chain D) in PDB entry 4WLU
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 TYR 287 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D ILE* 3.9 19.3 - - + -
149D PRO* 3.9 27.3 + - + +
152D ALA* 3.1 31.7 - - + +
153D GLU* 4.6 5.4 + - - +
156D LYS* 4.6 9.9 + - - -
161D TYR* 4.2 3.2 + - - -
166D ILE* 6.3 0.4 - - + -
277D PHE* 3.5 28.4 - + + -
278D VAL 3.3 6.3 - - - +
279D LYS* 3.6 40.6 - - + +
280D SER* 4.2 0.4 - - - +
285D CYS* 3.3 16.2 - - - +
286D THR* 1.3 95.7 - - + +
288D PHE* 1.3 67.0 + - - +
323D LEU* 4.8 1.0 - - - +
327D ILE* 3.7 27.7 - - + +
331D GLU* 4.1 6.2 + - - -
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Residues in contact with PHE 288 (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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197D ILE* 4.1 13.0 - - + -
198D GLY* 3.5 29.8 - - - -
206D ILE* 5.0 2.9 - - + -
276D SER 3.6 1.2 - - - +
277D PHE* 3.7 7.2 - - - -
278D VAL* 3.0 29.2 + - - +
280D SER* 3.7 21.1 - - - +
282D GLU* 5.1 0.7 - - + -
283D THR* 3.6 37.0 - - + +
285D CYS* 4.3 4.5 - - + +
287D TYR* 1.3 74.7 - - - +
289D SER* 1.3 79.5 + - - +
290D THR* 3.8 12.2 + - + -
305D ILE* 4.0 22.7 - - + -
316D ILE* 4.5 9.4 - - + -
319D ALA* 6.0 0.2 - - + -
320D ILE* 4.9 7.9 - - + -
323D LEU* 3.6 29.8 - - + -
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Residues in contact with SER 289 (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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170D THR* 3.6 14.3 + - - -
196D VAL 3.8 9.9 + - - -
197D ILE* 3.1 13.0 - - - +
198D GLY 2.8 43.9 + - - -
199D GLY 4.6 0.7 - - - -
275D CYS 3.9 0.3 - - - -
276D SER* 3.2 35.7 + - - -
277D PHE* 3.7 7.4 - - - -
288D PHE* 1.3 74.3 - - - +
290D THR* 1.3 64.7 + - - +
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Residues in contact with THR 290 (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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197D ILE* 4.1 4.5 - - + +
275D CYS* 3.3 15.1 - - - -
276D SER 3.5 2.3 + - - -
280D SER* 4.9 0.6 + - - +
282D GLU* 4.3 6.5 - - + -
288D PHE* 3.8 19.0 + - + -
289D SER* 1.3 79.9 + - - +
291D PRO* 1.3 75.0 - - + +
292D LEU* 3.3 16.1 + - - +
302D ASN* 2.6 36.9 + - - -
304D GLY* 3.8 22.9 - - - +
305D ILE* 3.9 13.5 - - + +
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Residues in contact with PRO 291 (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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195D PRO* 4.4 16.2 - - + -
197D ILE* 4.2 10.5 - - + -
208D LEU* 5.9 0.2 - - + -
211D GLN* 5.2 4.0 - - - +
273D VAL* 3.9 17.0 - - + -
274D GLU 3.9 4.7 - - - +
275D CYS* 3.9 22.9 - - - +
290D THR* 1.3 87.9 - - - +
292D LEU* 1.3 59.1 + - - +
302D ASN* 3.7 3.5 - - - +
303D LEU* 2.9 38.4 + - + +
304D GLY 3.5 15.9 - - - +
305D ILE* 5.4 1.1 - - - +
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Residues in contact with LEU 292 (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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167D PHE* 4.2 5.6 - - + -
273D VAL* 3.2 8.2 - - - +
274D GLU 2.9 33.3 + - - +
276D SER* 3.8 19.3 - - - +
278D VAL* 3.7 38.8 - - + -
290D THR* 3.3 17.7 - - - +
291D PRO* 1.3 71.9 - - - +
293D LEU* 1.3 62.4 + - - +
294D LEU* 3.4 13.7 + - + +
299D ILE* 3.9 20.0 - - + -
301D LYS 3.6 4.0 - - - +
302D ASN* 3.6 38.8 - - + +
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Residues in contact with LEU 293 (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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271D GLY* 4.2 12.1 - - - +
272D VAL 3.5 27.6 - - - +
273D VAL* 4.1 11.2 - - + -
292D LEU* 1.3 70.7 - - - +
294D LEU* 1.3 58.1 + - - +
299D ILE* 3.8 2.6 - - - -
300D GLU* 2.8 54.6 + - + +
301D LYS* 2.8 30.8 + - + +
303D LEU* 3.9 20.3 - - + +
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Residues in contact with LEU 294 (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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167D PHE* 4.1 28.3 - - + -
258D PHE* 4.8 6.3 - - + -
262D LEU* 4.0 34.1 - - + +
265D ALA* 3.4 22.6 - - + +
269D LYS 4.6 4.9 - - - +
271D GLY 5.7 0.2 + - - -
272D VAL* 2.9 25.5 + - + +
274D GLU* 4.1 27.8 - - + +
292D LEU* 3.9 24.7 - - + +
293D LEU* 1.3 83.3 - - - +
295D GLY* 1.3 59.1 + - - +
298D GLY 3.4 9.6 - - - +
299D ILE* 4.7 0.9 - - - -
300D GLU* 4.0 2.9 - - - +
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Residues in contact with GLY 295 (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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262D LEU* 5.0 0.9 - - - +
265D ALA* 3.5 20.2 - - - +
266D MET* 4.0 5.2 + - - +
269D LYS 5.8 0.7 - - - -
294D LEU* 1.3 73.6 - - - +
296D LYS* 1.3 65.7 + - - -
297D LYS 3.2 3.4 - - - -
298D GLY* 2.7 23.5 + - - +
300D GLU* 3.7 26.4 - - - +
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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