Contacts of the helix formed by residues 287 - 301 (chain Z) in PDB entry 5LN3
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 ASP 287 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260Z SER* 4.5 6.3 + - - -
262Z PHE* 4.3 17.0 - - + -
285Z CYS* 3.8 0.8 - - - +
286Z LYS* 1.3 84.0 + - - +
288Z VAL* 1.4 64.3 + - - +
289Z VAL* 4.1 9.5 - - + +
290Z VAL* 3.5 23.3 - - + +
291Z GLN* 3.2 23.7 + - - +
331Z LEU* 3.8 2.7 - - - -
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Residues in contact with VAL 288 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287Z ASP* 1.4 73.2 - - - +
289Z VAL* 1.3 64.1 + - + +
291Z GLN* 3.4 5.1 + - - +
292Z LYS* 3.2 41.3 + - - +
331Z LEU* 4.0 27.4 - - + -
333Z LEU* 5.6 4.3 - - + -
336Z GLU* 4.5 8.1 - - - +
901Z ARG* 3.7 22.0 - - - +
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Residues in contact with VAL 289 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287Z ASP* 4.1 16.8 - - + +
288Z VAL* 1.3 77.4 - - + +
290Z VAL* 1.3 61.5 + - + +
292Z LYS* 3.5 1.7 + - - +
293Z GLN* 3.1 26.9 + - - +
889Z PRO* 5.6 1.8 - - + -
890Z VAL* 6.0 5.4 - - + -
892Z PRO* 4.1 24.0 - - + -
899Z ILE* 3.5 19.8 - - + +
901Z ARG* 3.7 45.7 - - + +
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Residues in contact with VAL 290 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260Z SER* 4.7 3.8 - - - +
262Z PHE* 3.2 53.6 - - + -
266Z LEU* 5.7 3.8 - - + +
285Z CYS* 4.1 16.6 - - + -
287Z ASP* 3.5 26.7 + - + +
288Z VAL 3.4 0.2 - - - -
289Z VAL* 1.3 78.4 - - + +
291Z GLN* 1.4 64.9 - - - +
293Z GLN* 3.4 15.1 + - - +
294Z MET* 3.2 23.1 + - + +
892Z PRO* 4.5 13.5 - - + -
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Residues in contact with GLN 291 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282Z PHE* 3.5 45.0 + - - -
285Z CYS* 3.3 30.8 - - + +
287Z ASP 3.2 20.8 + - - +
288Z VAL* 3.6 6.5 - - - +
289Z VAL 3.2 0.2 - - - -
290Z VAL* 1.4 78.8 - - - +
292Z LYS* 1.4 58.0 + - - +
294Z MET* 3.5 9.0 + - - +
295Z ALA* 3.5 18.9 + - - +
321Z MET* 5.1 0.9 - - - +
330Z PHE 3.2 26.9 + - - +
331Z LEU* 4.0 9.7 - - + -
332Z ALA* 4.1 0.7 + - - -
336Z GLU* 3.4 29.1 - - - +
340Z MET* 5.6 1.0 - - - +
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Residues in contact with LYS 292 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288Z VAL* 3.2 32.2 + - + +
289Z VAL 3.9 4.0 - - - +
291Z GLN* 1.4 72.3 - - - +
293Z GLN* 1.4 61.3 + - - +
295Z ALA* 3.3 10.9 + - - +
296Z PHE* 3.3 26.9 + - + -
333Z LEU* 5.0 7.2 - - - -
335Z ARG* 4.9 8.0 - - - +
336Z GLU* 3.9 15.0 - - + +
834Z ASP 5.2 0.4 + - - -
835Z GLU* 3.8 41.5 + - - +
836Z GLU* 3.7 33.3 - - + +
899Z ILE* 3.9 18.5 - - + +
901Z ARG* 4.0 12.7 - - - +
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Residues in contact with GLN 293 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263Z PRO* 3.9 13.5 - - - +
266Z LEU* 5.0 6.5 - - + +
289Z VAL* 3.1 18.6 + - - +
290Z VAL* 3.4 13.6 + - - +
292Z LYS* 1.4 58.1 - - - +
294Z MET* 1.4 63.5 + - - +
296Z PHE* 3.4 8.1 + - - +
297Z MET* 3.3 22.5 + - - +
889Z PRO* 4.1 5.7 - - - +
892Z PRO* 3.5 33.9 + - - +
894Z LEU* 3.5 34.0 - - + +
897Z PHE 4.3 7.1 - - - +
898Z VAL* 4.3 4.4 - - - +
899Z ILE* 4.0 30.0 - - + +
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Residues in contact with MET 294 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266Z LEU* 4.3 28.4 - - + +
278Z VAL* 5.2 4.9 - - - +
281Z ILE* 4.0 28.3 - - + -
282Z PHE* 4.0 31.4 - - + +
285Z CYS* 4.1 13.5 - - - -
290Z VAL* 3.2 12.9 + - + +
291Z GLN* 3.9 10.5 - - - +
292Z LYS 3.4 0.2 - - - -
293Z GLN* 1.4 71.6 - - - +
295Z ALA* 1.3 57.7 - - - +
297Z MET* 3.2 2.7 + - - +
298Z LEU* 2.9 62.1 + - + +
340Z MET* 4.0 15.3 - - - +
785Z ARG* 5.2 0.2 - - - +
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Residues in contact with ALA 295 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291Z GLN 3.5 10.3 + - - +
292Z LYS* 3.3 14.5 + - - +
293Z GLN 3.3 0.6 - - - -
294Z MET* 1.3 76.1 - - - +
296Z PHE* 1.4 61.0 + - - +
299Z GLY 3.1 10.9 + - - -
321Z MET* 6.2 0.4 - - + -
336Z GLU* 4.0 16.4 - - + +
339Z ILE* 3.1 40.2 - - + +
340Z MET* 3.8 24.3 - - + +
836Z GLU* 5.3 0.9 - - - +
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Residues in contact with PHE 296 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292Z LYS* 3.3 15.5 + - + -
293Z GLN* 3.8 5.6 - - - +
294Z MET 3.2 0.6 - - - -
295Z ALA* 1.4 79.1 - - - +
297Z MET* 1.3 58.4 + - - +
299Z GLY* 3.1 15.9 + - - -
300Z ARG* 3.3 12.1 + - - +
339Z ILE* 3.4 26.2 - - + -
344Z VAL* 6.1 1.8 - - + -
345Z PRO* 4.4 18.2 - - + +
349Z TYR* 5.6 1.0 + - - -
833Z PHE* 3.4 45.3 - + + -
835Z GLU 5.2 0.4 - - - -
836Z GLU* 3.7 36.8 - - + -
897Z PHE* 3.7 48.3 - + + +
898Z VAL 5.3 4.9 - - - -
899Z ILE* 6.0 2.0 - - + -
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Residues in contact with MET 297 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266Z LEU* 4.9 2.5 - - + -
293Z GLN 3.3 16.6 + - - +
294Z MET* 3.2 5.6 + - - +
296Z PHE* 1.3 79.3 - - - +
298Z LEU* 1.3 57.3 - - - +
300Z ARG* 3.5 54.6 + - - +
301Z HIS* 4.2 5.5 + - - +
784Z ASP* 3.8 16.6 - - + +
785Z ARG* 3.5 54.4 + - + +
894Z LEU* 3.9 27.8 - - + -
895Z GLU 4.2 1.8 - - - +
897Z PHE* 3.4 31.2 - - - +
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Residues in contact with LEU 298 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266Z LEU* 5.9 1.6 - - + -
273Z ASN* 5.6 6.3 - - - +
278Z VAL* 4.2 20.6 - - + -
294Z MET* 2.9 53.3 + - + +
295Z ALA 4.6 1.6 - - - +
297Z MET* 1.3 69.0 - - - +
299Z GLY* 1.4 61.7 - - - +
300Z ARG 3.4 0.2 + - - -
301Z HIS 3.5 6.6 + - - +
302Z GLY* 3.3 28.6 + - - -
305Z LEU* 4.1 20.2 - - + +
306Z GLU 4.8 1.4 - - - +
340Z MET* 3.7 23.5 - - + +
785Z ARG* 4.3 18.8 - - - +
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Residues in contact with GLY 299 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295Z ALA 3.1 13.2 + - - -
296Z PHE* 3.1 10.0 + - - -
298Z LEU* 1.4 74.6 - - - +
300Z ARG* 1.4 57.2 + - - +
301Z HIS 3.3 0.2 - - - -
307Z LEU* 3.1 24.4 - - - +
339Z ILE 3.6 14.4 - - - -
340Z MET 4.4 5.8 + - - -
342Z PRO* 3.5 19.0 - - - +
345Z PRO* 4.7 8.8 - - - +
349Z TYR* 5.7 1.0 - - - -
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Residues in contact with ARG 300 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296Z PHE 3.3 7.6 + - - +
297Z MET* 3.5 51.4 + - - +
298Z LEU 3.3 0.2 - - - -
299Z GLY* 1.4 76.0 - - - +
301Z HIS* 1.4 92.6 + - - +
307Z LEU* 3.8 8.7 - - - +
345Z PRO* 5.4 0.2 - - - +
349Z TYR* 4.2 18.1 + - - +
782Z HIS* 3.4 20.2 - - - -
784Z ASP* 2.9 30.7 + - - +
785Z ARG* 4.6 5.7 - - - +
826Z GLN* 5.0 0.6 + - - +
827Z PRO* 3.8 38.3 + - + +
897Z PHE* 3.6 31.8 - - + -
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Residues in contact with HIS 301 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270Z LEU* 3.8 24.1 - - + +
297Z MET 4.2 4.2 + - - +
298Z LEU* 3.5 11.3 + - - +
300Z ARG* 1.4 111.7 - - - +
302Z GLY* 1.3 64.0 - - - +
303Z VAL* 5.0 3.3 - - + +
307Z LEU* 4.0 9.4 - - + -
782Z HIS* 3.2 31.8 + + - -
785Z ARG* 5.5 3.0 + - - -
789Z SER* 3.3 20.0 + - - -
791Z VAL* 4.7 12.1 - - + +
826Z GLN* 3.1 27.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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