Contacts of the helix formed by residues 280 - 295 (chain J) in PDB entry 5G04
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 LYS 280 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248J LYS* 4.9 7.9 - - - +
251J TYR* 3.4 45.0 + - + +
275J LEU* 3.2 14.6 + - + +
278J LEU* 3.6 41.1 - - + +
279J ASN* 1.3 72.3 - - - +
281J ALA* 1.3 64.0 + - - +
282J ASN* 3.2 3.4 - - - -
283J GLU* 3.0 22.9 + - + +
284J LEU* 3.1 10.4 + - - +
311J MET* 3.6 5.4 - - - +
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Residues in contact with ALA 281 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279J ASN* 2.9 10.0 + - - +
280J LYS* 1.3 71.6 - - - +
282J ASN* 1.3 58.8 + - - +
284J LEU* 3.2 1.8 + - - +
285J PHE* 2.8 33.1 + - - +
308J TYR* 3.8 9.2 - - + -
311J MET* 3.4 24.5 - - + -
312J VAL* 5.3 0.9 - - + -
26M TYR* 3.2 43.7 - - + +
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Residues in contact with ASN 282 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C SER 3.7 1.2 - - - +
318C TYR* 3.1 31.2 + - - +
321C HIS* 3.1 25.9 + - + +
322C ASN* 2.7 53.2 + - - +
325C GLU* 4.4 11.5 + - - +
280J LYS 3.2 0.8 - - - -
281J ALA* 1.3 78.1 - - - +
283J GLU* 1.3 64.0 + - - +
285J PHE* 3.3 6.6 + - - +
286J TYR* 3.0 20.3 + - - +
26M TYR* 5.0 0.2 - - - -
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Residues in contact with GLU 283 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C TYR* 3.1 31.4 + - - -
251J TYR* 4.1 14.4 - - - +
258J MET* 5.7 1.9 - - - +
271J HIS* 4.0 15.9 + - + +
275J LEU* 3.6 26.2 - - + -
280J LYS* 3.0 20.3 + - + +
282J ASN* 1.3 78.3 - - - +
284J LEU* 1.3 57.6 + - - +
286J TYR* 3.3 8.2 + - - +
287J LEU* 2.9 34.1 + - - +
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Residues in contact with LEU 284 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272J ILE* 4.3 27.4 - - + +
275J LEU* 3.6 22.0 - - + -
276J VAL* 4.4 4.9 - - + -
280J LYS 3.1 10.4 + - - +
281J ALA 3.2 6.7 + - - +
283J GLU* 1.3 79.0 - - - +
285J PHE* 1.3 56.5 + - - +
287J LEU* 3.2 7.4 + - + -
288J SER* 2.8 36.5 + - - +
304J ALA* 4.6 1.6 - - + +
307J CYS* 4.0 8.7 - - + -
308J TYR* 3.5 32.5 - - + +
311J MET* 3.3 33.4 - - + -
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Residues in contact with PHE 285 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C SER* 3.8 32.1 - - - -
317C SER* 3.8 26.9 - - - -
318C TYR 4.4 6.1 - - - -
321C HIS* 6.2 6.1 - + + +
281J ALA 2.8 11.8 + - - +
282J ASN* 3.7 8.3 - - - +
284J LEU* 1.3 74.6 - - - +
286J TYR* 1.3 71.3 + - + +
288J SER* 4.1 1.7 - - - +
289J HIS* 3.2 24.4 + - + +
308J TYR* 3.3 38.3 - + + +
27M GLU* 3.8 23.6 - - + -
28M ASP 4.2 1.6 - - - -
29M VAL* 3.6 41.5 - - + -
30M ALA 5.9 0.2 - - - -
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Residues in contact with TYR 286 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C SER* 4.6 12.6 - - - -
315C GLU* 2.8 44.8 + - + -
318C TYR* 3.5 59.2 - + + -
282J ASN 3.0 6.8 + - - +
283J GLU* 3.6 13.7 - - - +
285J PHE* 1.3 81.0 - + - +
287J LEU* 1.3 65.6 + - + +
289J HIS* 4.0 2.4 - + - +
290J LYS* 3.1 49.7 + - + +
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Residues in contact with LEU 287 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258J MET* 3.5 22.7 - - + -
262J PRO 5.4 0.7 - - - +
263J PHE* 3.9 27.1 - - + -
268J LEU* 4.6 5.8 - - + -
271J HIS* 3.4 32.3 - - + +
272J ILE* 4.6 16.2 - - + -
275J LEU* 4.5 5.8 - - + -
283J GLU* 2.9 24.1 + - - +
284J LEU* 3.2 8.5 + - + +
286J TYR* 1.3 80.1 - - + +
288J SER* 1.3 56.6 + - - +
290J LYS* 3.2 4.3 + - + +
291J LEU* 2.9 35.3 + - + +
304J ALA* 5.4 0.9 - - + -
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Residues in contact with SER 288 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284J LEU* 2.8 22.8 + - - +
285J PHE* 4.1 3.8 - - - -
287J LEU* 1.3 70.9 - - - +
289J HIS* 1.3 63.8 - - - +
291J LEU* 3.0 5.2 + - - +
292J VAL* 3.0 26.2 + - - +
304J ALA* 2.9 43.7 + - - +
305J VAL* 3.2 17.7 + - - -
308J TYR* 4.0 4.4 - - - +
29M VAL* 4.1 12.1 - - - -
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Residues in contact with HIS 289 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C SER* 2.9 40.5 + - - +
315C GLU* 6.0 0.6 - - - +
285J PHE* 3.2 23.9 + - + +
286J TYR* 4.1 5.8 - + - +
288J SER* 1.3 79.6 - - - +
290J LYS* 1.3 84.2 + - + +
292J VAL* 3.6 4.2 + - - +
293J ASP* 3.3 44.7 + - - -
29M VAL* 3.5 23.8 - - + +
30M ALA* 4.7 18.7 + - + +
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Residues in contact with LYS 290 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C GLU* 3.9 22.6 + - - +
263J PHE* 3.0 36.6 - - + -
286J TYR* 3.1 41.6 + - + +
287J LEU* 3.6 4.9 - - + +
289J HIS* 1.3 94.5 + - - +
291J LEU* 1.4 63.3 + - - +
293J ASP* 5.5 1.1 - - - -
294J LEU* 3.0 47.2 + - + +
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Residues in contact with LEU 291 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263J PHE* 3.3 33.9 - - + -
268J LEU* 3.8 27.6 - - + -
272J ILE* 4.8 3.1 - - + -
287J LEU* 2.9 25.6 + - + +
288J SER* 3.0 7.8 + - - +
290J LYS* 1.4 76.5 - - - +
292J VAL* 1.3 58.0 + - - +
295J TYR* 2.7 48.8 + - + +
298J ASN* 5.5 1.3 - - - +
300J VAL* 4.3 4.3 - - + -
301J SER* 3.1 34.4 + - - +
304J ALA* 3.9 17.5 - - + -
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Residues in contact with VAL 292 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288J SER 3.0 11.3 + - - +
289J HIS 3.6 10.5 - - - +
291J LEU* 1.3 73.8 - - - +
293J ASP* 1.3 76.4 - - - +
296J PRO* 3.4 26.9 - - + +
301J SER* 3.1 18.1 + - - +
302J TRP* 4.6 14.4 - - + -
305J VAL* 3.4 28.5 - - + -
29M VAL* 4.2 9.2 - - + -
30M ALA 3.7 23.3 - - - +
31M ILE* 4.3 7.9 - - + -
32M PRO* 4.1 16.6 - - + +
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Residues in contact with ASP 293 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289J HIS* 3.3 38.8 + - - +
290J LYS* 5.0 1.6 - - - -
291J LEU 3.3 0.2 - - - -
292J VAL* 1.3 92.4 - - - +
294J LEU* 1.3 75.1 + - + +
296J PRO* 3.7 7.8 - - - +
30M ALA* 4.4 7.1 - - - +
32M PRO* 5.2 3.6 - - - +
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Residues in contact with LEU 294 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263J PHE* 4.7 8.5 - - + -
290J LYS* 3.0 52.6 + - + +
293J ASP* 1.3 91.5 - - + +
295J TYR* 1.3 84.9 + - + +
296J PRO* 3.4 6.0 - - - +
54K HIS* 3.4 43.4 + - + +
85K GLU* 5.1 7.4 - - - +
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Residues in contact with TYR 295 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263J PHE* 3.9 29.9 - + + -
291J LEU* 2.7 32.1 + - + +
294J LEU* 1.3 89.0 - - + +
296J PRO* 1.3 65.7 - - - +
297J SER* 3.1 4.7 + - - +
298J ASN* 3.3 27.3 + - + +
301J SER* 3.2 19.0 - - - -
51K ALA 4.6 15.7 - - - -
52K GLN* 4.4 8.7 - - + -
53K TYR* 4.3 4.5 + + - -
54K HIS* 2.6 47.7 + + - +
55K ARG* 3.7 10.4 + - + +
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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
------------------------------------------------------------
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