Contacts of the helix formed by residues 286 - 301 (chain Y) in PDB entry 5A31
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 286 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F PHE* 3.0 50.6 - - + +
98F ASN* 4.4 3.6 - - - +
281Y TYR* 3.0 36.9 + - + +
284Y ALA* 3.8 19.8 - - + +
285Y GLY* 1.3 73.3 - - - +
287Y ASN* 1.3 62.6 - - - +
288Y LYS 3.5 1.8 - - - -
289Y ASN* 3.3 8.1 + - - +
290Y SER* 3.1 23.0 + - - -
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Residues in contact with ASN 287 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F PHE* 5.1 5.7 - - + -
281Y TYR 5.2 0.4 - - - -
282Y PHE* 6.0 0.4 - - - +
285Y GLY 3.0 11.5 + - - +
286Y ASP* 1.3 71.7 - - - +
288Y LYS* 1.3 69.5 + - + +
290Y SER* 3.4 21.0 - - - -
291Y VAL* 3.5 10.7 + - - +
314Y LEU* 3.3 29.8 - - - +
317Y ARG* 4.6 16.4 - - - +
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Residues in contact with LYS 288 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F GLN* 4.1 16.1 + - + +
95F GLY 5.7 2.2 - - - +
96F VAL* 4.4 31.6 - - + +
97F PHE* 6.0 8.5 - - + -
286Y ASP 3.5 0.6 - - - -
287Y ASN* 1.3 82.7 - - + +
289Y ASN* 1.3 69.3 + - - +
291Y VAL* 3.4 7.2 + - - +
292Y LEU* 3.3 19.6 + - - +
476Y ILE* 5.7 7.7 - - - +
507Y SER* 5.3 13.7 + - - +
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Residues in contact with ASN 289 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F GLN* 3.6 23.4 + - - +
94F GLY 5.2 2.3 - - - +
95F GLY 4.8 5.2 + - - +
96F VAL 3.6 14.3 + - - -
97F PHE* 4.6 1.6 - - - +
98F ASN* 3.6 29.5 + - - -
281Y TYR* 3.1 31.4 - - + -
286Y ASP* 3.3 11.6 + - - +
287Y ASN 3.2 0.4 - - - -
288Y LYS* 1.3 82.8 - - - +
290Y SER* 1.3 65.2 + - - +
292Y LEU* 3.5 3.4 + - - +
293Y LYS* 3.3 31.1 + - - +
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Residues in contact with SER 290 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278Y ALA* 4.3 12.2 - - - +
281Y TYR* 3.0 33.5 + - - +
282Y PHE* 3.0 18.0 + - - -
286Y ASP 3.1 10.8 + - - -
287Y ASN* 3.4 11.5 + - - -
289Y ASN* 1.3 77.1 - - - +
291Y VAL* 1.3 52.5 + - - -
293Y LYS* 3.2 2.6 + - - +
294Y PHE* 2.7 36.9 + - - +
314Y LEU* 3.8 19.2 - - - +
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Residues in contact with VAL 291 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287Y ASN* 3.7 12.6 - - - +
288Y LYS* 3.4 8.9 + - - +
289Y ASN 3.3 0.8 - - - -
290Y SER* 1.3 77.6 - - - +
292Y LEU* 1.3 57.7 + - - +
294Y PHE* 4.0 5.4 - - - -
295Y GLU* 2.7 40.8 + - - +
311Y TYR* 3.9 17.0 - - + -
314Y LEU* 3.4 39.9 - - + +
315Y LEU* 4.2 6.1 - - + -
320Y ARG* 4.0 22.9 - - - +
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Residues in contact with LEU 292 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F LYS* 3.4 37.2 - - + +
87F GLU* 4.0 15.3 - - + +
90F GLN* 3.1 42.2 - - - +
91F ILE* 5.4 6.1 - - + -
288Y LYS 3.3 5.4 + - - +
289Y ASN* 3.8 7.6 - - - +
290Y SER 3.4 0.4 - - - -
291Y VAL* 1.3 79.1 - - - +
293Y LYS* 1.3 67.1 + - + +
295Y GLU* 3.5 7.9 + - - +
296Y GLN* 3.2 25.1 + - + +
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Residues in contact with LYS 293 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259Y CYS* 4.8 8.3 - - - -
262Y GLU* 5.0 7.0 - - - +
274Y LEU* 4.2 20.3 - - + +
277Y LEU* 3.3 40.2 - - + -
278Y ALA* 5.2 3.4 - - - +
281Y TYR* 3.0 46.7 + - + -
289Y ASN* 3.3 14.2 + - - +
290Y SER* 3.2 7.8 + - - +
292Y LEU* 1.3 81.1 - - + +
294Y PHE* 1.3 60.9 + - - +
296Y GLN* 3.3 14.3 + - - +
297Y ALA* 3.1 24.3 + - - +
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Residues in contact with PHE 294 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275Y GLY* 6.1 1.6 - - - -
278Y ALA* 4.0 23.6 - - + +
290Y SER 2.7 19.5 + - - +
291Y VAL* 3.5 4.9 - - - +
293Y LYS* 1.3 75.5 - - - +
295Y GLU* 1.3 64.1 + - - +
297Y ALA* 3.0 21.1 + - + +
298Y GLN* 3.0 15.7 + - + -
304Y LEU* 6.4 0.7 - - + -
307Y GLY* 3.4 23.8 - - - -
308Y MET* 3.1 31.6 - - - -
310Y VAL* 5.8 1.8 - - + -
311Y TYR* 2.7 70.0 - + + -
314Y LEU* 5.6 2.9 - - + -
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Residues in contact with GLU 295 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F LYS* 2.6 39.0 + - - -
291Y VAL* 2.7 27.6 + - - +
292Y LEU* 3.7 6.1 - - - +
294Y PHE* 1.3 76.7 - - - +
296Y GLN* 1.3 61.7 + - - +
298Y GLN* 3.4 5.9 + - - +
299Y MET* 3.1 41.0 + - + +
311Y TYR* 3.3 21.3 + - + +
320Y ARG* 2.8 32.3 + - - -
323Y ASP* 4.5 3.3 - - - +
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Residues in contact with GLN 296 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F LYS* 3.6 18.1 - - - +
63F GLY 3.2 16.6 + - - +
64F HIS* 3.2 6.3 - - - +
65F SER* 2.8 48.7 - - - +
262Y GLU* 4.8 1.9 - - - +
268Y ARG 5.6 0.2 + - - -
269Y ASP* 4.6 3.8 + - - -
274Y LEU* 3.9 22.3 - - + +
292Y LEU* 3.2 17.8 + - + +
293Y LYS* 3.4 13.2 - - - +
294Y PHE 3.1 0.4 - - - -
295Y GLU* 1.3 76.0 - - - +
297Y ALA* 1.3 59.9 + - - +
299Y MET* 3.2 4.4 + - - +
300Y LEU* 2.9 44.3 + - + +
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Residues in contact with ALA 297 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271Y VAL* 4.7 3.0 - - - +
274Y LEU* 3.8 30.5 - - + -
275Y GLY* 4.5 9.4 - - - +
293Y LYS 3.1 9.1 + - - +
294Y PHE* 3.0 19.4 + - + +
296Y GLN* 1.3 76.3 - - - +
298Y GLN* 1.3 61.4 + - - +
300Y LEU* 3.3 5.2 + - - +
301Y ASP 3.1 14.0 + - - -
304Y LEU* 3.1 27.5 - - + +
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Residues in contact with GLN 298 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530H ASN* 5.4 0.7 + - - +
294Y PHE* 3.0 15.0 + - + +
295Y GLU* 3.8 9.3 - - - +
297Y ALA* 1.3 76.1 - - - +
299Y MET* 1.3 64.5 + - + +
301Y ASP 2.7 25.1 - - - +
302Y PRO* 4.2 8.7 - - - +
304Y LEU* 3.9 6.5 - - - +
308Y MET* 3.7 21.7 - - + +
311Y TYR* 4.0 22.8 + - - -
327Y LEU* 3.5 30.1 - - - +
330Y ARG* 3.7 38.4 + - - +
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Residues in contact with MET 299 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F TYR* 6.1 0.9 - - + -
59F ARG* 4.4 22.9 - - + +
62F LYS* 4.7 13.0 - - + -
63F GLY* 3.9 31.0 - - - -
527H ARG 4.4 10.4 - - - +
528H ILE 5.1 3.8 - - - +
530H ASN* 3.2 40.8 + - - +
295Y GLU* 3.1 38.4 + - + +
296Y GLN 3.7 4.7 - - - +
297Y ALA 3.2 0.4 - - - -
298Y GLN* 1.3 78.6 - - + +
300Y LEU* 1.3 66.5 + - - +
301Y ASP 4.9 0.5 - - - -
330Y ARG* 5.9 3.4 - - - +
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Residues in contact with LEU 300 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F GLY 2.9 31.4 - - - +
64F HIS* 4.8 6.5 - - + +
527H ARG 5.1 2.4 - - - +
528H ILE* 6.1 0.5 - - - -
62X THR* 6.1 0.2 - - + -
269Y ASP* 3.6 42.6 - - + +
270Y ASN 4.4 5.4 - - - +
271Y VAL* 4.8 7.0 - - + +
274Y LEU* 3.9 15.7 - - + -
296Y GLN* 2.9 33.7 + - + +
297Y ALA* 3.6 8.1 - - - +
299Y MET* 1.3 79.3 - - - +
301Y ASP* 1.3 69.3 + - + +
302Y PRO* 4.0 5.4 - - - +
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Residues in contact with ASP 301 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95X ASN* 5.7 2.4 + - - +
99X LYS* 5.3 8.4 + - - -
271Y VAL* 3.2 39.7 - - + +
297Y ALA 3.1 3.0 + - - +
298Y GLN* 2.7 21.4 - - - +
299Y MET 4.9 0.2 - - - -
300Y LEU* 1.3 86.1 - - - +
302Y PRO* 1.3 72.0 - - + +
303Y TYR* 3.2 6.5 + - - +
304Y LEU* 3.6 31.5 - - + +
308Y MET* 5.3 0.2 - - - +
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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