Contacts of the helix formed by residues 286 - 296 (chain A) in PDB entry 5HOO
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 HIS 286 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A TRP* 4.3 7.2 - - + -
282A PRO 3.1 13.1 + - - +
285A TYR* 1.3 94.2 - - + +
287A LEU* 1.3 68.4 + - - +
288A PHE 3.6 0.2 - - - -
289A ALA* 3.4 2.5 + - - +
290A SER* 3.2 23.7 + - - -
321A PHE* 3.1 65.2 + + - -
322A TYR* 4.6 2.7 - - - -
324A ARG* 4.2 11.8 - - + +
325A GLY* 3.4 27.4 + - - -
328A LYS* 3.9 18.4 - - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A VAL* 4.7 13.0 - - + -
197A TRP* 3.4 53.8 - - + +
202A VAL* 5.3 1.8 - - + -
282A PRO 3.2 4.4 + - - -
283A SER* 3.5 7.2 - - - +
286A HIS* 1.3 85.7 + - - +
288A PHE* 1.3 79.6 + - + +
290A SER* 3.6 4.2 + - - -
291A MET* 3.4 19.1 + - + +
313A TRP* 4.2 3.7 - - + -
314A PHE* 4.3 16.4 - - + -
317A LYS* 3.4 29.8 - - - +
321A PHE* 4.5 4.7 - - + -
322A TYR* 4.4 6.5 - - + -
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Residues in contact with PHE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ASP* 3.6 37.2 - - + -
157A GLU 4.3 2.0 - - - -
158A LYS* 3.4 47.9 - - + -
193A LEU* 4.5 2.7 - - + -
195A VAL* 3.7 21.8 - - + -
283A SER* 2.9 28.0 + - - +
284A ASP* 3.3 29.2 - - - +
287A LEU* 1.3 78.5 - - + +
289A ALA* 1.3 60.7 + - - +
291A MET* 3.0 23.9 + - + +
292A GLY 2.8 25.3 + - - -
55F G 3.7 17.7 - - - +
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ASP 3.5 2.2 + - - -
285A TYR 3.0 28.7 - - - +
286A HIS 3.4 2.7 + - - +
288A PHE* 1.3 78.0 - - - +
290A SER* 1.3 62.6 + - - +
292A GLY* 3.1 12.3 + - - -
293A HIS* 3.3 18.6 + - - -
54F T 4.1 18.1 + - - +
55F G 3.2 28.7 + - - +
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Residues in contact with SER 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A HIS 3.2 7.0 + - - -
287A LEU 3.7 9.4 - - - -
289A ALA* 1.3 77.3 - - - +
291A MET* 1.3 63.0 + - - +
293A HIS* 3.4 20.5 + - - +
294A ALA* 3.5 8.1 + - - +
313A TRP* 3.4 20.9 - - - -
317A LYS* 4.9 0.7 - - - +
321A PHE* 3.7 30.5 - - - -
5E G 6.1 2.5 - - - -
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Residues in contact with MET 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LYS* 4.3 11.0 - - - -
160A ILE* 4.1 24.5 - - - -
193A LEU* 3.9 15.3 - - + -
195A VAL* 5.9 0.2 - - + -
287A LEU* 3.4 12.8 + - + +
288A PHE* 3.0 41.6 + - + +
290A SER* 1.3 79.6 - - - +
292A GLY* 1.3 51.5 + - - +
294A ALA* 3.0 3.4 + - - +
295A LEU* 2.8 47.1 + - + +
309A TRP* 4.2 17.0 - - + -
310A LEU* 4.2 15.5 - - + -
313A TRP* 3.8 26.4 - - + -
314A PHE* 5.0 3.4 - - + -
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Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LYS* 5.2 4.9 + - - -
288A PHE 2.8 13.3 + - - -
289A ALA 3.1 3.5 + - - -
291A MET* 1.3 76.0 - - - +
293A HIS* 1.3 59.3 + - - +
295A LEU* 3.6 10.9 + - - +
296A ALA* 3.4 18.0 + - - +
54F T 3.4 31.9 - - - +
55F G 3.9 10.5 + - - -
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Residues in contact with HIS 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ALA 3.3 24.6 + - - -
290A SER* 3.4 10.5 + - - +
291A MET 3.2 0.6 - - - -
292A GLY* 1.3 71.2 - - - +
294A ALA* 1.3 66.9 + - - +
295A LEU 3.1 1.6 - - - -
296A ALA* 3.1 21.6 + - - +
4E G 4.9 1.4 + - - -
5E G 4.6 27.7 + - - +
6E T 5.2 15.3 - - - -
53F C 3.3 24.7 + - - -
54F T 3.1 42.7 + - - -
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A SER 3.5 5.2 + - - +
291A MET 3.0 5.4 + - - +
293A HIS* 1.3 76.8 - - - +
295A LEU* 1.3 57.3 + - - +
296A ALA 3.4 2.2 - - - +
298A GLN* 3.4 20.4 + - - +
309A TRP* 3.5 23.3 - - + -
313A TRP* 3.5 31.9 - - + +
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LYS* 4.1 24.0 - - - +
160A ILE* 4.4 26.2 - - + -
164A ASN* 3.3 27.5 - - + +
291A MET* 2.8 37.8 + - + +
292A GLY* 3.8 8.7 - - - +
293A HIS 3.1 0.4 - - - -
294A ALA* 1.3 75.4 - - - +
296A ALA* 1.3 68.3 + - - +
298A GLN* 3.2 17.7 + - + +
300A PHE* 4.5 17.9 - - + -
309A TRP* 4.2 21.5 - - + -
55F G 5.6 1.6 - - - +
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Residues in contact with ALA 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ASN* 4.2 4.5 - - - -
166A LYS* 4.0 27.8 - - + +
292A GLY 3.4 8.2 + - - +
293A HIS* 3.1 17.2 + - - +
294A ALA 4.0 2.6 - - - +
295A LEU* 1.3 78.8 - - - +
297A GLU* 1.3 72.8 + - + +
298A GLN* 3.0 8.8 + - - +
54F T 5.2 3.1 - - - +
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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