Contacts of the helix formed by residues 276 - 286 (chain B) in PDB entry 5H8N
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 GLY 276 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A PHE* 4.2 18.1 - - - -
272B SER 4.1 1.1 - - - -
273B HIS 3.5 9.1 + - - -
274B GLU 3.4 4.2 + - - -
275B ASN* 1.3 78.9 - - - +
277B PHE* 1.3 59.3 + - - +
278B MET 3.3 2.9 - - - -
279B GLU* 3.0 9.9 + - - +
280B ASP* 2.8 36.2 + - - +
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Residues in contact with PHE 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ASP* 4.1 8.5 - - + -
71B LEU* 4.1 9.9 - - + -
74B LYS* 3.6 53.6 - - + -
272B SER* 3.1 26.3 + - - +
275B ASN* 3.1 19.9 + - - +
276B GLY* 1.3 76.5 - - - +
278B MET* 1.3 56.6 + - - +
280B ASP* 3.3 19.0 + - + +
281B LEU* 3.1 66.0 + - + +
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Residues in contact with MET 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 4.5 10.6 - - + -
71B LEU* 4.1 22.9 - - + -
142B PHE* 3.6 34.8 - - + +
269B ILE* 3.9 16.2 - - + +
272B SER* 2.9 37.2 + - - +
273B HIS* 3.4 36.3 - - + +
277B PHE* 1.3 76.4 - - - +
279B GLU* 1.3 63.8 + - - +
281B LEU* 3.5 15.9 + - - +
282B ASP* 3.3 20.3 + - - +
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Residues in contact with GLU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TYR* 2.9 37.9 + - - +
238A ILE 4.4 1.0 - - - +
239A PHE* 3.2 36.1 - - + +
240A ALA 4.4 2.3 + - - -
273B HIS 5.5 0.6 + - - +
276B GLY* 3.0 17.2 + - - +
278B MET* 1.3 75.0 - - - +
280B ASP* 1.4 59.5 + - - +
282B ASP* 3.2 8.9 + - + +
283B LYS* 2.9 59.4 + - - +
287B ARG* 4.7 2.3 + - - +
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Residues in contact with ASP 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B GLY* 2.8 22.8 + - - +
277B PHE* 3.4 22.4 - - + +
279B GLU* 1.4 71.4 - - - +
281B LEU* 1.4 57.0 + - + +
283B LYS* 3.0 15.2 + - - +
284B THR* 2.9 34.8 + - - +
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B PHE* 3.6 47.8 - - + +
70B ASP* 3.6 33.0 - - + +
71B LEU* 4.4 7.6 - - + +
277B PHE* 3.1 51.7 + - + +
278B MET* 3.7 13.2 - - - +
279B GLU 3.4 0.2 - - - -
280B ASP* 1.4 74.4 - - + +
282B ASP* 1.3 57.7 + - - +
284B THR* 3.2 3.3 + - - +
285B TRP* 2.8 43.2 + - + +
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Residues in contact with ASP 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TYR* 6.1 0.4 - - - +
67B PHE* 3.8 7.7 - - - -
143B LYS* 3.5 31.6 + - - +
278B MET 3.3 8.8 + - - +
279B GLU* 3.2 13.1 + - + +
281B LEU* 1.3 77.7 - - - +
283B LYS* 1.3 57.6 + - - +
286B VAL* 3.0 34.4 + - - +
287B ARG* 2.8 57.2 + - - +
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Residues in contact with LYS 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B VAL* 4.0 12.3 - - - +
36B ASN* 4.6 9.2 + - - +
279B GLU* 2.9 45.6 + - + +
280B ASP* 3.0 14.4 + - - +
282B ASP* 1.3 75.9 - - - +
284B THR* 1.3 61.7 + - - +
287B ARG* 3.3 56.1 - - + +
288B TYR* 4.4 1.4 - - - +
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Residues in contact with THR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B THR* 3.9 28.9 - - + +
35B VAL* 3.9 11.0 + - - +
36B ASN* 3.8 17.3 + - - +
70B ASP* 4.9 2.2 - - - +
280B ASP* 2.9 17.5 + - - +
281B LEU* 3.6 6.5 - - - +
283B LYS* 1.3 78.4 - - - +
285B TRP* 1.3 89.2 + - + +
286B VAL 3.9 0.2 - - - -
288B TYR* 3.5 15.2 - - - -
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Residues in contact with TRP 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PRO* 3.3 24.2 - - - +
19B TYR* 3.8 32.1 - + - -
34B THR* 4.8 7.0 - - + -
40B VAL* 4.0 23.3 - - + -
65B TYR* 3.6 28.0 - + + -
66B GLY* 3.5 19.6 - - - -
67B PHE* 3.6 32.1 - - + -
70B ASP* 2.9 33.3 + - - -
231B PHE* 3.6 11.1 - - - -
281B LEU* 2.8 32.7 + - + +
284B THR* 1.3 94.9 - - + +
286B VAL* 1.3 61.5 + - + +
288B TYR* 3.6 10.3 + - - -
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PRO* 4.2 11.0 - - + -
17B PHE* 5.1 8.3 - - + -
67B PHE* 3.9 22.2 - - + -
143B LYS* 5.3 7.0 - - - -
227B ALA* 4.3 19.7 - - + +
230B GLU* 6.5 1.1 - - + -
231B PHE* 3.7 24.1 - - + +
234B SER* 4.6 6.2 + - - -
282B ASP* 3.0 39.7 + - - +
285B TRP* 1.3 81.7 - - + +
287B ARG* 1.3 58.2 + - + +
288B TYR* 3.7 5.2 + - - +
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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
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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