Contacts of the helix formed by residues 272 - 282 (chain B) in PDB entry 4PEI
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 272 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B CYS* 3.1 43.6 + - + +
120B ASN* 2.8 29.8 + - - +
125B ARG* 2.8 39.5 + - - -
168B LEU* 4.1 0.5 - - - +
270B GLU 3.8 1.4 + - - -
271B TYR* 1.3 72.3 - - - +
273B LYS* 1.3 66.4 + - - +
274B ASP* 3.4 5.0 + - - +
275B TRP* 3.1 23.1 + - + +
276B VAL* 3.0 21.8 + - - +
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Residues in contact with LYS 273 (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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120B ASN* 4.5 14.1 - - - +
270B GLU* 4.5 11.1 + - - -
271B TYR 3.6 3.4 + - - +
272B ASP* 1.3 73.7 + - - +
274B ASP* 1.3 65.1 + - - +
276B VAL* 3.0 6.5 + - - +
277B CYS* 2.9 28.1 + - - -
315B ILE* 3.9 37.0 - - + -
324B LEU* 4.0 32.8 - - + +
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Residues in contact with ASP 274 (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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125B ARG* 3.8 9.7 + - - +
167B ASN* 5.5 1.8 - - - +
168B LEU* 3.8 19.2 - - + +
171B SER* 2.6 35.0 + - - -
272B ASP* 3.4 11.5 + - - +
273B LYS* 1.3 80.4 - - - +
275B TRP* 1.3 62.9 + - - +
277B CYS* 3.3 4.7 + - - +
278B ASN* 3.0 25.3 + - - +
306B ARG* 3.0 29.3 + - - +
311B ASP* 4.9 0.3 - - - +
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Residues in contact with TRP 275 (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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102B ASN* 5.4 3.1 + - - -
116B CYS* 3.3 35.4 - - - -
117B SER* 3.3 21.2 - - - -
118B CYS* 3.7 28.5 - - + +
164B MET* 3.7 46.7 - - + -
165B LEU* 4.0 10.8 - - + -
168B LEU* 4.1 14.6 - - + -
271B TYR* 5.6 7.2 - + + -
272B ASP* 3.1 21.4 + - - +
273B LYS 3.1 1.0 - - - -
274B ASP* 1.3 76.8 - - - +
276B VAL* 1.3 68.2 + - + +
278B ASN* 3.1 9.7 + - + +
279B LEU* 2.8 56.6 + - + +
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Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B TYR* 3.7 17.5 - - + -
272B ASP 3.0 16.1 + - - +
273B LYS* 3.5 9.4 - - - +
275B TRP* 1.3 81.2 - - + +
277B CYS* 1.3 64.3 + - - +
279B LEU* 3.1 7.8 + - - +
280B ILE* 2.9 25.4 + - - +
314B ILE* 3.7 19.5 - - + -
315B ILE* 3.9 11.0 - - + -
318B TRP* 3.7 56.1 - - + +
324B LEU* 5.1 2.7 - - + -
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Residues in contact with CYS 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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273B LYS* 2.9 17.5 + - - -
274B ASP* 3.5 7.9 - - - +
276B VAL* 1.3 77.2 - - - +
278B ASN* 1.3 57.5 + - - +
280B ILE* 3.3 1.2 + - - +
281B MET* 2.8 36.1 + - - +
306B ARG* 3.6 23.6 - - - +
311B ASP* 3.5 37.5 - - - +
314B ILE* 4.0 13.2 - - + -
315B ILE* 3.5 22.0 - - - -
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Residues in contact with ASN 278 (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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164B MET* 2.9 30.0 + - + +
167B ASN* 2.9 30.0 + - - +
168B LEU* 3.9 11.7 - - - +
274B ASP 3.0 10.6 + - - -
275B TRP* 3.1 19.3 + - + +
277B CYS* 1.3 75.8 - - - +
279B LEU* 1.3 55.1 + - - +
281B MET 3.4 0.2 + - - -
282B THR* 2.7 38.7 + - - +
303B LEU* 3.6 16.4 - - + +
306B ARG* 2.9 27.9 + - - -
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Residues in contact with LEU 279 (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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101B TYR* 5.9 0.4 - - + -
102B ASN* 3.2 32.1 - - + +
164B MET* 4.9 9.6 - - + -
275B TRP* 2.8 44.2 + - + +
276B VAL* 3.1 7.6 + - - +
278B ASN* 1.3 77.9 - - - +
280B ILE* 1.3 62.3 + - + +
282B THR* 3.2 15.4 + - - +
283B TRP* 3.6 6.2 + - - -
286B PHE* 5.7 4.6 - - + -
318B TRP* 3.9 27.6 - - + -
340B ARG* 5.3 1.3 - - - +
344B ILE* 3.8 34.5 - - + +
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Residues in contact with ILE 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 VAL* 2.9 23.9 + - + +
277B CYS 4.0 1.8 - - - +
279B LEU* 1.3 76.3 - - + +
281B MET* 1.3 66.6 + - - +
282B THR 3.0 3.7 + - - -
283B TRP* 3.1 12.5 + - - +
314B ILE* 3.8 14.8 - - + -
318B TRP* 3.7 34.5 - - + -
344B ILE* 3.9 31.9 - - + +
347B ILE* 3.9 17.0 - - + -
348B TYR* 3.1 25.6 - - - +
351B LEU* 3.8 29.2 - - + -
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Residues in contact with MET 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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277B CYS 2.8 24.9 + - - +
278B ASN 4.2 2.5 - - - +
280B ILE* 1.3 72.3 - - - +
282B THR* 1.3 60.2 + - - +
283B TRP 3.4 0.2 - - - -
284B PRO* 3.6 10.0 - - - +
302B LEU* 3.7 22.2 - - - +
303B LEU* 4.2 12.6 - - + -
305B LYS* 3.3 45.1 - - + +
306B ARG* 3.7 17.5 - - + +
310B LEU* 4.6 10.5 - - + -
314B ILE* 3.7 26.2 - - + -
348B TYR* 4.2 6.9 - - - -
351B LEU* 3.9 16.6 - - - -
353B ILE* 4.4 18.4 - - + -
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Residues in contact with THR 282 (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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164B MET* 3.5 18.1 - - - +
278B ASN 2.7 21.4 + - - +
279B LEU 3.2 8.0 + - - -
280B ILE 3.0 0.2 - - - -
281B MET* 1.3 77.5 - - - +
283B TRP* 1.3 65.7 + - - +
284B PRO* 3.0 4.9 - - - -
285B ALA* 2.9 15.1 + - - +
286B PHE* 3.4 23.8 - - - -
299B ILE* 4.0 22.7 - - + -
302B LEU* 4.2 11.2 - - + -
303B LEU* 3.4 27.6 - - + -
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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