Contacts of the helix formed by residues 272 - 282 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118E CYS* 3.1 38.4 + - + +
119E ILE* 4.1 0.2 - - - +
120E ASN* 3.0 23.3 + - - +
125E ARG* 2.8 45.8 + - - -
168E LEU* 3.9 1.7 - - - +
270E GLU 3.6 2.2 + - - -
271E TYR* 1.3 70.1 - - - +
273E LYS* 1.3 55.8 + - - +
274E ASP* 3.3 5.5 + - - +
275E TRP* 2.9 26.4 + - + +
276E VAL* 2.7 36.4 + - - +
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Residues in contact with LYS 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E ASN* 4.4 13.7 - - - +
270E GLU* 4.6 10.1 + - - -
271E TYR 3.5 1.4 + - - -
272E ASP* 1.3 73.6 + - - +
274E ASP* 1.3 59.4 + - - +
276E VAL* 3.1 7.1 + - - +
277E CYS* 2.9 32.5 + - - -
315E ILE* 3.4 37.2 - - + +
324E LEU* 3.9 32.6 - - + +
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Residues in contact with ASP 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E ARG* 4.0 13.2 + - - +
167E ASN* 5.2 2.7 - - - +
168E LEU* 3.8 19.5 - - + +
171E SER* 4.2 24.6 + - - -
272E ASP* 3.3 9.3 + - - +
273E LYS* 1.3 75.2 - - - +
275E TRP* 1.3 67.6 + - - +
277E CYS* 3.1 3.3 + - - +
278E ASN* 3.0 26.5 + - - +
306E ARG* 2.8 36.7 + - - +
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Residues in contact with TRP 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E ASN* 5.3 4.5 + - - -
116E CYS* 3.2 34.8 - - - -
117E SER* 3.5 23.7 - - - -
118E CYS* 3.7 18.6 - - + +
164E MET* 3.7 43.3 - - + -
165E LEU* 3.9 12.3 - - + -
168E LEU* 3.6 21.4 - - + +
271E TYR* 5.7 7.6 - + + -
272E ASP* 2.9 29.5 + - + +
274E ASP* 1.3 76.4 - - - +
276E VAL* 1.3 70.8 + - + +
278E ASN* 3.1 8.6 + - + +
279E LEU* 2.9 51.6 + - + +
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Residues in contact with VAL 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E TYR* 3.7 25.8 - - + +
272E ASP 2.7 30.7 + - - +
273E LYS* 3.1 12.1 + - - +
275E TRP* 1.3 77.2 - - + +
277E CYS* 1.3 63.8 + - - +
279E LEU* 3.1 9.3 + - - +
280E ILE* 3.1 21.5 + - - +
314E ILE* 3.9 17.7 - - + -
315E ILE* 4.2 7.6 - - + -
318E TRP* 3.5 48.5 - - + +
324E LEU* 5.0 2.2 - - + -
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Residues in contact with CYS 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273E LYS 2.9 19.8 + - - -
274E ASP* 3.1 2.6 + - - +
276E VAL* 1.3 75.0 - - - +
278E ASN* 1.3 59.1 + - - +
280E ILE* 3.3 1.9 + - - +
281E MET* 2.9 36.4 + - - +
306E ARG* 3.6 28.5 - - - +
311E ASP* 3.6 44.6 - - - +
314E ILE* 4.2 14.8 - - + -
315E ILE* 4.0 12.1 - - - -
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Residues in contact with ASN 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E MET* 2.9 30.8 + - + +
167E ASN* 3.1 30.7 + - - +
168E LEU* 4.1 10.7 - - - +
274E ASP 3.0 12.1 + - - -
275E TRP* 3.4 15.8 - - + +
277E CYS* 1.3 75.8 - - - +
279E LEU* 1.3 63.6 + - - +
282E THR* 3.0 32.4 + - + +
303E LEU* 3.6 17.3 - - + +
306E ARG* 2.9 27.7 + - - -
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Residues in contact with LEU 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E ASN* 3.4 31.4 - - + +
164E MET* 4.8 11.4 - - + -
275E TRP* 2.9 45.3 + - + +
276E VAL* 3.1 9.8 + - - +
278E ASN* 1.3 79.2 - - - +
280E ILE* 1.3 62.6 + - + +
282E THR* 3.4 14.1 + - - +
283E TRP* 3.7 5.0 + - - -
286E PHE* 5.9 1.5 - - + -
318E TRP* 4.0 31.0 - - + -
340E ARG* 5.6 1.1 - - - +
344E ILE* 4.0 27.1 - - + +
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Residues in contact with ILE 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276E VAL* 3.1 16.6 + - + +
277E CYS 3.8 4.9 - - - +
279E LEU* 1.3 75.7 - - - +
281E MET* 1.3 60.4 + - - +
283E TRP* 2.9 27.0 + - - +
314E ILE* 3.5 33.9 - - + -
318E TRP* 4.3 10.1 - - + -
344E ILE* 3.8 39.0 - - + +
347E ILE* 4.0 24.5 - - + -
348E TYR* 3.4 34.1 - - + +
351E LEU* 4.1 5.2 - - + -
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Residues in contact with MET 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277E CYS 2.9 20.9 + - - +
278E ASN 4.2 2.5 - - - +
280E ILE* 1.3 77.7 - - - +
282E THR* 1.3 60.7 + - - +
283E TRP 3.2 0.2 - - - -
284E PRO* 3.4 12.6 - - - +
302E LEU* 4.0 23.5 - - - +
303E LEU* 4.2 10.3 - - + -
305E LYS* 3.5 44.4 - - + +
306E ARG* 3.7 18.6 - - + +
310E LEU* 4.9 10.1 - - + -
314E ILE* 3.8 23.6 - - + -
348E TYR* 4.2 14.3 - - + -
351E LEU* 3.9 18.8 - - - -
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Residues in contact with THR 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E MET* 3.5 31.8 - - - +
278E ASN 3.0 19.7 + - - +
279E LEU* 3.4 7.8 + - - +
280E ILE 3.2 0.2 - - - -
281E MET* 1.3 74.9 - - - +
283E TRP* 1.3 65.9 + - - +
284E PRO* 3.1 4.3 - - - -
285E ALA* 2.8 19.3 + - - +
286E PHE* 3.5 18.4 - - - -
299E ILE* 4.2 9.6 - - + -
302E LEU* 3.9 15.3 - - + -
303E LEU* 3.5 25.8 - - + -
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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