Contacts of the helix formed by residues 283 - 287 (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 TRP 283 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101E TYR* 5.6 0.2 - - - -
279E LEU 3.7 4.7 + - - -
280E ILE 2.9 16.7 + - - +
282E THR* 1.3 77.3 + - - +
284E PRO* 1.3 71.2 - - + +
286E PHE* 2.8 27.0 + - + +
287E SER* 3.1 34.1 + - - -
341E ARG* 3.4 57.0 - - + -
344E ILE* 3.7 26.0 - - + -
345E GLU* 3.4 51.5 + - + +
348E TYR* 3.7 31.4 - + + -
349E ASN* 4.8 3.1 + - - -
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Residues in contact with PRO 284 (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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281E MET 3.4 12.1 - - - +
282E THR 3.1 5.8 - - - -
283E TRP* 1.3 98.3 - - + +
285E ALA* 1.3 59.8 + - - +
287E SER* 3.0 22.4 + - - +
294E ASP* 5.2 0.5 - - - +
297E TYR* 3.5 40.5 - - + +
302E LEU* 4.2 12.1 - - + -
348E TYR* 3.4 34.8 - - + +
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Residues in contact with ALA 285 (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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282E THR 2.8 12.9 + - - +
284E PRO* 1.3 80.7 - - - +
286E PHE* 1.3 65.1 + - + +
287E SER 3.5 0.6 + - - -
288E ASN 5.3 0.5 + - - -
291E GLN 5.2 0.3 - - - +
292E PHE* 4.3 0.7 - - - +
293E PRO* 3.3 4.1 - - + +
294E ASP* 2.5 45.6 + - - +
297E TYR* 3.9 12.6 - - + -
299E ILE* 4.0 17.0 - - + -
302E LEU* 3.7 16.2 - - + +
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Residues in contact with PHE 286 (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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101E TYR* 4.1 18.4 - + - +
160E TYR* 3.6 39.7 - + - -
164E MET* 3.8 18.8 - - + -
279E LEU* 5.9 1.1 - - + -
282E THR* 3.5 35.0 - - - -
283E TRP* 2.8 16.8 + - + +
285E ALA* 1.3 82.6 - - + +
287E SER* 1.3 59.0 + - - +
288E ASN 3.3 6.6 + - - +
292E PHE* 3.7 29.6 - + + +
293E PRO* 3.8 20.0 - - + -
299E ILE* 4.5 2.2 - - + -
341E ARG* 2.7 40.1 + - - +
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Residues in contact with SER 287 (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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283E TRP* 3.1 39.3 + - - -
284E PRO* 3.0 19.8 + - - +
285E ALA 3.5 0.8 - - - -
286E PHE* 1.3 79.1 - - - +
288E ASN* 1.3 58.7 + - - +
289E LYS* 3.5 1.7 + - - +
297E TYR* 4.9 3.1 + - - -
341E ARG* 3.5 7.3 + - - -
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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