Contacts of the helix formed by residues 250 - 255 (chain E) in PDB entry 3FZ7
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 LEU 250 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E TYR* 3.7 2.9 - - - +
246E SER 3.5 17.3 - - - +
247E GLY* 2.9 6.8 + - - +
248E GLY 3.6 0.2 - - - -
249E PHE* 1.3 79.2 - - - +
251E ALA* 1.3 68.0 + - - +
252E PRO* 3.3 1.3 - - - +
253E PHE* 3.0 17.7 + - - +
254E VAL* 3.1 17.0 + - - +
277E PHE* 3.6 32.5 - - + -
343E GLN* 3.7 25.6 - - + +
347E TYR* 3.6 15.3 - - + +
375E ILE* 3.5 40.8 - - + -
376E PRO* 3.6 19.7 - - + -
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Residues in contact with ALA 251 (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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209E PHE* 3.5 37.5 - - + -
217E TYR* 3.5 10.8 + - + +
247E GLY 3.2 1.4 + - - -
250E LEU* 1.3 79.7 - - - +
252E PRO* 1.4 65.1 - - + +
254E VAL* 4.5 1.1 - - - -
255E ALA* 2.7 52.1 + - + +
258E ILE* 4.8 1.6 - - + -
260E TRP* 3.9 9.0 - - + +
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Residues in contact with PRO 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E LEU* 3.9 38.8 - - + +
108E TRP* 4.3 2.5 - - + -
109E HIS* 6.4 0.4 - - + -
247E GLY 3.7 3.8 - - - +
248E GLY 3.3 26.7 - - - +
249E PHE* 4.3 1.3 - - - -
250E LEU 3.4 6.7 - - - +
251E ALA* 1.4 92.3 - - + +
253E PHE* 1.3 60.7 + - + +
256E PRO* 4.0 19.8 - - + +
260E TRP* 4.0 18.8 - - + +
261E ASP* 5.9 0.4 - - - +
263E ARG* 6.3 1.1 - - - +
336E ARG* 4.4 11.1 + - - +
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Residues in contact with PHE 253 (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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32D PHE* 4.0 13.5 - + - -
107E LEU* 3.6 38.1 - - + -
249E PHE* 3.2 43.5 - + + -
250E LEU 3.0 3.4 + - - +
252E PRO* 1.3 83.5 - - + +
254E VAL* 1.3 63.3 + - + +
255E ALA 3.6 0.7 - - - -
256E PRO* 4.4 7.4 - - - +
336E ARG* 4.0 27.1 - - + -
339E TYR* 3.5 46.0 - + + +
340E THR* 3.3 37.2 + - - +
343E GLN* 4.5 2.7 - - + -
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Residues in contact with VAL 254 (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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250E LEU 3.1 16.4 + - - +
251E ALA* 4.5 0.7 - - - +
253E PHE* 1.3 80.0 - - + +
255E ALA* 1.3 65.5 + - + +
256E PRO* 3.6 5.5 - - - +
340E THR* 4.1 6.1 - - + +
343E GLN* 4.0 23.6 - - + -
344E ASN* 3.1 35.9 - - - +
347E TYR* 3.6 27.6 - - + +
371E PRO* 3.7 21.5 - - + +
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Residues in contact with ALA 255 (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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251E ALA* 2.7 27.2 + - - +
254E VAL* 1.3 76.7 - - + +
256E PRO* 1.3 61.9 - - - +
257E ASP* 2.8 13.8 + - - -
258E ILE* 3.1 40.8 + - + +
260E TRP* 5.6 0.3 + - - -
371E PRO 3.9 16.6 - - - +
372E ASP* 4.8 2.7 - - + -
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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