Contacts of the helix formed by residues 324 - 332 (chain B) in PDB entry 4FE1
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 324 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B MET* 5.1 0.2 - - - +
305B ASP* 3.6 11.7 + - - -
322B HIS 3.2 0.8 + - - -
323B GLN* 1.3 72.3 - - - +
325B ILE* 1.3 57.5 + - - +
326B TYR 3.2 3.7 - - - +
327B GLU* 3.1 21.0 + - - +
328B THR* 2.9 33.6 + - - -
405B GLN 3.8 16.0 - - - +
406B ASN* 4.2 2.5 - - - -
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Residues in contact with ILE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B MET* 3.7 24.5 - - + -
322B HIS* 3.0 21.2 + - + +
324B GLY* 1.3 76.8 - - - +
326B TYR* 1.3 57.2 + - - +
328B THR* 3.7 7.2 - - + -
329B TYR* 2.9 35.2 + - + +
335B PHE* 6.0 6.9 - - + -
406B ASN* 4.4 3.1 - - - +
409B ASN* 3.1 44.2 - - + +
410B VAL* 3.8 23.8 - - + -
411B LEU* 4.5 9.2 - - + +
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Residues in contact with TYR 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LYS 4.5 2.8 + - - -
170B ALA* 4.1 15.2 + - + +
171B GLU* 2.6 31.0 + - - -
300B ILE* 3.4 34.5 - - + -
301B LYS* 3.8 25.4 - - + -
304B MET* 3.8 22.7 - - + +
305B ASP* 5.0 0.4 - - - +
324B GLY 3.2 0.4 - - - -
325B ILE* 1.3 80.9 - - - +
327B GLU* 1.3 83.3 + - + +
329B TYR* 4.0 3.1 - - - +
330B ASN* 2.9 47.9 + - + +
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Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LYS* 3.7 18.1 - - - +
305B ASP* 4.3 6.0 - - - +
324B GLY* 3.3 27.2 + - - +
326B TYR* 1.3 98.5 - - + +
328B THR* 1.3 66.9 + - - +
330B ASN* 4.8 1.6 - - - -
331B ASN* 2.8 45.0 + - - +
405B GLN* 5.7 12.1 - - + +
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Residues in contact with THR 328 (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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324B GLY 2.9 11.9 + - - -
325B ILE* 3.7 7.4 - - + -
327B GLU* 1.3 78.6 - - - +
329B TYR* 1.3 60.6 + - - +
331B ASN* 4.1 2.0 - - - +
332B SER* 3.3 23.7 + - - -
335B PHE* 4.5 6.5 - - + +
396B PHE* 3.4 32.8 - - + -
400B ASP 6.0 0.2 - - - +
401B TYR* 5.0 0.7 - - + -
402B ASP 6.0 0.2 - - - +
405B GLN* 4.5 1.0 + - - +
406B ASN* 2.4 37.7 + - - +
411B LEU* 3.7 16.2 - - + -
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Residues in contact with TYR 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ALA* 6.6 0.2 - - + -
173B ARG* 5.7 4.3 - - - -
325B ILE* 2.9 21.8 + - + +
326B TYR* 4.0 3.8 - - - +
328B THR* 1.3 74.3 - - - +
330B ASN* 1.3 69.7 + - + +
331B ASN 3.3 0.9 + - - -
332B SER 3.4 6.8 + - - +
335B PHE* 3.4 39.5 - + + -
336B GLN* 2.9 46.9 + - + +
339B TRP* 4.2 24.9 - + + -
340B HIS* 2.7 33.4 + + - -
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Residues in contact with ASN 330 (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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42B TYR* 4.2 6.6 + - - -
167B PHE 5.1 1.0 - - - +
168B LYS* 2.6 56.4 + - - +
170B ALA* 3.8 18.9 - - + +
173B ARG* 5.5 4.2 + - - -
326B TYR* 2.9 37.5 + - + +
327B GLU* 4.2 1.3 - - - +
329B TYR* 1.3 83.7 - - + +
331B ASN* 1.3 63.7 + - - +
336B GLN* 3.0 21.3 + - - +
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Residues in contact with ASN 331 (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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38B GLU* 5.4 1.2 - - - +
42B TYR* 4.5 6.4 + - - -
168B LYS* 3.6 32.4 - - - +
327B GLU* 2.8 39.0 + - - +
328B THR* 4.5 2.2 - - - +
330B ASN* 1.3 82.5 - - - +
332B SER* 1.3 58.8 + - - +
333B LEU* 4.0 1.6 + - - +
336B GLN* 4.7 0.2 - - - -
400B ASP* 5.0 2.9 - - - +
405B GLN* 5.6 2.1 - - - +
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Residues in contact with SER 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B THR 3.3 19.0 + - - -
329B TYR 3.4 1.5 + - - +
331B ASN* 1.3 79.0 - - - +
333B LEU* 1.3 59.9 + - - +
334B HIS* 3.9 0.5 - - - -
335B PHE* 3.1 11.3 + - - -
336B GLN* 3.1 28.7 + - - +
396B PHE* 3.0 30.3 - - - -
400B ASP* 2.9 28.3 + - - -
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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