Contacts of the helix formed by residues 327 - 335 (chain B) in PDB entry 4HY4
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 CYS 327 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300B CYS* 3.9 1.6 - - - -
302B CYS* 4.0 3.6 - - - -
303B CYS* 3.7 19.9 - - + +
320B HIS* 3.5 4.5 - - - +
324B PHE 3.1 17.7 + - - +
325B PRO 3.3 0.8 - - - -
326B ARG* 1.3 75.5 - - - +
328B GLU* 1.3 61.9 + - - +
329B PHE* 3.5 19.7 - - - -
330B LEU* 3.4 13.9 + - + +
331B ILE* 3.0 29.7 + - - +
401B ZN 2.3 36.6 - - - -
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Residues in contact with GLU 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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254B SER* 5.9 5.2 - - - +
302B CYS* 4.1 14.3 - - - -
326B ARG 3.2 5.7 + - - +
327B CYS* 1.3 72.0 - - - +
329B PHE* 1.3 60.0 + - - +
331B ILE* 3.4 21.6 + - - +
332B ARG* 3.0 44.3 + - + +
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Residues in contact with PHE 329 (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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261B GLN 5.6 1.3 - - - -
266B ARG* 4.1 14.4 - - - -
286B SER 4.0 6.5 - - - -
287B ALA 4.2 2.5 - - - -
288B GLY* 3.5 27.1 - - - -
300B CYS* 4.9 0.4 - - - -
301B PHE* 3.6 31.0 - + + -
302B CYS* 3.7 26.1 - - + -
317B TRP* 3.6 22.7 - + - -
320B HIS* 4.6 4.0 - + - -
327B CYS* 3.4 4.7 - - - -
328B GLU* 1.3 73.8 - - - +
330B LEU* 1.3 62.0 + - - +
332B ARG* 3.3 4.2 + - + +
333B MET* 2.9 66.4 + - + +
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Residues in contact with LEU 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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317B TRP* 3.6 45.1 - - + +
320B HIS* 3.8 11.9 - - + +
321B ALA* 3.6 27.6 - - + -
324B PHE 3.5 23.3 - - - +
325B PRO* 3.9 8.3 - - + +
327B CYS* 3.4 18.1 + - + +
329B PHE* 1.3 80.5 - - - +
331B ILE* 1.3 58.2 + - - +
334B LYS* 2.9 43.2 + - + +
335B GLY 3.7 0.3 + - - -
338B PHE* 4.3 1.1 - - + -
339B VAL* 3.7 19.0 - - + +
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Residues in contact with ILE 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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325B PRO 3.9 16.8 - - - +
326B ARG* 3.9 20.9 - - - +
327B CYS 3.0 18.6 + - - +
328B GLU* 3.8 20.4 - - - +
329B PHE 3.3 0.2 - - - -
330B LEU* 1.3 75.7 - - - +
332B ARG* 1.3 63.5 + - + +
335B GLY* 2.8 34.7 + - - +
336B GLN* 3.8 35.9 - - + +
339B VAL* 4.5 7.2 - - + -
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Residues in contact with ARG 332 (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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328B GLU* 3.0 31.2 + - - +
329B PHE* 4.0 4.3 - - + +
331B ILE* 1.3 83.8 - - + +
333B MET* 1.3 86.5 + - + +
335B GLY* 4.7 0.5 + - - -
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Residues in contact with MET 333 (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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317B TRP* 3.6 22.7 - - + -
329B PHE* 2.9 56.0 + - + +
332B ARG* 1.3 109.8 - - + +
334B LYS* 1.3 64.7 + - - +
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Residues in contact with LYS 334 (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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317B TRP* 3.5 56.0 - - + +
330B LEU* 2.9 11.6 + - + +
333B MET* 1.3 81.7 - - - +
335B GLY* 1.3 63.5 + - - +
338B PHE* 3.4 62.6 + - + +
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Residues in contact with GLY 335 (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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330B LEU 3.7 0.8 + - - -
331B ILE* 2.8 21.2 + - - -
332B ARG 4.5 1.2 + - - -
333B MET 3.8 0.6 - - - -
334B LYS* 1.3 78.5 - - - +
336B GLN* 1.3 66.3 + - - -
337B GLU* 3.2 3.8 - - - -
338B PHE* 3.2 4.2 + - - +
339B VAL* 3.2 23.5 + - - +
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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