Contacts of the helix formed by residues 324 - 338 (chain B) in PDB entry 4F5D
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 SER 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B ASP* 3.5 6.3 + - - -
218B ASN* 4.9 4.5 + - - -
322B SER 4.0 2.9 + - - -
323B PHE* 1.3 76.3 - - - +
325B LEU* 1.3 64.4 + - - +
326B SER* 3.0 21.5 + - - -
327B GLN* 3.0 30.9 + - - +
328B GLU* 3.0 14.9 + - - +
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Residues in contact with LEU 325 (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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201B LEU* 4.0 23.8 - - + -
212B LEU* 4.3 0.7 - - + -
215B ALA* 4.1 15.9 - - + +
216B ASP* 3.4 15.6 + - + +
219B ILE* 4.0 15.7 - - + -
261B TYR* 3.6 24.2 - - - +
314B TYR* 3.7 33.7 - - + +
323B PHE* 3.6 24.4 + - + -
324B SER* 1.3 72.1 - - - +
326B SER* 1.3 63.9 + - - +
328B GLU* 3.1 7.8 + - + +
329B VAL* 3.0 30.4 + - + +
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Residues in contact with SER 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ASP* 3.0 17.2 + - - -
218B ASN* 3.7 28.6 + - - +
219B ILE* 4.1 15.7 - - - +
247B LEU* 4.1 9.2 - - - +
248B LEU 4.2 8.0 + - - -
324B SER* 3.0 16.8 + - - -
325B LEU* 1.3 76.8 - - - +
327B GLN* 1.3 61.5 + - - +
329B VAL* 3.3 5.4 + - - +
330B LEU* 2.8 35.3 + - - +
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Residues in contact with GLN 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU 5.5 1.0 - - - +
249B GLU* 2.7 34.3 + - - +
324B SER* 3.0 30.0 + - - +
326B SER* 1.3 82.5 + - - +
328B GLU* 1.3 66.0 + - - +
330B LEU* 3.3 9.2 + - - +
331B ARG* 3.0 31.5 + - + +
334B ARG* 4.3 13.0 + - - +
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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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312B ILE* 4.5 9.1 - - + +
313B ALA 4.7 3.5 - - - +
314B TYR* 4.4 13.7 - - + +
323B PHE* 3.3 38.5 - - + -
324B SER 3.0 8.9 + - - +
325B LEU* 3.4 13.7 - - + +
327B GLN* 1.3 78.9 - - - +
329B VAL* 1.3 60.6 + - + +
331B ARG* 2.7 41.4 + - - +
332B HIS* 2.8 40.2 + - - -
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Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TYR* 5.1 1.3 - - + -
201B LEU* 3.7 27.4 - - + -
219B ILE* 4.7 1.8 - - + -
247B LEU* 3.4 23.6 - - + -
257B CYS* 4.5 9.4 - - - -
259B LEU* 4.1 24.7 - - + -
312B ILE* 4.3 17.7 - - + -
325B LEU* 3.0 24.3 + - + +
326B SER* 3.7 3.6 - - - +
328B GLU* 1.3 73.9 - - + +
330B LEU* 1.3 65.2 + - - +
332B HIS* 3.4 5.5 + - - +
333B LEU* 3.3 22.4 + - + +
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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
----------------------------------------------------------
247B LEU* 3.8 26.7 - - + -
248B LEU 4.7 4.7 - - - +
249B GLU* 4.1 15.9 - - + +
254B ALA* 3.6 40.4 - - + +
255B GLY 4.2 0.9 - - - +
326B SER 2.8 20.3 + - - +
327B GLN* 3.7 13.0 - - - +
329B VAL* 1.3 74.5 - - - +
331B ARG* 1.3 66.3 + - - +
333B LEU* 3.1 11.1 + - + +
334B ARG* 2.9 62.4 + - + +
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Residues in contact with ARG 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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327B GLN* 3.0 17.5 + - + +
328B GLU* 2.7 47.8 + - - +
329B VAL 3.3 0.2 - - - -
330B LEU* 1.3 75.8 - - - +
332B HIS* 1.3 76.3 + - - +
334B ARG* 3.8 13.0 - - - +
335B GLN* 2.8 44.1 + - - +
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Residues in contact with HIS 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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199B TYR* 4.4 8.7 - - + -
310B ARG* 4.1 17.3 - - + -
311B LEU 4.2 6.6 + - - -
312B ILE* 3.8 35.3 - - + +
313B ALA 5.5 1.3 + - - -
328B GLU* 2.8 41.3 + - - -
329B VAL 3.8 6.5 - - - +
330B LEU 3.3 0.8 - - - -
331B ARG* 1.3 95.1 + - - +
333B LEU* 1.3 63.3 + - - +
335B GLN* 3.8 13.8 - - - +
336B GLU* 3.0 41.7 + - - +
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Residues in contact with LEU 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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195B SER* 3.9 16.6 - - - +
199B TYR* 3.0 49.8 - - + +
247B LEU* 4.0 23.3 - - + -
255B GLY* 4.3 20.2 - - - -
256B THR 4.5 0.2 - - - +
257B CYS* 4.1 15.0 - - + -
329B VAL* 3.3 13.9 + - + +
330B LEU* 3.1 12.0 + - + +
332B HIS* 1.3 78.3 - - - +
334B ARG* 1.3 58.8 + - + +
336B GLU* 3.3 3.3 + - - +
337B GLU* 2.8 30.9 + - + +
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Residues in contact with ARG 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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249B GLU* 2.6 43.4 + - - -
254B ALA* 4.6 3.4 + - - +
327B GLN* 4.3 6.9 + - - +
330B LEU* 2.9 56.8 + - + +
331B ARG* 3.8 11.7 - - - +
333B LEU* 1.3 69.6 - - + +
335B GLN* 1.3 60.5 + - - +
337B GLU* 2.7 39.7 + - - +
338B LYS* 2.9 13.7 + - - +
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Residues in contact with GLN 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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331B ARG* 2.8 32.5 + - - +
332B HIS* 3.8 15.7 - - - +
334B ARG* 1.3 74.8 - - - +
336B GLU* 1.3 62.5 + - + +
338B LYS* 2.8 51.3 - - - +
339B GLU* 3.4 2.1 + - - +
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Residues in contact with GLU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ARG* 2.8 43.8 + - - +
199B TYR* 3.1 34.4 + - - +
310B ARG* 3.8 20.6 - - - +
332B HIS* 3.0 28.9 + - - +
333B LEU* 3.6 4.0 - - - +
335B GLN* 1.3 75.1 - - + +
337B GLU* 1.3 59.8 + - - +
338B LYS 2.9 1.1 - - - -
339B GLU* 2.7 43.5 + - + +
340B GLU* 2.9 4.5 + - - +
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Residues in contact with GLU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 2.8 13.4 + - - +
334B ARG* 2.7 30.2 + - - +
336B GLU* 1.3 76.0 - - - +
338B LYS* 1.3 54.9 + - - +
340B GLU* 2.4 37.1 + - - +
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Residues in contact with LYS 338 (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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334B ARG 2.9 12.2 + - - +
335B GLN* 2.8 46.6 - - - +
337B GLU* 1.3 78.6 - - - +
339B GLU* 1.3 53.4 + - - +
340B GLU* 2.5 27.4 - - - +
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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