Contacts of the helix formed by residues 314 - 328 (chain B) in PDB entry 5FFG
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 THR 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ASP* 5.7 0.9 - - - +
253B SER 3.5 3.8 + - - +
254B ASP* 3.5 31.6 + - + +
313B VAL* 1.3 79.4 - - - +
315B GLN* 1.3 68.4 + - - +
316B GLU* 3.3 2.0 + - - +
317B GLN* 2.9 36.6 + - - +
318B VAL* 3.1 7.6 + - - +
335B LEU* 3.8 1.1 - - - -
336B LEU* 3.3 24.2 - - + +
337B GLN 4.1 15.3 - - - +
338B LYS* 4.6 8.7 - - - +
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Residues in contact with GLN 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B THR* 1.3 75.7 - - - +
316B GLU* 1.3 65.9 + - + +
317B GLN 3.1 1.2 + - - -
318B VAL* 3.2 15.8 + - + +
319B HIS* 4.6 4.9 + - - -
335B LEU* 3.4 31.1 - - + +
336B LEU 4.2 0.6 + - - -
2004B PEG 3.2 53.0 + - - +
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Residues in contact with GLU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ARG* 3.0 24.5 + - - +
314B THR* 3.3 2.1 + - - +
315B GLN* 1.3 79.4 - - + +
317B GLN* 1.3 76.6 + - - +
318B VAL 3.6 0.2 - - - -
319B HIS* 5.2 1.8 + - - +
320B LEU* 5.1 1.6 + - - +
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Residues in contact with GLN 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ARG* 3.8 6.7 - - - +
254B ASP 3.1 16.4 + - - +
255B ALA* 3.4 23.5 - - - +
256B ASP* 2.9 31.9 + - - +
313B VAL* 3.7 11.0 - - + -
314B THR* 2.9 32.9 + - - +
316B GLU* 1.3 106.0 + - - +
318B VAL* 1.3 63.8 + - - +
319B HIS 3.5 2.0 - - - -
320B LEU* 3.5 2.9 + - - -
321B TYR* 3.0 39.3 + - + +
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Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B VAL* 3.5 22.4 - - + +
314B THR 3.1 15.4 + - - +
315B GLN* 3.2 10.7 + - + +
317B GLN* 1.3 77.7 - - - +
319B HIS* 1.3 65.8 + - + +
321B TYR* 3.2 0.7 + - - -
322B GLU* 2.7 61.8 + - + +
333B VAL* 3.9 8.8 - - + +
334B GLY 4.5 0.4 - - - +
335B LEU* 3.6 36.8 - - + +
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Residues in contact with HIS 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B GLN 4.6 4.8 + - - -
316B GLU 5.2 1.9 + - - +
317B GLN 3.5 0.2 - - - -
318B VAL* 1.3 87.7 - - + +
320B LEU* 1.3 62.3 + - - +
322B GLU* 3.4 25.5 + - - +
323B ASN* 3.2 29.2 + - - +
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ARG* 3.3 50.5 - - + +
249A THR* 4.0 2.0 - - + +
272A MET* 3.5 17.5 - - + -
256B ASP* 4.3 15.3 - - + +
257B SER 5.2 0.2 - - - +
316B GLU 5.2 0.6 + - - -
317B GLN 3.5 6.4 + - - +
318B VAL 3.3 0.4 - - - -
319B HIS* 1.3 78.7 - - - +
321B TYR* 1.3 85.6 + - + +
323B ASN* 3.2 18.2 + - - +
324B TYR* 3.2 51.5 + - + +
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Residues in contact with TYR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PHE* 4.7 2.5 - + - -
251B PHE* 3.7 24.9 - + - -
255B ALA 2.7 28.2 + - - -
256B ASP* 3.3 3.6 + - - -
257B SER* 2.5 29.9 + - - -
311B PHE* 3.6 43.4 - + + -
313B VAL* 3.9 14.6 - - + -
317B GLN* 3.0 42.7 + - + +
318B VAL 4.0 2.0 - - - +
320B LEU* 1.3 91.7 - - + +
322B GLU* 1.3 60.2 + - - +
324B TYR* 3.2 16.8 + + - +
325B ALA* 2.9 24.6 + - - +
333B VAL* 3.5 9.9 - - + +
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Residues in contact with GLU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B VAL* 2.7 43.2 + - - +
319B HIS* 3.4 26.9 + - - +
321B TYR* 1.3 72.3 - - - +
323B ASN* 1.3 65.6 + - - +
325B ALA* 3.2 4.3 + - - +
326B LYS* 3.0 42.9 + - - +
333B VAL* 3.7 23.3 - - + +
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Residues in contact with ASN 323 (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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248A ARG* 6.1 1.4 - - - +
272A MET* 3.6 39.1 - - + +
319B HIS* 3.3 18.7 + - - +
320B LEU* 3.2 8.4 + - - +
322B GLU* 1.3 74.3 - - - +
324B TYR* 1.3 68.3 + - - +
326B LYS* 3.3 30.1 + - - +
327B LEU* 3.6 17.0 + - - +
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Residues in contact with TYR 324 (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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249A THR* 3.0 42.0 + - - +
272A MET* 3.7 22.4 - - + -
273A ALA* 4.3 5.8 - - + -
226B PHE* 3.9 27.6 - + - -
256B ASP* 6.1 0.2 - - - +
257B SER* 4.7 8.2 + - - -
259B PHE* 4.1 8.2 - + - -
295B ILE* 3.6 26.5 - - + +
311B PHE* 4.3 9.2 - - + -
320B LEU* 3.2 36.7 + - + +
321B TYR* 3.2 22.2 + + - +
323B ASN* 1.3 78.1 - - - +
325B ALA* 1.3 62.1 + - - +
327B LEU* 3.1 15.7 + - - +
328B ILE* 3.3 21.6 + - + +
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B PHE* 4.2 5.8 - - + -
321B TYR 2.9 16.7 + - - +
322B GLU* 3.2 5.1 + - - +
324B TYR* 1.3 77.1 - - - +
326B LYS* 1.3 61.1 + - + +
328B ILE* 2.7 26.9 - - - +
331B ALA* 3.7 36.7 - - + +
332B THR* 4.6 0.7 - - - -
333B VAL* 3.8 17.7 - - + -
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Residues in contact with LYS 326 (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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309A LEU* 5.6 0.3 - - - +
322B GLU* 3.0 34.1 + - - +
323B ASN* 3.7 27.0 + - - +
324B TYR 3.2 1.0 - - - -
325B ALA* 1.3 78.0 - - + +
327B LEU* 1.3 64.0 + - + +
328B ILE 4.9 0.8 - - - -
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Residues in contact with LEU 327 (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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271A GLN* 4.5 17.5 - - + +
272A MET* 3.9 43.1 - - + +
301A MET* 5.4 3.4 - - - -
303A ARG* 6.3 0.7 - - - +
309A LEU* 4.0 29.2 - - + +
295B ILE* 4.2 26.2 - - + -
299B ILE* 3.1 16.9 - - + +
323B ASN 3.6 10.8 - - - +
324B TYR 3.1 4.9 + - - +
326B LYS* 1.3 84.0 - - + +
328B ILE* 1.3 57.7 + - - +
329B PRO* 3.5 7.4 - - - +
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Residues in contact with ILE 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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226B PHE* 6.1 1.6 - - + -
295B ILE* 4.3 14.4 - - + -
298B LEU* 5.2 11.9 - - + -
299B ILE* 3.9 17.0 - - + -
302B LEU* 3.7 28.0 - - + -
309B LEU* 4.4 7.6 - - + -
311B PHE* 4.3 23.3 - - + -
324B TYR* 3.3 25.8 - - + +
325B ALA 2.7 19.2 + - - +
326B LYS 5.0 0.2 - - - -
327B LEU* 1.3 79.0 - - - +
329B PRO* 1.3 76.8 - - + +
330B GLY 3.5 0.3 + - - -
331B ALA* 3.3 24.4 + - + +
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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