Contacts of the helix formed by residues 308 - 327 (chain B) in PDB entry 4F4W
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 308 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B TYR* 3.4 1.9 + - - -
306B GLY 3.8 4.2 + - - -
307B ILE* 1.3 78.5 - - - +
309B LYS* 1.3 64.6 + - - +
310B GLU* 3.6 15.6 + - - +
311B THR* 3.1 27.9 + - - -
312B ALA 3.0 17.8 + - - -
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Residues in contact with LYS 309 (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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270B ILE* 4.3 1.8 - - + -
271B GLU* 3.0 39.4 + - - +
274B TYR* 3.6 49.5 - - + -
308B SER* 1.3 73.7 - - - +
310B GLU* 1.3 77.9 + - - +
312B ALA* 3.2 3.8 + - - +
313B TYR* 3.1 34.3 + - + -
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Residues in contact with GLU 310 (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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308B SER* 3.7 15.2 + - - +
309B LYS* 1.3 97.5 + - + +
311B THR* 1.3 61.4 + - - +
313B TYR* 3.4 11.3 + - - +
314B SER* 3.3 19.8 + - - -
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Residues in contact with THR 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PHE* 4.6 24.2 - - + -
305B HIS* 5.3 7.7 + - - +
307B ILE* 4.1 15.3 - - + -
308B SER* 3.1 24.5 + - - +
310B GLU* 1.3 74.2 - - - +
312B ALA* 1.3 61.5 + - - +
314B SER* 3.3 8.5 + - - +
315B GLU* 2.9 30.1 + - + +
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Residues in contact with ALA 312 (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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270B ILE* 3.9 7.9 - - + -
274B TYR* 3.6 28.0 - - + +
285B ILE* 3.7 7.7 - - - +
307B ILE* 3.6 10.4 - - + +
308B SER 3.0 12.4 + - - +
309B LYS 3.2 10.8 - - - +
310B GLU 3.2 0.2 - - - -
311B THR* 1.3 74.4 - - - +
313B TYR* 1.3 66.0 + - - +
315B GLU* 4.9 0.7 - - - -
316B SER* 2.8 28.1 + - - +
338B PHE* 3.9 13.5 - - + -
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Residues in contact with TYR 313 (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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267B PHE* 3.2 55.0 - + + +
270B ILE* 4.0 24.7 - - + -
271B GLU* 2.3 41.9 + - - +
309B LYS* 3.1 27.9 + - + -
310B GLU* 3.4 12.8 - - - +
312B ALA* 1.3 77.6 - - - +
314B SER* 1.3 63.8 + - - +
316B SER* 2.7 22.4 + - - -
317B VAL* 3.2 13.0 + - - +
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Residues in contact with SER 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B GLU 3.3 8.8 + - - -
311B THR* 3.3 14.2 + - - +
313B TYR* 1.3 80.4 - - - +
315B GLU* 1.3 63.7 + - - +
317B VAL* 3.2 16.8 + - - +
318B LYS* 3.4 22.9 + - - +
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Residues in contact with GLU 315 (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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285B ILE* 4.0 15.0 - - + -
301B ARG* 3.6 19.8 + - - -
303B PHE* 3.6 41.3 - - + -
311B THR* 2.9 18.8 + - + +
312B ALA* 4.3 2.2 - - - +
314B SER* 1.3 75.2 + - - +
316B SER* 1.3 66.1 + - - +
318B LYS* 3.1 29.3 + - - +
319B LEU* 3.0 39.7 + - + +
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Residues in contact with SER 316 (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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266B LEU* 3.7 16.4 - - - +
267B PHE* 3.9 3.5 - - - -
270B ILE* 3.4 23.2 - - - +
285B ILE* 3.9 12.7 - - - +
287B VAL* 3.7 22.6 - - - +
312B ALA 2.8 17.0 + - - -
313B TYR* 2.7 19.8 + - - -
315B GLU* 1.3 76.8 - - - +
317B VAL* 1.3 57.9 + - - +
319B LEU* 3.3 1.1 + - - -
320B LEU* 2.9 28.9 + - - +
336B VAL* 4.7 0.2 - - - -
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Residues in contact with VAL 317 (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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259B LEU* 4.2 24.9 - - + -
263B LYS* 4.5 16.4 - - + +
266B LEU* 4.8 2.2 - - + -
267B PHE* 3.7 28.3 - - + -
313B TYR 3.2 16.3 + - - +
314B SER* 3.6 8.7 - - - +
315B GLU 3.1 0.8 - - - -
316B SER* 1.3 83.7 + - - +
318B LYS* 1.3 56.9 + - + +
320B LEU* 3.2 6.4 + - - +
321B GLN* 2.9 46.5 + - - +
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Residues in contact with LYS 318 (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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314B SER* 3.4 18.8 + - - +
315B GLU* 3.1 32.5 + - - +
317B VAL* 1.3 77.2 - - + +
319B LEU* 1.3 62.2 + - - +
321B GLN* 3.4 17.2 + - - +
322B LYS* 3.1 22.7 + - - +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ILE* 3.7 33.0 - - + +
287B VAL* 3.7 24.7 - - + +
299B ARG* 3.6 28.4 - - + +
300B GLY* 3.8 20.6 - - - +
301B ARG* 4.3 2.5 - - + +
315B GLU* 3.0 34.9 + - + +
316B SER 3.7 1.1 - - - +
318B LYS* 1.3 73.9 - - - +
320B LEU* 1.3 65.0 + - - +
322B LYS* 3.1 27.2 + - - +
323B ILE* 3.0 26.8 + - - +
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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
----------------------------------------------------------
259B LEU* 3.6 27.4 - - + +
262B ILE* 3.7 30.5 - - + -
263B LYS* 5.0 4.5 - - + +
266B LEU* 4.0 18.2 - - + -
287B VAL* 4.4 3.7 - - + +
316B SER 2.9 17.3 + - - +
317B VAL* 3.6 5.8 - - - +
319B LEU* 1.3 75.6 - - - +
321B GLN* 1.3 64.3 + - - +
323B ILE* 3.1 12.4 + - + +
324B LEU* 2.9 27.7 + - + +
331B ILE* 3.9 27.8 - - + -
334B ILE* 4.1 14.8 - - + -
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Residues in contact with GLN 321 (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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259B LEU* 4.2 25.8 - - + +
317B VAL* 2.9 33.4 + - - +
318B LYS* 3.5 21.1 + - - +
319B LEU 3.3 0.2 - - - -
320B LEU* 1.3 74.1 - - - +
322B LYS* 1.3 57.8 + - - +
324B LEU* 3.1 10.4 + - + +
325B GLU* 2.8 33.6 + - - +
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Residues in contact with LYS 322 (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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299B ARG* 3.7 27.6 - - + +
300B GLY 4.9 5.7 + - - -
301B ARG* 6.1 2.0 - - - +
318B LYS 3.1 13.7 + - - +
319B LEU* 3.1 30.6 + - - +
321B GLN* 1.3 76.3 - - - +
323B ILE* 1.3 62.9 + - - +
325B GLU* 3.2 10.3 + - - +
326B GLU* 3.0 51.6 + - - +
8E A 4.7 4.9 + - - +
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Residues in contact with ILE 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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287B VAL* 3.7 43.1 - - + +
289B ALA* 4.1 21.3 - - + -
291B THR* 6.1 1.1 - - + -
297B VAL* 4.1 34.8 - - + +
299B ARG* 3.5 24.2 - - + +
319B LEU 3.0 13.1 + - - +
320B LEU* 3.1 11.4 + - + +
322B LYS* 1.3 75.9 - - - +
324B LEU* 1.3 59.8 + - + +
326B GLU* 5.0 1.8 - - - -
327B ASP* 2.9 36.2 + - + +
331B ILE* 4.4 12.8 - - + -
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Residues in contact with LEU 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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257B ARG* 3.0 74.8 + - + +
259B LEU* 4.0 28.5 - - + +
262B ILE* 4.7 3.1 - - + -
320B LEU* 2.9 27.1 + - + +
321B GLN* 3.6 10.1 - - + +
323B ILE* 1.3 77.1 - - + +
325B GLU* 1.3 60.5 + - - +
327B ASP 3.0 12.5 - - - +
328B GLU* 5.8 0.3 - - - +
331B ILE* 3.7 25.1 - - + -
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Residues in contact with GLU 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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321B GLN* 2.8 17.7 + - - +
322B LYS* 3.5 10.7 - - - +
323B ILE 3.2 0.2 - - - -
324B LEU* 1.3 80.3 - - - +
326B GLU* 1.3 74.5 + - + +
327B ASP 3.8 0.9 + - - -
328B GLU* 5.8 3.1 - - - +
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Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ARG* 2.8 40.4 + - - +
322B LYS* 3.0 34.7 + - + +
323B ILE 4.3 0.7 - - - +
325B GLU* 1.3 94.5 - - + +
327B ASP* 1.3 61.5 + - - +
328B GLU* 6.0 0.7 - - - -
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Residues in contact with ASP 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ARG* 2.6 25.6 + - - -
291B THR* 4.2 3.4 - - + +
297B VAL* 3.7 18.2 - - + +
299B ARG* 6.0 0.4 - - - +
323B ILE* 2.9 23.1 + - + +
324B LEU* 3.0 9.9 - - - +
325B GLU 3.5 0.4 - - - -
326B GLU* 1.3 81.3 - - - +
328B GLU* 1.3 53.7 + - - +
329B ARG* 2.7 70.6 + - - +
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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
------------------------------------------------------------
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