Contacts of the helix formed by residues 323 - 341 (chain B) in PDB entry 6VSU
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 323 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B ASP* 3.2 18.6 - - - -
320B THR* 3.0 12.3 + - - -
321B VAL 3.4 1.2 + - - -
322B ASP* 1.3 78.9 - - - +
324B MET* 1.3 65.0 + - - +
326B ALA* 3.1 19.0 + - - +
327B MET* 3.3 15.7 + - - +
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Residues in contact with MET 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PRO* 3.5 38.8 - - + +
277A ALA* 4.1 2.2 - - - +
280A PRO* 4.6 12.3 - - + -
285A ILE* 4.3 26.4 - - + +
277B ALA 3.6 23.8 - - - +
278B PHE 3.8 10.1 - - - +
280B PRO* 3.7 26.0 - - + -
319B ASP* 3.4 0.8 + - - -
320B THR* 3.1 24.7 + - + +
322B ASP* 3.6 2.5 - - + -
323B GLY* 1.3 76.6 - - - +
325B THR* 1.3 57.6 + - - +
327B MET* 3.1 6.4 + - - +
328B VAL* 3.1 26.9 + - + +
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Residues in contact with THR 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B VAL* 3.8 22.4 - - + -
278B PHE 5.1 0.4 - - - -
279B ALA* 4.1 8.5 - - + -
280B PRO* 3.3 13.2 - - - +
281B GLY 2.9 40.6 + - - +
314B PHE* 3.6 11.2 - - + -
319B ASP* 2.7 32.1 + - - -
324B MET* 1.3 69.6 - - - +
326B ALA* 1.3 59.8 + - - +
328B VAL* 3.2 7.9 + - + +
329B ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ARG* 4.1 19.7 - - + +
89B ILE* 4.6 2.1 - - - -
92B ALA* 3.3 14.6 - - + +
314B PHE* 3.4 30.7 - - + -
319B ASP* 3.0 9.6 + - - +
323B GLY* 3.1 14.1 + - - +
325B THR* 1.3 77.6 - - - +
327B MET* 1.4 56.4 + - + +
329B ALA* 3.5 1.9 + - - +
330B ALA* 2.9 22.9 + - - +
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Residues in contact with MET 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ILE* 3.7 42.6 - - + +
287A PRO* 3.9 9.4 - - + +
92B ALA* 3.7 30.5 - - - +
95B CYS* 4.4 13.2 - - + -
97B SER* 4.6 4.0 - - - +
98B THR* 3.4 32.8 - - + -
322B ASP 5.4 1.8 - - - +
323B GLY 3.3 14.3 + - - +
324B MET 3.1 8.5 + - - +
326B ALA* 1.4 73.2 - - - +
328B VAL* 1.3 60.5 + - - +
330B ALA* 3.4 3.0 + - + +
331B LYS* 2.9 31.5 + - - +
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PRO* 6.0 1.3 - - + -
287A PRO* 3.9 24.7 - - + -
271B VAL* 4.8 3.4 - - + -
274B LEU* 3.4 32.3 - - + -
278B PHE* 3.6 22.9 - - + +
279B ALA* 4.5 8.1 - - + -
292B PHE* 3.6 11.2 - - + -
324B MET* 3.1 19.4 + - + +
325B THR* 3.4 12.6 - - + +
327B MET* 1.3 74.0 - - - +
329B ALA* 1.3 60.0 + - - +
331B LYS 3.2 1.9 + - - -
332B LEU* 2.9 38.4 + - + +
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Residues in contact with ALA 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 4.1 29.2 - - + -
271B VAL* 4.4 4.5 - - + -
311B VAL* 4.2 14.0 - - + +
314B PHE* 4.1 17.0 - - + -
325B THR 2.9 18.5 + - - +
326B ALA 3.9 3.8 - - - +
328B VAL* 1.3 73.0 - - - +
330B ALA* 1.3 63.7 + - - +
332B LEU* 3.3 8.3 + - - +
333B VAL* 3.1 26.7 + - - +
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 3.8 12.3 - - - +
92B ALA* 3.4 23.8 - - + +
93B ILE* 3.5 24.0 - - + +
326B ALA 2.9 19.1 + - - +
327B MET* 3.7 5.6 - - + +
328B VAL 3.2 0.2 - - - -
329B ALA* 1.3 77.3 - - - +
331B LYS* 1.3 57.7 + - - +
333B VAL* 3.3 4.0 + - - +
334B ARG* 3.0 34.6 + - - +
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Residues in contact with LYS 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ARG* 3.6 9.3 + - - +
286A GLU* 2.9 28.0 + - - +
287A PRO* 3.0 34.1 + - + +
103B GLU* 2.7 41.8 + - - -
292B PHE* 3.6 20.4 - - + -
296B LEU* 4.2 7.0 - - - -
327B MET 2.9 17.0 + - - +
328B VAL 3.8 0.2 - - - +
330B ALA* 1.3 72.8 - - - +
332B LEU* 1.3 65.7 + - - +
334B ARG* 3.2 17.4 + - - +
335B GLU* 2.9 31.6 + - + +
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ILE* 4.0 30.5 - - + -
271B VAL* 4.4 9.4 - - + -
273B CYS* 5.9 0.2 - - - -
274B LEU* 4.4 9.2 - - + -
292B PHE* 3.6 22.2 - - + -
295B VAL* 3.8 28.5 - - + -
296B LEU* 4.7 2.9 - - + -
299B LEU* 4.6 5.6 - - + +
311B VAL* 4.3 11.4 - - + -
328B VAL* 2.9 35.1 + - + +
329B ALA* 3.6 11.2 - - - +
331B LYS* 1.3 76.4 - - - +
333B VAL* 1.3 55.8 + - - +
335B GLU* 3.3 4.0 + - - +
336B LEU* 2.9 36.6 + - - +
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Residues in contact with VAL 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.7 30.5 - - + -
89B ILE* 4.0 8.5 - - + -
93B ILE* 3.9 18.8 - - + -
114B LEU* 5.4 4.9 - - + -
155B LEU* 3.5 13.5 - - + +
157B LEU* 3.5 24.7 - - + -
311B VAL* 3.8 18.4 - - + -
329B ALA 3.1 19.0 + - - +
330B ALA 3.5 7.4 - - - +
331B LYS 3.3 0.2 - - - -
332B LEU* 1.3 72.8 - - - +
334B ARG* 1.3 59.9 + - - +
336B LEU* 3.5 1.1 + - - -
337B ALA* 3.0 27.2 + - - +
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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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286A GLU* 5.8 3.1 + - - -
92B ALA 5.5 0.7 - - - -
93B ILE* 3.3 41.6 + - + +
98B THR* 3.8 14.8 + - - +
99B ASN* 2.9 27.3 + - - -
100B SER* 4.6 1.0 - - - +
101B ALA 2.8 34.1 + - - -
102B THR* 3.7 15.8 - - + +
108B LEU* 3.4 35.9 - - + +
114B LEU* 5.9 0.9 - - + -
330B ALA* 3.0 24.3 + - - +
331B LYS* 3.2 18.4 + - - +
333B VAL* 1.3 74.2 - - - +
335B GLU* 1.3 68.6 + - - +
337B ALA* 3.4 5.6 + - - +
338B ALA 3.2 17.2 + - - -
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Residues in contact with GLU 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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102B THR* 3.6 13.1 - - - +
103B GLU* 3.0 41.0 + - - +
104B GLU* 4.7 3.5 + - - +
296B LEU* 3.9 31.6 - - + -
299B LEU* 5.1 7.0 - - + -
300B HIS* 2.9 29.8 + - + +
331B LYS* 2.9 25.2 + - + +
332B LEU 4.0 2.7 - - - +
334B ARG* 1.3 76.4 + - + +
336B LEU* 1.3 65.6 + - - +
338B ALA* 3.3 7.6 + - - +
339B LYS* 3.1 22.8 + - - +
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Residues in contact with LEU 336 (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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155B LEU* 3.6 17.0 - - + -
267B ILE* 3.9 35.0 - - + -
269B ILE* 3.7 24.7 - - + -
299B LEU* 4.3 15.3 - - + -
309B ALA* 4.0 21.3 - - + -
310B ASP 4.5 0.9 - - - +
311B VAL* 3.7 21.1 - - + -
332B LEU 2.9 20.7 + - - +
335B GLU* 1.3 78.3 - - - +
337B ALA* 1.3 55.0 + - - +
339B LYS* 3.1 9.3 + - + +
340B ILE* 2.8 38.5 + - + +
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Residues in contact with ALA 337 (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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65B THR* 3.3 31.9 - - + -
108B LEU* 4.6 8.5 - - + -
113B VAL* 4.0 9.6 - - + +
114B LEU* 4.3 10.8 - - + -
155B LEU* 3.9 0.8 - - - +
333B VAL 3.0 17.6 + - - +
334B ARG* 3.5 9.4 - - - +
335B GLU 3.3 0.4 - - - -
336B LEU* 1.3 72.2 - - - +
338B ALA* 1.3 61.5 + - - +
341B SER* 2.8 36.3 + - - -
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Residues in contact with ALA 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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102B THR* 3.6 28.9 - - + +
104B GLU* 5.9 4.7 - - + -
106B LYS* 2.7 46.2 + - + -
113B VAL* 5.0 1.6 - - - -
334B ARG 3.2 10.5 + - - +
335B GLU* 3.7 12.6 - - - +
336B LEU 3.3 0.2 - - - -
337B ALA* 1.3 77.4 - - - +
339B LYS* 1.3 58.4 + - - +
341B SER 3.0 6.1 - - - +
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Residues in contact with LYS 339 (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 ILE* 4.4 10.5 - - + -
299B LEU* 2.8 37.4 + - + +
300B HIS* 3.7 11.4 + - + +
302B LEU* 3.0 42.0 + - - -
304B ALA* 5.3 3.8 + - - +
306B VAL* 4.2 23.4 + - + +
335B GLU 3.1 12.8 + - - +
336B LEU* 3.1 13.6 + - + +
337B ALA 3.1 0.2 - - - -
338B ALA* 1.3 79.2 - - - +
340B ILE* 1.3 63.7 + - + +
341B SER 3.8 2.9 - - - +
342B LYS* 5.2 4.5 - - - +
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Residues in contact with ILE 340 (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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63B ALA* 3.4 15.4 - - - +
64B SER 5.1 0.2 - - - -
65B THR* 3.2 21.8 - - - +
153B ARG* 3.6 37.1 - - + +
154B PRO 4.7 1.8 - - - +
155B LEU* 4.4 13.9 - - + -
306B VAL* 3.6 33.8 - - + +
308B GLY* 4.4 1.8 - - - -
309B ALA* 3.8 34.5 - - + +
336B LEU* 2.8 27.2 + - + +
339B LYS* 1.3 73.0 - - + +
341B SER* 1.3 64.9 + - - +
342B LYS* 3.6 7.6 + - - +
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Residues in contact with SER 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA 3.3 12.6 - - - -
65B THR* 2.8 21.8 + - - -
106B LYS* 2.7 29.0 + - - -
112B ARG 3.8 8.7 - - - -
113B VAL* 2.6 38.3 + - - -
337B ALA 2.8 14.4 + - - -
338B ALA 3.0 5.2 - - - +
339B LYS 3.8 1.9 - - - +
340B ILE* 1.3 77.5 - - - +
342B LYS* 1.3 57.4 + - - +
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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
------------------------------------------------------------
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