Contacts of the helix formed by residues 323 - 341 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D ASP* 3.2 19.1 - - - -
320D THR* 3.1 8.9 + - - -
321D VAL 3.5 0.8 + - - -
322D ASP* 1.3 80.4 - - - +
324D MET* 1.3 66.2 + - - +
326D ALA* 3.2 18.9 + - - +
327D MET* 3.2 18.3 + - - +
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Residues in contact with MET 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D ALA 3.6 24.5 - - - +
278D PHE* 3.7 10.3 - - - +
280D PRO* 3.6 26.7 - - + -
319D ASP* 3.5 0.8 + - - -
320D THR* 3.1 24.2 + - + +
322D ASP* 3.5 1.6 - - + -
323D GLY* 1.3 75.5 - - - +
325D THR* 1.3 63.0 + - - +
327D MET* 3.0 20.2 + - + +
328D VAL* 3.1 15.0 + - + +
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Residues in contact with THR 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D VAL* 3.7 23.3 - - + -
279D ALA* 4.0 8.7 - - + -
280D PRO* 3.3 13.0 - - - +
281D GLY 2.9 40.0 + - - +
314D PHE* 3.7 11.9 - - + -
319D ASP* 2.7 29.7 + - - -
324D MET* 1.3 69.7 - - - +
326D ALA* 1.3 60.4 + - - +
328D VAL* 3.2 8.2 + - + -
329D ALA* 2.8 29.5 + - - +
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Residues in contact with ALA 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ARG* 4.2 18.4 - - + +
89D ILE* 4.7 2.1 - - - -
92D ALA* 3.2 17.0 - - + +
314D PHE* 3.5 29.7 - - + -
319D ASP* 3.1 9.3 + - - +
323D GLY* 3.3 14.8 - - - +
325D THR* 1.3 76.3 - - - +
327D MET* 1.3 56.1 + - - +
329D ALA* 3.8 1.7 - - - +
330D ALA 2.9 22.0 + - - -
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Residues in contact with MET 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D ALA* 3.8 30.3 - - - +
95D CYS* 4.5 12.8 - - + -
97D SER* 4.5 4.9 - - - +
98D THR* 3.5 32.1 - - + -
322D ASP 5.5 2.2 - - - +
323D GLY 3.2 15.7 + - - +
324D MET* 3.0 11.0 + - + +
326D ALA* 1.3 73.7 - - - +
328D VAL* 1.3 56.4 + - + +
330D ALA* 3.2 3.5 + - + +
331D LYS* 2.9 35.2 + - - +
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Residues in contact with VAL 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D VAL* 4.6 6.3 - - + -
274D LEU* 3.3 31.0 - - + -
278D PHE* 3.4 26.2 - - + +
279D ALA* 4.6 6.7 - - + -
292D PHE* 3.5 23.5 - - + -
324D MET* 3.1 16.0 + - + +
325D THR* 3.4 9.6 - - - +
327D MET* 1.3 72.7 - - + +
329D ALA* 1.3 67.1 + - - +
331D LYS* 3.1 2.1 + - - -
332D LEU* 3.0 33.1 + - + +
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Residues in contact with ALA 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ILE* 3.8 30.3 - - + -
271D VAL* 4.4 3.8 - - + -
311D VAL* 4.2 15.1 - - + +
314D PHE* 4.2 14.6 - - + -
325D THR 2.8 16.7 + - - +
326D ALA 3.8 1.8 - - - +
328D VAL* 1.3 76.2 - - - +
330D ALA* 1.3 64.1 + - - +
332D LEU* 3.4 7.6 + - - +
333D VAL* 3.0 28.7 + - - +
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Residues in contact with ALA 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ILE* 3.9 7.5 - - - +
92D ALA* 3.4 34.1 - - + +
93D ILE* 3.5 28.3 - - + +
326D ALA 2.9 8.5 + - - +
327D MET* 3.2 7.4 + - + +
329D ALA* 1.3 76.6 - - - +
331D LYS* 1.3 56.7 + - - +
333D VAL* 3.2 4.0 + - - +
334D ARG* 2.9 35.5 + - - +
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Residues in contact with LYS 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D GLU* 2.7 41.7 + - - +
292D PHE* 3.6 26.9 - - + -
293D ARG* 4.4 3.6 - - - +
296D LEU* 4.2 8.5 - - - -
327D MET 2.9 16.4 + - - +
328D VAL* 3.1 0.4 + - - -
330D ALA* 1.3 74.0 - - - +
332D LEU* 1.3 60.7 + - - +
334D ARG* 3.1 15.7 + - - +
335D GLU* 2.9 38.3 + - + +
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Residues in contact with LEU 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D ILE* 4.0 29.8 - - + -
271D VAL* 4.2 22.7 - - + -
273D CYS* 5.8 0.4 - - - -
274D LEU* 4.6 8.1 - - + -
292D PHE* 3.8 21.0 - - + -
295D VAL* 3.8 28.7 - - + -
296D LEU* 4.8 2.2 - - + -
299D LEU* 4.6 5.3 - - + +
311D VAL* 4.3 14.4 - - + -
328D VAL* 3.0 25.8 + - + +
329D ALA* 3.6 6.1 - - - +
331D LYS* 1.3 75.6 - - - +
333D VAL* 1.3 62.8 + - - +
335D GLU* 3.8 4.1 - - - +
336D LEU* 2.9 31.6 + - - +
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Residues in contact with VAL 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D LEU* 3.8 28.0 - - + -
89D ILE* 3.9 9.6 - - + -
93D ILE* 3.9 18.8 - - + -
114D LEU* 5.4 4.5 - - + -
155D LEU* 3.6 12.8 - - + +
157D LEU* 3.6 25.1 - - + -
311D VAL* 3.9 19.1 - - + -
329D ALA 3.0 18.7 + - - +
330D ALA 3.4 7.6 - - - +
331D LYS 3.2 0.2 - - - -
332D LEU* 1.3 76.6 - - - +
334D ARG* 1.3 60.1 + - + +
336D LEU* 3.3 1.3 + - - -
337D ALA* 2.9 27.2 + - - +
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Residues in contact with ARG 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ALA 5.7 0.2 - - - -
93D ILE* 3.2 43.4 + - + +
94D TRP* 6.1 0.2 - - - -
98D THR* 3.9 13.9 + - - +
99D ASN* 2.8 30.3 + - - +
100D SER* 4.6 0.6 - - - +
101D ALA 3.0 25.9 + - - -
102D THR* 3.6 17.4 - - + +
108D LEU* 3.4 32.0 - - + +
114D LEU* 5.8 1.6 - - + -
330D ALA* 2.9 27.0 + - - +
331D LYS* 3.1 16.0 + - - +
333D VAL* 1.3 78.2 - - + +
335D GLU* 1.3 60.6 + - - +
337D ALA* 3.2 9.5 + - - +
338D ALA 3.1 21.8 + - - -
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Residues in contact with GLU 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D THR* 3.3 14.2 - - - +
103D GLU* 2.9 39.8 + - - +
104D GLU* 4.7 2.8 + - - +
296D LEU* 3.9 31.9 - - + -
299D LEU* 5.2 7.4 - - + +
300D HIS* 2.8 34.1 + - + +
331D LYS* 2.9 28.2 + - + +
332D LEU* 4.1 2.9 - - - +
334D ARG* 1.3 75.6 + - - +
336D LEU* 1.3 66.2 + - - +
338D ALA* 3.4 8.1 + - - +
339D LYS* 3.2 21.8 + - - +
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Residues in contact with LEU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D LEU* 3.8 12.3 - - + -
267D ILE* 4.0 34.5 - - + -
269D ILE* 3.9 15.0 - - + -
299D LEU* 4.2 20.6 - - + -
309D ALA* 4.2 19.3 - - + -
310D ASP 4.5 0.7 - - - +
311D VAL* 3.6 27.8 - - + -
332D LEU 2.9 21.4 + - - +
333D VAL* 3.6 4.9 - - - +
335D GLU* 1.3 77.3 - - - +
337D ALA* 1.3 56.9 + - - +
339D LYS* 3.1 8.8 + - + +
340D ILE* 2.9 40.3 + - + +
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Residues in contact with ALA 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D THR* 3.1 32.4 + - + +
108D LEU* 4.5 8.3 - - + -
113D VAL* 4.1 9.9 - - + +
114D LEU* 4.1 12.8 - - + -
155D LEU* 4.1 0.4 - - - +
333D VAL 2.9 14.2 + - - +
334D ARG* 3.2 13.6 + - - +
336D LEU* 1.3 75.3 - - - +
338D ALA* 1.3 57.3 + - - +
341D SER* 2.9 33.5 + - - -
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Residues in contact with ALA 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D THR* 3.7 27.3 - - + +
104D GLU* 5.7 7.9 - - + +
106D LYS* 3.0 45.3 + - + -
113D VAL* 5.1 2.4 - - - +
334D ARG 3.1 12.0 + - - +
335D GLU* 3.5 14.6 - - - +
337D ALA* 1.3 73.6 - - - +
339D LYS* 1.3 56.9 + - - +
341D SER 3.1 6.4 - - - +
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Residues in contact with LYS 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D ILE* 4.6 9.2 - - + -
299D LEU* 2.8 33.4 + - + +
300D HIS* 3.8 10.9 + - + +
302D LEU* 2.8 45.8 + - + -
304D ALA 4.9 5.6 - - - +
306D VAL* 4.1 22.7 + - + +
335D GLU 3.2 9.6 + - - +
336D LEU* 3.1 13.3 + - + +
338D ALA* 1.3 80.9 - - - +
340D ILE* 1.3 63.3 + - + +
341D SER 3.9 3.1 - - - +
342D LYS* 5.1 5.5 + - - +
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Residues in contact with ILE 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ALA* 3.4 15.6 - - - +
65D THR* 3.1 24.9 - - + +
153D ARG* 3.7 36.7 - - + +
154D PRO 4.6 2.7 - - - +
155D LEU* 4.4 14.4 - - + -
306D VAL* 3.6 32.9 - - + +
308D GLY 4.4 2.0 - - - +
309D ALA* 3.9 33.7 - - + +
336D LEU* 2.9 22.5 + - + +
339D LYS* 1.3 77.8 - - + +
341D SER* 1.3 62.0 + - - +
342D LYS* 3.7 8.0 + - - +
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Residues in contact with SER 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ALA 3.3 7.9 - - - -
65D THR* 2.8 22.7 + - - -
106D LYS* 2.7 30.0 + - - -
112D ARG 3.6 15.3 - - - -
113D VAL* 2.5 38.6 + - - -
337D ALA 2.9 10.2 + - - -
338D ALA 3.1 4.7 - - - +
339D LYS 3.9 1.9 - - - +
340D ILE* 1.3 76.3 - - - +
342D LYS* 1.3 59.2 + - - +
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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
------------------------------------------------------------
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