Contacts of the helix formed by residues 321 - 344 (chain D) in PDB entry 2VT4
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 PRO 321 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D VAL* 1.3 96.0 - - + +
322D ASP* 1.3 67.3 + - - +
323D TRP* 3.4 36.3 - - + +
324D LEU* 2.7 30.4 + - + +
325D PHE 3.4 2.6 + - - -
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Residues in contact with ASP 322 (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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320D VAL 3.9 2.7 + - - +
321D PRO* 1.3 69.8 - - - +
323D TRP* 1.3 56.0 + - - +
325D PHE* 2.7 36.2 + - + +
326D VAL* 3.0 17.6 + - + +
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Residues in contact with TRP 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D PRO* 2.9 36.1 + - + +
322D ASP* 1.3 77.3 - - - +
324D LEU* 1.3 88.7 + - + +
326D VAL* 3.5 9.4 + - - +
327D ALA* 3.1 32.5 + - + +
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Residues in contact with LEU 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D VAL* 4.5 5.6 - - + -
320D VAL* 4.1 25.4 - - + -
321D PRO* 2.7 28.0 + - + +
323D TRP* 1.3 104.2 - - + +
325D PHE* 1.3 63.3 + - - +
327D ALA* 4.5 3.6 - - + +
328D PHE* 3.1 63.3 + - + +
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Residues in contact with PHE 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D PHE* 4.0 21.5 - + - -
309D VAL* 3.6 28.9 - - + -
310D ASN* 3.5 26.7 - - - -
313D ASN* 2.7 40.2 - - + -
320D VAL* 4.2 13.2 - - + -
321D PRO 3.4 3.1 + - - -
322D ASP* 2.7 22.3 + - - +
324D LEU* 1.3 78.0 - - - +
326D VAL* 1.3 64.9 + - + +
328D PHE* 3.5 2.1 + - - -
329D ASN* 2.9 27.2 + - + +
400D P32 6.6 0.2 - - + -
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Residues in contact with VAL 326 (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 VAL* 4.3 24.2 - - + -
322D ASP* 3.0 17.9 + - + +
323D TRP* 3.9 9.9 - - - +
324D LEU 3.4 0.2 - - - -
325D PHE* 1.3 77.3 - - + +
327D ALA* 1.3 64.7 + - - +
329D ASN* 3.4 3.7 + - - +
330D TRP* 2.8 53.0 + - + +
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Residues in contact with ALA 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D TRP* 3.1 28.8 + - + +
324D LEU* 4.0 9.9 - - + +
325D PHE 3.2 0.4 - - - -
326D VAL* 1.3 78.4 - - - +
328D PHE* 1.3 60.6 + - + +
330D TRP* 3.1 7.1 + - - +
331D LEU* 2.9 27.6 + - - +
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Residues in contact with PHE 328 (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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302D CYS 4.1 2.3 - - - +
305D PRO* 3.5 32.8 - - + -
306D PHE* 3.8 25.7 + - + +
309D VAL* 3.5 34.5 - - + -
324D LEU* 3.1 46.4 + - + +
325D PHE* 4.1 3.1 - - - +
327D ALA* 1.3 80.6 - - + +
329D ASN* 1.3 61.4 + - - +
331D LEU* 3.3 14.8 + - + +
332D GLY* 3.2 17.3 + - - -
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Residues in contact with ASN 329 (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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303D TRP* 3.7 13.5 - - - -
306D PHE* 3.5 21.8 - - + -
325D PHE* 2.9 19.5 + - + +
326D VAL* 3.7 6.1 - - - +
328D PHE* 1.3 77.4 - - - +
330D TRP* 1.3 61.7 + - + +
332D GLY* 3.5 2.6 + - - -
333D TYR* 3.2 33.7 + - - -
400D P32 2.8 54.8 + - - +
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Residues in contact with TRP 330 (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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48D MET* 4.3 30.3 - - + +
51D VAL* 5.0 8.5 - - + -
95D VAL* 4.0 28.0 - - + -
98D GLY* 3.9 10.3 - - - -
99D ALA* 3.8 24.2 - - + -
102D VAL* 3.6 28.3 - - + +
326D VAL* 2.8 50.5 + - + +
327D ALA* 3.1 5.6 + - - +
329D ASN* 1.3 77.3 - - + +
331D LEU* 1.3 67.6 + - - +
333D TYR* 3.6 33.7 - + + +
334D ALA* 2.9 24.8 + - - +
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Residues in contact with LEU 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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301D LEU 3.7 20.9 - - - +
302D CYS* 3.5 28.6 - - - +
305D PRO* 3.9 17.3 - - + -
327D ALA 2.9 12.5 + - - +
328D PHE* 3.3 19.5 + - + +
330D TRP* 1.3 77.3 - - - +
332D GLY* 1.3 61.0 + - - +
334D ALA* 3.2 16.6 + - + +
335D ASN 3.4 7.8 + - - -
338D MET* 5.1 6.7 - - + -
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Residues in contact with GLY 332 (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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302D CYS* 3.1 21.8 + - - -
303D TRP* 3.3 35.2 + - - -
328D PHE 3.2 6.1 + - - -
329D ASN 3.5 3.1 + - - -
330D TRP 3.2 0.2 - - - -
331D LEU* 1.3 77.5 - - - +
333D TYR* 1.3 64.2 + - - +
335D ASN* 3.1 18.2 - - - +
336D SER* 4.3 1.2 + - - -
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Residues in contact with TYR 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D VAL* 5.4 1.8 - - + -
55D ILE* 3.8 6.8 - - + +
90D VAL* 4.1 17.3 - - + -
94D VAL* 3.5 24.2 - - + +
95D VAL* 3.7 22.9 - - + -
98D GLY* 5.8 1.1 - - - -
117D TRP* 4.3 8.0 - + - -
121D ASP* 2.5 28.8 + - - -
303D TRP* 4.4 8.5 - + - -
329D ASN* 3.2 30.6 + - - -
330D TRP* 3.2 46.2 + + + +
332D GLY* 1.3 70.8 - - - +
334D ALA* 1.3 65.2 + - - +
335D ASN 2.9 5.4 - - - -
336D SER* 2.8 24.1 + - - -
400D P32 3.8 23.1 + - - +
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Residues in contact with ALA 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D LEU* 4.4 24.0 - - + -
48D MET* 4.5 10.5 - - + -
51D VAL* 4.3 13.5 - - + -
330D TRP 2.9 13.3 + - - +
331D LEU* 3.2 15.0 + - + +
333D TYR* 1.3 76.6 - - - +
335D ASN* 1.3 55.7 - - - +
337D ALA* 2.9 25.6 + - - +
338D MET* 3.6 19.4 + - + +
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Residues in contact with ASN 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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87D ASP* 5.1 5.1 + - - -
295D ILE 5.2 0.2 - - - +
298D VAL* 3.3 14.0 - - - +
299D PHE* 3.2 49.6 + - - +
302D CYS* 3.7 15.2 - - + -
303D TRP* 4.4 4.3 - - - +
331D LEU 3.4 4.0 + - - -
332D GLY 3.1 17.9 + - - +
333D TYR 2.9 0.2 + - - -
334D ALA* 1.3 78.0 - - - +
336D SER* 1.3 62.7 + - - +
337D ALA 3.1 1.3 + - - -
338D MET* 3.3 20.5 + - - +
339D ASN* 3.7 20.2 + - - +
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Residues in contact with SER 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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55D ILE* 3.4 25.0 - - - +
59D ASN* 2.9 28.9 + - - -
87D ASP* 2.8 35.3 + - - +
90D VAL* 3.6 22.7 - - - +
332D GLY 5.1 1.2 + - - -
333D TYR* 2.8 18.3 + - - -
335D ASN* 1.3 72.8 + - - +
337D ALA* 1.3 56.6 + - - +
339D ASN 4.9 1.1 - - - -
340D PRO* 4.4 1.7 - - - +
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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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47D LEU* 5.6 3.6 - - + -
51D VAL* 4.5 8.7 - - + -
54D LEU* 3.8 32.5 - - + +
55D ILE* 3.4 22.6 - - + +
334D ALA 2.9 11.2 + - - +
336D SER* 1.3 79.1 - - - +
338D MET* 1.3 62.5 + - - +
339D ASN 3.6 0.9 - - - -
340D PRO* 3.6 10.9 - - - +
341D ILE* 3.9 16.9 - - - +
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Residues in contact with MET 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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47D LEU* 5.9 4.0 - - + -
298D VAL* 3.1 35.2 - - + -
302D CYS* 3.7 24.0 - - - -
331D LEU* 5.1 6.3 - - + -
334D ALA* 4.1 18.8 - - + +
335D ASN* 3.3 14.7 + - - +
337D ALA* 1.3 78.6 - - - +
339D ASN* 1.3 69.0 + - - +
341D ILE* 3.1 16.9 + - + +
342D ILE* 3.0 28.8 + - + +
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Residues in contact with ASN 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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59D ASN* 5.2 2.2 - - - +
83D LEU* 4.3 15.0 - - - +
87D ASP* 4.6 13.6 + - - +
295D ILE* 2.9 47.6 - - + +
298D VAL* 6.0 1.0 - - - +
335D ASN* 3.7 22.6 + - - +
338D MET* 1.3 74.6 - - - +
340D PRO* 1.3 73.4 - - + +
342D ILE* 2.9 15.3 + - - +
343D TYR* 3.0 36.8 + - + +
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Residues in contact with PRO 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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54D LEU 4.8 1.8 - - - +
58D GLY* 3.4 42.4 - - - +
59D ASN* 3.9 20.2 - - - +
62D VAL* 3.9 7.2 - - + -
336D SER 4.4 0.7 - - - +
337D ALA 3.6 13.9 - - - +
338D MET 3.5 3.8 - - - -
339D ASN* 1.3 93.8 - - + +
341D ILE* 1.3 63.4 + - + +
343D TYR* 3.3 22.0 + - + +
344D CYS* 3.5 15.5 + - - -
353D PHE* 4.1 6.7 - - + -
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Residues in contact with ILE 341 (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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47D LEU* 6.5 0.4 - - + -
54D LEU* 5.5 15.5 - - + -
337D ALA* 3.9 16.8 - - + +
338D MET* 3.1 15.7 + - + +
340D PRO* 1.3 78.4 - - + +
342D ILE* 1.3 68.8 + - + +
344D CYS* 2.9 26.9 + - - +
345D ARG* 4.2 1.0 + - - +
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Residues in contact with ILE 342 (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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291D THR* 3.8 21.1 - - + +
294D ILE* 3.5 37.5 - - + -
295D ILE* 3.7 24.2 - - + -
298D VAL* 3.9 20.2 - - + -
338D MET* 3.0 22.3 + - + +
339D ASN* 2.9 13.5 + - - +
341D ILE* 1.3 77.0 - - + +
343D TYR* 1.3 58.9 + - - +
344D CYS 3.1 0.2 - - - -
345D ARG* 3.1 33.5 + - - +
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Residues in contact with TYR 343 (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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59D ASN* 6.0 0.2 - - - -
62D VAL* 3.5 34.5 - - + -
80D ILE* 3.4 46.0 + - + +
83D LEU* 4.9 3.1 - - - +
84D ALA* 6.4 0.4 - - + -
291D THR* 4.0 19.5 - - + -
292D LEU* 5.8 1.6 - - + -
295D ILE* 3.9 21.7 - - + +
339D ASN* 3.0 45.2 + - + +
340D PRO* 3.7 5.2 - - + +
341D ILE 3.1 0.6 + - - -
342D ILE* 1.3 71.9 - - - +
344D CYS* 1.3 56.8 + - - +
345D ARG 3.0 5.8 - - - -
346D SER* 3.0 22.2 + - - +
349D PHE* 3.4 45.4 - + + +
353D PHE* 4.6 1.1 - - + -
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Residues in contact with CYS 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D PRO 3.5 10.8 - - - -
341D ILE* 2.9 16.4 + - - +
343D TYR* 1.3 78.6 - - - +
345D ARG* 1.3 59.5 + - - +
346D SER 3.1 4.1 - - - +
350D ARG* 3.0 40.3 + - + -
353D PHE* 3.5 31.4 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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