Contacts of the helix formed by residues 321 - 344 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A VAL* 1.3 97.3 - - + +
322A ASP* 1.3 67.6 + - - +
323A TRP* 3.4 36.8 - - + +
324A LEU* 2.7 30.7 + - + +
325A PHE* 3.5 2.6 + - - -
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Residues in contact with ASP 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A VAL 3.9 3.5 + - - +
321A PRO* 1.3 70.0 - - - +
323A TRP* 1.3 54.6 + - - +
325A PHE* 2.7 36.6 + - + +
326A VAL* 2.9 18.6 + - + +
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Residues in contact with TRP 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A PRO* 2.9 35.7 + - + +
322A ASP* 1.3 78.0 - - - +
324A LEU* 1.3 88.8 + - + +
326A VAL* 3.4 9.4 + - - +
327A ALA* 3.1 32.3 + - + +
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Residues in contact with LEU 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A VAL* 4.5 5.6 - - + -
320A VAL* 4.2 25.6 - - + -
321A PRO* 2.7 28.1 + - + +
323A TRP* 1.3 103.1 - - + +
325A PHE* 1.3 64.5 + - - +
327A ALA* 3.9 4.0 - - + +
328A PHE* 3.2 61.8 + - + -
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Residues in contact with PHE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A PHE* 4.0 21.3 - + - -
309A VAL* 3.6 28.7 - - + -
310A ASN* 3.5 26.5 - - - -
313A ASN* 2.7 40.2 - - + -
320A VAL* 4.2 12.8 - - + +
321A PRO 3.5 3.1 + - - -
322A ASP* 2.7 23.2 + - - +
324A LEU* 1.3 78.1 - - - +
326A VAL* 1.3 64.0 + - + +
328A PHE* 3.5 1.9 + - - -
329A ASN* 2.9 27.4 + - + +
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Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A VAL* 4.3 24.2 - - + -
322A ASP* 2.9 18.3 + - + +
323A TRP* 3.9 9.9 - - - +
324A LEU 3.4 0.2 - - - -
325A PHE* 1.3 79.1 - - + +
327A ALA* 1.3 63.1 + - - +
329A ASN* 3.4 3.7 + - - +
330A TRP* 2.8 53.8 + - + +
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A TRP* 3.1 29.5 + - + +
324A LEU* 4.0 9.2 - - + +
325A PHE 3.2 0.2 - - - -
326A VAL* 1.3 79.7 - - - +
328A PHE* 1.3 60.8 + - + +
330A TRP* 3.1 7.5 + - - +
331A LEU* 2.9 27.8 + - - +
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Residues in contact with PHE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A CYS 4.1 2.1 - - - +
305A PRO* 3.5 34.3 - - + -
306A PHE* 3.8 25.6 + - + +
309A VAL* 3.5 34.3 - - + -
324A LEU* 3.2 45.5 + - + +
325A PHE* 4.1 3.1 - - - +
327A ALA* 1.3 80.3 - - + +
329A ASN* 1.3 62.1 + - - +
331A LEU* 3.3 15.0 + - + +
332A GLY* 3.2 17.0 + - - -
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Residues in contact with ASN 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A TRP* 3.7 13.5 - - - -
306A PHE* 3.5 22.5 - - + -
325A PHE* 2.9 19.2 + - + +
326A VAL* 3.7 6.1 - - - +
328A PHE* 1.3 76.3 - - - +
330A TRP* 1.3 61.7 + - + +
332A GLY* 3.5 2.8 + - - -
333A TYR* 3.2 34.3 + - - -
400A P32 2.9 54.7 + - - +
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Residues in contact with TRP 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A MET* 4.3 30.1 - - + +
51A VAL* 5.1 8.5 - - + -
95A VAL* 4.0 27.6 - - + -
98A GLY* 3.9 11.0 - - - -
99A ALA* 3.8 24.7 - - + -
102A VAL* 3.6 27.6 - - + +
326A VAL* 2.8 50.7 + - + +
327A ALA* 3.1 4.9 + - - +
329A ASN* 1.3 77.7 - - + +
331A LEU* 1.3 66.5 + - - +
332A GLY 3.2 0.2 - - - -
333A TYR* 3.7 32.7 - + + +
334A ALA* 2.9 24.6 + - - +
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Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A LEU 3.8 20.2 - - - +
302A CYS* 3.5 28.0 - - - +
305A PRO* 3.9 17.5 - - + -
327A ALA 2.9 13.3 + - - +
328A PHE* 3.4 19.3 - - + +
329A ASN 3.3 0.2 - - - -
330A TRP* 1.3 77.7 - - - +
332A GLY* 1.3 60.6 + - - +
334A ALA* 3.2 16.8 + - + +
335A ASN 3.4 8.1 + - - -
338A MET* 5.1 6.5 - - + -
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Residues in contact with GLY 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A CYS* 3.1 20.9 + - - -
303A TRP* 3.3 35.8 + - - -
328A PHE 3.2 5.7 + - - -
329A ASN 3.5 3.1 + - - -
330A TRP 3.2 0.4 - - - -
331A LEU* 1.3 76.6 - - - +
333A TYR* 1.3 64.1 + - - +
335A ASN* 3.1 18.5 - - - +
336A SER* 4.2 1.2 + - - -
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Residues in contact with TYR 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 5.4 1.3 - - + -
55A ILE* 3.8 6.4 - - + +
90A VAL* 4.1 17.9 - - + +
94A VAL* 3.5 24.8 - - + +
95A VAL* 3.7 24.0 - - + -
98A GLY* 5.8 0.9 - - - -
117A TRP* 4.3 8.3 - + - -
121A ASP* 2.5 28.7 + - - -
303A TRP* 4.4 9.0 - + - -
329A ASN* 3.2 31.1 + - - -
330A TRP* 3.2 46.6 + + + +
332A GLY* 1.3 76.0 - - - +
334A ALA* 1.3 66.1 + - - +
336A SER* 2.8 24.1 + - - -
400A P32 3.8 23.4 + - - +
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Residues in contact with ALA 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 4.4 24.0 - - + -
48A MET* 4.5 10.1 - - + -
51A VAL* 4.3 14.3 - - + +
330A TRP 2.9 13.7 + - - +
331A LEU* 3.2 14.8 + - + +
333A TYR* 1.3 76.6 - - - +
335A ASN* 1.3 56.0 - - - +
337A ALA* 2.9 26.9 + - - +
338A MET* 3.6 18.6 + - + +
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Residues in contact with ASN 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ASP* 5.1 5.1 + - - -
295A ILE 5.2 0.3 - - - +
298A VAL* 3.4 13.5 - - - +
299A PHE* 3.2 49.9 + - - +
302A CYS* 3.7 16.4 - - + -
303A TRP* 4.4 3.6 - - - +
331A LEU 3.4 3.8 + - - -
332A GLY 3.1 18.1 + - - +
334A ALA* 1.3 77.4 - - - +
336A SER* 1.3 61.9 + - - +
337A ALA 3.0 1.4 + - - -
338A MET* 3.3 20.2 + - - +
339A ASN* 3.7 20.1 + - - +
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Residues in contact with SER 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ILE* 3.4 26.1 - - - +
59A ASN* 2.9 28.4 + - - -
87A ASP* 2.8 35.3 + - - +
90A VAL* 3.6 22.6 - - - +
332A GLY 5.1 0.9 + - - -
333A TYR* 2.8 18.4 + - - -
335A ASN* 1.3 73.5 + - - +
337A ALA* 1.3 56.3 + - - +
339A ASN 4.9 1.1 - - - -
340A PRO* 4.4 1.7 - - - +
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 5.6 3.4 - - + -
51A VAL* 4.5 8.5 - - + -
54A LEU* 3.8 33.4 - - + +
55A ILE* 3.5 22.8 - - + +
334A ALA 2.9 11.4 + - - +
336A SER* 1.3 80.3 - - - +
338A MET* 1.3 62.9 + - + +
339A ASN 3.6 0.7 - - - -
340A PRO* 3.6 10.6 - - - +
341A ILE* 3.9 16.8 - - - +
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Residues in contact with MET 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 5.9 4.7 - - + -
298A VAL* 3.1 36.1 - - + -
302A CYS* 3.7 24.2 - - - -
331A LEU* 5.1 5.8 - - + -
334A ALA* 4.1 18.8 - - + +
335A ASN* 3.3 14.1 + - - +
337A ALA* 1.3 79.3 - - - +
339A ASN* 1.3 68.7 + - - +
341A ILE* 3.1 16.7 + - + +
342A ILE* 3.0 28.5 + - + +
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Residues in contact with ASN 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASN* 5.2 2.5 - - - +
83A LEU* 4.3 15.4 - - - +
87A ASP* 4.6 12.9 + - - +
295A ILE* 3.0 48.2 - - + +
298A VAL* 6.0 1.2 - - - +
335A ASN* 3.7 22.5 + - - +
337A ALA 3.6 0.2 - - - -
338A MET* 1.3 75.3 - - - +
340A PRO* 1.3 74.4 - - + +
342A ILE* 2.9 14.7 + - - +
343A TYR* 3.0 37.0 + - + +
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Residues in contact with PRO 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU 4.8 1.3 - - - +
58A GLY* 3.4 43.5 - - - +
59A ASN* 3.9 20.2 - - - +
62A VAL* 3.9 8.1 - - + -
336A SER 4.4 0.9 - - - +
337A ALA 3.6 14.1 - - - +
338A MET 3.5 3.8 - - - -
339A ASN* 1.3 93.8 - - + +
341A ILE* 1.3 63.7 + - + +
343A TYR* 3.2 21.9 + - + +
344A CYS* 3.5 16.0 + - - -
353A PHE* 4.1 5.8 - - + -
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Residues in contact with ILE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 6.5 0.4 - - + -
54A LEU* 5.6 14.8 - - + -
337A ALA 3.9 17.0 - - - +
338A MET* 3.1 15.6 + - + +
340A PRO* 1.3 78.0 - - + +
342A ILE* 1.3 69.4 + - + +
344A CYS* 2.9 26.4 + - - +
345A ARG* 4.2 1.0 + - - +
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Residues in contact with ILE 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A THR* 3.8 21.5 - - + +
294A ILE* 3.5 37.5 - - + -
295A ILE* 3.7 25.4 - - + -
298A VAL* 3.9 19.5 - - + -
338A MET* 3.0 22.7 + - + +
339A ASN* 2.9 12.4 + - - +
341A ILE* 1.3 76.6 - - + +
343A TYR* 1.3 58.8 + - - +
344A CYS 3.1 0.2 - - - -
345A ARG* 3.1 33.2 + - - +
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Residues in contact with TYR 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASN* 6.0 0.4 - - - -
62A VAL* 3.6 33.7 - - + -
80A ILE* 3.4 47.3 + - + +
83A LEU* 4.9 2.9 - - - +
291A THR* 4.0 19.5 - - + -
292A LEU* 5.8 1.3 - - + -
295A ILE* 3.9 21.8 - - + +
339A ASN* 3.0 45.5 + - + +
340A PRO* 3.7 5.6 - - + +
341A ILE 3.1 0.6 + - - -
342A ILE* 1.3 71.6 - - - +
344A CYS* 1.3 55.4 + - - +
345A ARG 3.0 5.6 - - - -
346A SER* 3.0 22.1 + - - +
349A PHE* 3.4 46.5 - + + +
353A PHE* 4.6 1.1 - - + -
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Residues in contact with CYS 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A PRO 3.6 10.5 - - - -
341A ILE* 2.9 15.7 + - - +
343A TYR* 1.3 77.9 - - - +
345A ARG* 1.3 61.4 + - - +
346A SER 3.1 4.1 - - - +
350A ARG* 3.0 40.0 + - + -
353A PHE* 3.5 32.5 - - - -
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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