Contacts of the helix formed by residues 310 - 335 (chain A) in PDB entry 3DVA
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 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A GLU* 4.6 4.3 - - - -
309A TRP* 1.3 91.2 + - - +
311A GLU* 1.3 71.2 + - - +
312A GLU* 4.0 10.1 + - - +
313A GLU* 3.1 26.4 + - - +
314A GLU 3.1 17.7 + - - -
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU* 4.5 10.8 + - - +
310A SER* 1.3 79.9 - - - +
312A GLU* 1.3 73.2 + - - +
314A GLU* 3.8 10.8 - - + +
315A ASN* 3.0 40.7 + - - +
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Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A SER* 3.1 9.1 - - - +
311A GLU* 1.3 89.8 - - + +
313A GLU* 1.3 66.3 + - - +
315A ASN* 3.3 14.0 + - - +
316A ASN* 3.1 33.4 + - - +
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS* 2.5 39.8 + - - +
51A ARG* 4.7 13.1 + - - +
308A LEU 3.5 8.3 - - - +
309A TRP* 3.5 35.3 - - + -
310A SER* 3.1 20.8 + - - +
312A GLU* 1.3 81.0 - - - +
314A GLU* 1.3 60.6 + - - +
316A ASN* 3.5 12.1 + - - +
317A VAL* 3.3 24.9 + - - +
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Residues in contact with GLU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET* 4.1 0.4 - - - +
54A VAL* 3.9 27.0 - - + +
296A LEU* 5.5 0.5 - - - +
300A ARG* 2.7 47.1 + - - -
309A TRP* 2.9 34.0 + - + +
310A SER 3.1 9.3 + - - +
311A GLU* 3.8 10.3 - - - +
312A GLU 3.2 0.2 - - - -
313A GLU* 1.3 77.1 - - - +
315A ASN* 1.3 65.9 + - - +
317A VAL* 3.2 5.8 + - - +
318A ILE* 3.1 34.5 + - + +
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Residues in contact with ASN 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A GLU* 3.0 33.4 + - - +
312A GLU* 3.6 18.6 + - - +
314A GLU* 1.3 78.8 - - - +
316A ASN* 1.3 59.3 + - - +
318A ILE* 3.2 17.2 + - - +
319A GLU* 2.9 34.7 + - + +
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Residues in contact with ASN 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 4.9 11.2 + - - +
312A GLU* 3.1 20.8 + - - +
313A GLU* 3.6 12.2 - - - +
314A GLU 3.2 0.2 - - - -
315A ASN* 1.3 78.0 - - - +
317A VAL* 1.3 57.7 + - - +
319A GLU* 3.4 8.0 + - - +
320A GLN* 3.0 28.9 + - - +
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Residues in contact with VAL 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 3.4 65.5 - - + +
54A VAL* 4.1 9.9 - - + -
55A TYR* 4.0 20.7 - - + +
309A TRP* 4.1 12.8 - - + -
313A GLU 3.3 15.7 - - - +
314A GLU* 3.2 9.1 + - - +
316A ASN* 1.3 74.7 - - - +
318A ILE* 1.3 59.7 + - - +
320A GLN* 3.2 8.4 + - + +
321A ALA* 2.9 27.7 + - - +
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Residues in contact with ILE 318 (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 VAL* 3.9 14.4 - - + -
58A ILE* 3.6 39.7 - - + -
314A GLU* 3.1 23.2 + - + +
315A ASN* 3.2 21.5 + - - +
317A VAL* 1.3 77.2 - - - +
319A GLU* 1.3 58.2 + - + +
321A ALA* 3.3 2.6 + - - +
322A LYS* 3.0 50.0 + - - +
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Residues in contact with GLU 319 (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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315A ASN* 2.9 21.0 + - + +
316A ASN* 3.7 8.1 - - - +
318A ILE* 1.3 75.5 - - + +
320A GLN* 1.3 65.3 + - - +
322A LYS* 3.5 17.3 + - - +
323A GLU* 3.1 35.1 + - + +
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Residues in contact with GLN 320 (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 ARG* 2.9 35.2 + - - +
55A TYR* 4.7 9.3 - - + -
316A ASN 3.0 15.9 + - - +
317A VAL* 3.5 7.1 - - - +
319A GLU* 1.3 76.2 - - - +
321A ALA* 1.3 62.0 + - - +
323A GLU* 4.0 3.6 - - - +
324A GLU* 3.1 55.3 + - + +
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Residues in contact with ALA 321 (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 TYR* 3.5 35.8 - - + +
58A ILE* 3.8 24.9 - - + -
317A VAL 2.9 16.8 + - - +
318A ILE* 3.5 5.6 - - - +
319A GLU 3.2 0.2 - - - -
320A GLN* 1.3 76.7 - - - +
322A LYS* 1.3 53.8 + - - +
324A GLU* 3.3 2.4 + - - +
325A ILE* 2.8 43.0 + - + +
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Residues in contact with LYS 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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58A ILE* 4.2 16.6 - - + -
61A GLN* 5.7 2.2 - - - -
62A ARG* 4.9 17.3 + - - +
318A ILE* 3.0 42.2 + - + +
319A GLU* 4.0 18.9 + - - +
321A ALA* 1.3 75.3 - - - +
323A GLU* 1.3 61.4 + - - +
325A ILE* 3.2 8.9 + - - +
326A LYS* 3.0 32.5 + - + +
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Residues in contact with GLU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLU* 3.1 26.7 + - - +
320A GLN* 4.0 5.2 - - - +
322A LYS* 1.3 75.1 - - + +
324A GLU* 1.3 65.5 + - + +
326A LYS* 3.3 25.0 + - - +
327A GLU* 3.2 24.7 + - - +
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Residues in contact with GLU 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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55A TYR* 2.6 36.1 + - - +
115A LEU* 3.8 5.8 - - + +
320A GLN* 3.1 47.2 + - + +
321A ALA 3.8 0.2 - - - +
323A GLU* 1.3 81.5 - - + +
325A ILE* 1.3 62.3 + - - +
327A GLU* 3.3 23.4 - - - +
328A ALA* 3.1 24.8 + - - +
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Residues in contact with ILE 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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55A TYR* 4.9 2.7 - - + +
58A ILE* 4.1 6.1 - - + +
59A LEU* 3.9 27.6 - - + -
62A ARG* 3.7 48.2 - - + +
66A LEU* 4.3 11.0 - - + -
115A LEU* 4.0 20.2 - - + -
119A PHE* 3.7 17.4 - - + -
321A ALA* 2.8 32.7 + - + +
322A LYS* 3.6 5.6 - - - +
323A GLU 3.2 0.4 - - - -
324A GLU* 1.3 78.3 - - - +
326A LYS* 1.3 56.9 + - + +
328A ALA* 3.5 0.4 + - - -
329A ILE* 3.1 26.7 + - - +
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Residues in contact with LYS 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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62A ARG* 4.7 18.4 - - - +
71A ARG* 6.0 4.5 - - - +
322A LYS* 3.0 21.0 + - + +
323A GLU* 3.3 25.6 + - - +
325A ILE* 1.3 76.6 - - + +
327A GLU* 1.3 59.6 + - - +
329A ILE* 3.2 12.3 - - + +
330A LYS* 3.0 30.1 + - - +
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Residues in contact with GLU 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 GLU* 3.2 11.7 + - - +
324A GLU* 3.3 35.8 - - - +
326A LYS* 1.3 77.2 - - - +
328A ALA* 1.3 58.8 + - - +
330A LYS* 3.7 11.0 - - + +
331A LYS* 2.9 29.0 + - - +
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Residues in contact with ALA 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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115A LEU* 3.7 9.9 - - + -
116A TYR* 3.2 34.8 - - - +
119A PHE* 3.5 21.5 - - + -
324A GLU 3.1 18.3 + - - +
325A ILE 3.8 0.2 - - - +
327A GLU* 1.3 75.7 - - + +
329A ILE* 1.3 60.5 + - - +
330A LYS 3.1 1.3 - - - -
331A LYS* 3.2 2.0 + - - -
332A ALA* 2.9 26.9 + - - +
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Residues in contact with ILE 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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66A LEU* 3.8 28.0 - - + -
71A ARG* 3.4 50.0 - - - +
72A LEU* 5.0 2.2 - - + -
119A PHE* 3.7 14.1 - - + -
123A ARG* 2.9 33.9 - - - +
325A ILE* 3.1 17.0 + - + +
326A LYS* 3.2 20.6 - - + +
328A ALA* 1.3 77.6 - - - +
330A LYS* 1.3 60.5 + - - +
332A ALA* 3.5 4.4 + - - +
333A ASP* 3.1 23.1 + - - +
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Residues in contact with LYS 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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71A ARG* 5.3 2.2 - - - +
326A LYS 3.0 18.6 + - - +
327A GLU* 3.7 10.5 - - + +
328A ALA 3.1 0.2 - - - -
329A ILE* 1.3 78.8 - - + +
331A LYS* 1.3 63.7 + - - +
333A ASP* 3.2 18.3 + - + +
334A GLU* 3.2 40.3 + - + +
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Residues in contact with LYS 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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116A TYR* 3.7 48.6 + - + -
327A GLU 2.9 19.5 + - - +
328A ALA* 3.2 5.8 + - - +
330A LYS* 1.3 77.3 - - - +
332A ALA* 1.3 61.3 + - - +
334A GLU* 3.4 21.7 + - - +
335A THR* 3.3 18.9 + - + +
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Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TYR* 4.1 14.5 - - - +
119A PHE* 4.4 7.4 - - + -
120A LEU* 3.8 25.3 - - + +
123A ARG* 3.8 15.0 + - - +
328A ALA 2.9 16.9 + - - +
329A ILE* 3.6 10.1 - - - +
330A LYS 3.1 0.2 - - - -
331A LYS* 1.3 74.9 - - - +
333A ASP* 1.3 63.9 + - - +
335A THR* 2.6 28.1 + - - +
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Residues in contact with ASP 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG* 3.8 19.4 + - - -
123A ARG* 2.5 46.3 + - - +
329A ILE* 3.1 13.0 + - - +
330A LYS* 3.2 10.9 + - + +
332A ALA* 1.3 77.1 - - - +
334A GLU* 1.3 62.3 + - + +
335A THR 3.5 6.2 + - - +
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Residues in contact with GLU 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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330A LYS* 3.2 40.6 + - + +
331A LYS* 3.8 18.0 - - + +
332A ALA 3.2 1.0 - - - -
333A ASP* 1.3 77.7 - - + +
335A THR* 1.3 63.2 + - - +
336A PRO* 3.3 7.3 - - - +
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Residues in contact with THR 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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116A TYR* 4.1 12.6 - - + -
120A LEU* 3.4 34.3 - - + +
125A HIS* 4.3 13.9 + - - -
127A HIS* 4.4 7.2 - - + -
331A LYS 3.3 17.5 + - - +
332A ALA* 2.6 19.0 + - - +
333A ASP 3.8 6.9 - - - +
334A GLU* 1.3 76.5 - - - +
336A PRO* 1.3 75.9 - - + +
337A LYS* 3.6 2.3 + - - +
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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