Contacts of the helix formed by residues 311 - 336 (chain A) in PDB entry 1UMD
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 ASN 311 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ARG* 5.7 2.6 - - - +
308A GLY 6.0 0.2 + - - -
310A TRP* 1.3 96.9 - - - +
312A GLU* 1.3 62.2 + - - +
313A GLU* 3.3 10.9 + - + +
314A TRP* 2.7 40.0 + - - +
315A GLU 3.1 15.2 + - - -
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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 TRP* 3.5 26.8 - - + -
311A ASN* 1.3 73.4 - - - +
313A GLU* 1.3 62.6 + - - +
315A GLU* 3.2 16.0 + - - +
316A GLU* 2.9 44.2 + - - +
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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
----------------------------------------------------------
311A ASN* 3.3 9.7 + - - +
312A GLU* 1.3 78.8 - - - +
314A TRP* 1.3 64.5 + - - +
316A GLU* 3.3 10.8 + - - +
317A ASP* 3.0 41.4 + - - +
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Residues in contact with TRP 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG* 3.1 84.7 - - + +
42A TYR* 3.6 28.9 - + - -
43A ARG* 4.8 6.7 - - + -
304A LEU* 4.4 2.5 - - + -
309A LEU 4.2 4.3 - - - -
310A TRP* 3.6 25.1 - + - -
311A ASN* 2.7 26.6 + - - +
313A GLU* 1.3 70.8 - - - +
315A GLU* 1.3 66.6 + - - +
317A ASP* 3.1 11.9 + - + +
318A VAL* 2.8 53.2 + - + +
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Residues in contact with GLU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 2.6 32.2 + - - -
46A LEU* 4.0 4.7 - - - +
301A ARG* 5.1 1.8 - - - -
310A TRP* 2.8 27.6 + - + +
311A ASN 3.1 13.9 + - - +
312A GLU* 3.2 21.8 - - - +
314A TRP* 1.3 79.6 - - - +
316A GLU* 1.3 64.6 + - + +
318A VAL* 3.4 5.2 + - - +
319A ARG* 2.7 65.1 + - - +
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Residues in contact with GLU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 2.9 36.5 + - - +
313A GLU* 3.7 10.6 - - - +
314A TRP 3.2 0.2 - - - -
315A GLU* 1.3 78.3 - - + +
317A ASP* 1.3 66.9 + - - +
319A ARG* 3.3 8.1 + - - +
320A GLU* 3.0 25.9 + - - +
323A ARG* 4.9 1.0 + - - -
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Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A GLU* 3.0 29.5 + - - +
314A TRP* 3.5 15.9 - - + +
316A GLU* 1.3 78.8 - - - +
318A VAL* 1.3 61.9 + - - +
320A GLU* 3.4 4.9 + - - +
321A GLU* 2.9 38.9 + - + +
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Residues in contact with VAL 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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42A TYR* 6.2 0.2 - - + -
43A ARG* 3.5 30.3 - - + +
46A LEU* 4.0 16.4 - - + -
314A TRP* 2.8 63.4 + - + +
315A GLU* 3.7 5.2 - - - +
317A ASP* 1.3 71.5 - - - +
319A ARG* 1.3 57.4 + - - +
321A GLU* 3.2 16.1 + - - +
322A ILE* 3.0 48.6 + - + +
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Residues in contact with ARG 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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46A LEU* 3.4 30.8 - - + +
49A ARG* 6.1 3.2 - - - +
50A MET* 3.6 42.0 - - + +
53A GLU* 5.5 1.8 + - - -
297A ILE* 5.0 5.1 - - - +
315A GLU* 2.7 51.0 + - - +
316A GLU* 3.3 8.0 + - - +
318A VAL* 1.3 76.2 - - - +
320A GLU* 1.3 56.3 + - - +
322A ILE* 3.3 1.2 + - - -
323A ARG* 3.0 48.8 + - - +
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Residues in contact with GLU 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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316A GLU 3.0 17.8 + - - +
317A ASP* 3.9 5.6 - - - +
319A ARG* 1.3 75.8 - - - +
321A GLU* 1.3 63.5 + - + +
323A ARG* 3.2 37.8 + - - +
324A ALA* 3.1 24.7 + - + +
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Residues in contact with GLU 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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43A ARG* 3.5 21.2 + - - +
317A ASP* 2.9 28.1 + - + +
318A VAL* 3.5 18.0 - - - +
319A ARG 3.2 0.2 - - - -
320A GLU* 1.3 79.5 - - + +
322A ILE* 1.3 55.7 + - - +
324A ALA* 3.4 6.8 + - - +
325A GLU* 2.8 35.6 + - - +
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Residues in contact with ILE 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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43A ARG* 3.7 23.1 - - - +
46A LEU* 3.9 10.3 - - + -
47A ALA* 3.6 42.6 - - + +
50A MET* 3.7 28.5 - - + -
318A VAL* 3.0 39.5 + - + +
319A ARG* 3.6 4.3 - - - +
321A GLU* 1.3 75.2 - - - +
323A ARG* 1.3 63.0 + - - +
325A GLU* 3.0 11.8 + - - +
326A LEU* 2.9 35.0 + - + +
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Residues in contact with ARG 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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50A MET* 4.0 15.3 - - + +
316A GLU 4.9 1.0 + - - -
319A ARG* 3.0 32.5 + - - +
320A GLU* 3.2 62.7 + - - +
322A ILE* 1.3 76.3 - - - +
324A ALA* 1.3 56.3 + - - +
326A LEU* 3.6 13.6 - - + +
327A GLU* 3.0 36.8 + - + +
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Residues in contact with ALA 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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320A GLU* 3.1 25.2 + - + +
321A GLU* 3.5 8.1 - - - +
322A ILE 3.1 0.4 - - - -
323A ARG* 1.3 76.7 - - - +
325A GLU* 1.3 59.6 + - + +
327A GLU* 3.3 7.1 + - - +
328A ARG* 2.9 30.9 + - - +
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Residues in contact with GLU 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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43A ARG* 3.2 38.3 + - - -
47A ALA* 5.5 1.7 - - - +
108A LEU* 3.4 21.8 - - + +
321A GLU* 2.8 23.6 - - - +
322A ILE* 3.0 13.1 + - - +
324A ALA* 1.3 78.8 - - + +
326A LEU* 1.3 57.2 + - - +
328A ARG* 3.4 5.0 + - - +
329A GLY* 2.8 24.8 + - - -
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Residues in contact with LEU 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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47A ALA 5.4 0.7 - - - +
50A MET* 3.8 37.5 - - + +
51A LEU* 3.9 33.2 - - + -
54A ARG* 3.3 29.3 + - + +
102A LEU* 5.8 1.3 - - + -
108A LEU* 3.9 18.8 - - + -
112A LEU* 4.2 6.6 - - + +
322A ILE* 2.9 24.0 + - + +
323A ARG* 3.6 13.5 - - + +
325A GLU* 1.3 77.9 - - - +
327A GLU* 1.3 57.3 + - - +
329A GLY* 3.3 0.7 + - - -
330A LEU* 2.9 31.7 + - - +
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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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54A ARG* 2.5 33.6 + - - +
323A ARG* 3.0 24.6 + - + +
324A ALA* 3.3 6.5 + - - +
326A LEU* 1.3 74.7 - - - +
328A ARG* 1.3 57.8 + - - +
330A LEU* 3.9 9.5 - - - +
331A LYS* 3.0 28.6 + - - +
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Residues in contact with ARG 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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324A ALA 2.9 17.2 + - - +
325A GLU* 3.8 6.3 - - - +
327A GLU* 1.3 77.3 - - - +
329A GLY* 1.3 64.0 + - - +
331A LYS* 3.3 34.9 + - - +
332A GLU* 3.0 65.6 + - - +
335A GLU* 4.5 10.1 + - - -
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Residues in contact with GLY 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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108A LEU* 4.1 17.9 - - - -
109A LYS* 3.8 7.0 - - - -
112A LEU* 3.6 6.1 - - - -
325A GLU 2.8 17.6 + - - -
326A LEU 3.3 1.3 + - - -
328A ARG* 1.3 78.2 - - - +
330A LEU* 1.3 56.5 + - - +
332A GLU* 3.4 13.4 + - - +
333A ALA* 3.0 28.9 + - - +
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Residues in contact with LEU 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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54A ARG* 4.4 22.4 - - - +
58A LEU* 4.0 28.3 - - + -
63A LYS* 5.3 4.7 - - - +
112A LEU* 3.3 19.8 - - + +
116A LEU* 3.9 26.7 - - + -
326A LEU 2.9 18.3 + - - +
327A GLU* 3.9 8.7 - - - +
329A GLY* 1.3 72.2 - - - +
331A LYS* 1.3 66.9 + - - +
333A ALA* 3.3 1.8 + - - +
334A GLU* 2.9 47.8 + - + +
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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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327A GLU 3.0 18.6 + - - +
328A ARG* 3.6 30.0 - - - +
330A LEU* 1.3 78.5 - - - +
332A GLU* 1.3 58.4 + - - +
334A GLU* 3.3 9.9 + - - +
335A GLU* 2.9 44.7 + - + +
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Residues in contact with GLU 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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109A LYS* 3.7 41.3 + - + +
120A ALA* 4.4 1.2 - - - +
328A ARG* 3.0 60.5 + - - +
329A GLY* 3.7 13.3 - - - +
331A LYS* 1.3 75.4 - - - +
333A ALA* 1.3 63.6 + - - +
335A GLU* 3.0 29.0 - - - +
336A ALA* 3.3 11.1 + - - +
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Residues in contact with ALA 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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109A LYS* 3.8 5.3 - - - +
112A LEU* 3.8 11.4 - - + +
113A GLY* 3.7 29.6 - - - +
116A LEU* 4.4 5.8 - - + -
118A THR* 2.7 24.6 + - - -
120A ALA* 3.7 11.7 - - - -
329A GLY 3.0 17.7 + - - +
330A LEU 3.3 5.6 + - - +
332A GLU* 1.3 76.7 - - - +
334A GLU* 1.3 62.2 + - - +
336A ALA* 3.3 9.9 - - - +
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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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63A LYS* 2.8 41.7 + - - +
116A LEU* 3.7 17.2 - - + +
118A THR* 4.6 8.8 - - - +
330A LEU* 2.9 34.7 + - + +
331A LYS* 3.8 7.0 - - - +
333A ALA* 1.3 73.0 - - - +
335A GLU* 1.3 62.2 + - - +
336A ALA 3.1 5.8 + - - -
337A GLY* 3.3 12.5 + - - -
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Residues in contact with GLU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ARG* 4.5 9.4 + - - -
331A LYS* 2.9 36.7 + - + +
332A GLU* 3.0 33.3 - - - +
334A GLU* 1.3 75.5 - - - +
336A ALA* 1.3 62.1 + - - +
337A GLY* 3.2 2.2 + - - -
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Residues in contact with ALA 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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118A THR* 3.9 1.3 - - - +
119A LYS* 3.9 21.8 - - + +
120A ALA* 3.4 35.0 - - + +
332A GLU 3.3 8.4 + - - +
333A ALA 3.3 15.3 - - - +
334A GLU 3.1 0.6 - - - -
335A GLU* 1.3 79.1 - - - +
337A GLY* 1.3 60.7 + - - +
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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