Contacts of the helix formed by residues 343 - 363 (chain A) in PDB entry 1U5U
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 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A VAL* 6.4 2.0 - - - -
197A THR* 4.5 5.0 - - - +
287A PHE* 3.6 36.1 - - - +
334A LEU* 3.3 43.2 - - + +
335A GLU 3.6 24.7 + - - +
336A ALA* 3.6 8.3 - - - +
341A ASP* 2.8 18.6 + - - +
342A TYR* 1.3 74.5 - - - +
344A SER* 1.3 63.1 + - - +
345A ILE 3.3 2.3 + - - -
346A GLY* 3.4 12.0 + - - +
347A GLU 3.7 5.5 + - - -
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Residues in contact with SER 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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42A LEU* 4.2 7.8 - - - +
146A ASN* 3.3 13.5 - - - -
147A SER 3.5 3.0 + - - -
336A ALA* 3.5 13.4 - - - +
338A SER 3.5 18.6 - - - -
339A PRO* 3.3 19.1 + - - -
341A ASP 2.7 21.3 + - - -
343A ASN* 1.3 76.0 - - - +
345A ILE* 1.3 68.3 + - - +
347A GLU* 3.1 4.7 + - - +
348A LEU* 2.9 28.6 + - - +
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Residues in contact with ILE 345 (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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144A PHE* 3.8 26.5 - - + +
145A TRP* 3.5 29.2 - - - +
146A ASN* 3.6 28.7 - - - +
150A LEU* 4.5 2.5 - - + -
196A VAL* 4.6 7.2 - - + -
289A ALA* 6.1 2.7 - - + -
342A TYR 4.3 4.7 - - - +
343A ASN 3.3 0.6 - - - -
344A SER* 1.3 75.8 + - - +
346A GLY* 1.3 63.6 + - - +
348A LEU* 3.2 13.0 + - + +
349A ARG* 2.9 46.6 + - - +
999A HEM 4.0 27.4 - - + -
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Residues in contact with GLY 346 (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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196A VAL* 4.7 15.2 - - - +
324A ILE* 3.8 18.5 - - - +
333A LEU* 5.0 10.1 - - - -
334A LEU 5.6 2.9 - - - -
343A ASN* 3.4 8.1 + - - +
344A SER 3.3 1.0 - - - -
345A ILE* 1.3 80.2 - - - +
347A GLU* 1.3 61.6 + - - +
349A ARG* 3.4 3.7 + - - +
350A VAL* 3.2 25.7 + - - +
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Residues in contact with GLU 347 (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 LEU* 3.8 8.1 - - + +
46A LYS* 2.6 41.9 + - - +
333A LEU* 5.9 2.0 - - + -
334A LEU 4.1 13.2 + - - +
335A GLU* 3.3 11.4 - - - +
336A ALA* 2.7 40.1 + - + +
343A ASN 3.7 2.9 + - - +
344A SER 3.1 8.5 + - - +
346A GLY* 1.3 73.2 - - - +
348A LEU* 1.3 65.4 + - - +
350A VAL* 3.3 8.6 + - - +
351A ALA* 3.0 23.6 + - - +
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Residues in contact with LEU 348 (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 LEU* 4.3 12.1 - - + -
45A LYS* 4.2 3.6 - - + -
46A LYS* 3.8 37.2 - - + +
49A PHE* 4.1 14.8 - - + -
147A SER* 4.4 19.5 - - - -
150A LEU* 4.3 16.2 - - + -
344A SER* 2.9 28.2 + - - +
345A ILE* 3.6 20.4 - - + +
347A GLU* 1.3 75.4 - - - +
349A ARG* 1.3 58.7 + - - +
351A ALA* 3.3 4.0 + - - +
352A VAL* 2.9 36.2 + - + +
999A HEM 4.2 12.8 - - + -
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Residues in contact with ARG 349 (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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135A VAL* 3.4 30.3 + - - +
194A SER 4.5 1.4 + - - -
196A VAL* 3.6 21.2 - - - +
198A MET* 5.3 1.0 - - - +
323A ASN* 5.2 0.9 - - - -
324A ILE* 3.8 33.7 - - + +
345A ILE* 2.9 29.9 + - - +
346A GLY* 3.7 4.9 - - - +
348A LEU* 1.3 76.5 - - - +
350A VAL* 1.3 55.9 + - - +
352A VAL* 4.8 1.6 - - - -
353A TYR* 2.8 73.0 + - + +
999A HEM 3.2 67.2 - - + +
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Residues in contact with VAL 350 (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 ASN* 4.2 7.0 - - - -
324A ILE* 4.2 5.2 - - + -
325A ALA* 3.9 27.1 - - + -
333A LEU* 3.4 33.9 - - + -
346A GLY 3.2 8.6 + - - +
347A GLU* 3.6 8.5 - - - +
349A ARG* 1.3 77.7 - - - +
351A ALA* 1.3 63.3 + - - +
354A THR* 2.7 36.4 + - - +
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Residues in contact with ALA 351 (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 LYS* 3.9 34.8 - - + +
50A LYS* 3.8 15.2 - - + +
347A GLU 3.0 16.7 + - - +
348A LEU 3.7 3.6 - - - +
350A VAL* 1.3 80.9 - - - +
352A VAL* 1.3 61.4 + - + +
354A THR* 4.1 2.9 - - - -
355A TRP* 3.3 21.8 + - - +
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Residues in contact with VAL 352 (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 LYS* 4.6 2.9 - - - +
49A PHE* 3.7 21.1 - - + +
50A LYS* 3.9 17.0 - - + +
53A PHE* 3.8 21.1 - - + -
348A LEU* 2.9 23.8 + - + +
349A ARG 4.1 1.1 - - - +
351A ALA* 1.3 73.4 - - + +
353A TYR* 1.3 67.6 + - + +
355A TRP* 3.1 3.5 + - - +
356A VAL* 2.9 25.6 + - + +
999A HEM 3.7 51.8 - - + -
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Residues in contact with TYR 353 (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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135A VAL* 4.8 5.2 - - + -
322A PHE 3.3 23.8 - - - -
323A ASN* 3.6 21.8 - - - +
324A ILE 5.0 3.1 - - - -
349A ARG* 2.8 76.4 + - + +
352A VAL* 1.3 71.2 - - + +
354A THR* 1.3 63.6 + - - +
356A VAL* 3.9 7.9 - - - -
357A GLN* 2.8 40.0 + - - +
999A HEM 2.2 83.3 + + + -
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Residues in contact with THR 354 (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 ASN* 3.1 19.0 + - - +
325A ALA* 5.0 1.4 - - - +
350A VAL* 2.7 31.3 + - - +
351A ALA* 4.1 3.6 - - - -
353A TYR* 1.3 78.5 - - - +
355A TRP* 1.3 61.8 + - - +
357A GLN* 4.2 3.5 - - - +
358A HIS* 3.3 20.4 + - - +
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Residues in contact with TRP 355 (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 LYS* 3.7 37.7 - - + -
54A THR* 2.9 33.9 + - - +
351A ALA 3.3 16.0 + - - +
352A VAL 3.1 4.1 + - - +
354A THR* 1.3 80.8 - - - +
356A VAL* 1.3 65.9 + - + +
358A HIS* 3.3 23.5 + + + +
359A LEU* 3.4 13.1 + - + +
51B THR* 3.7 26.4 + - + +
52B LEU* 4.3 20.4 - - + -
55B LEU* 3.7 37.9 - - + +
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Residues in contact with VAL 356 (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 LYS 4.6 0.7 - - - +
53A PHE* 3.8 38.6 - - + +
54A THR* 3.9 13.9 - - - +
57A THR* 3.6 13.2 - - - +
352A VAL* 2.9 25.8 + - + +
353A TYR* 3.5 11.4 - - - +
355A TRP* 1.3 75.3 - - + +
357A GLN* 1.3 63.6 + - - +
359A LEU* 2.9 11.7 - - - +
360A ARG* 2.9 29.7 + - - +
999A HEM 3.8 32.5 - - + +
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Residues in contact with GLN 357 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A ALA* 3.6 28.4 - - + +
322A PHE 2.8 28.2 + - - +
323A ASN* 3.2 25.6 + - - +
353A TYR* 2.8 30.3 + - - +
354A THR* 4.2 3.6 - - - +
356A VAL* 1.3 73.4 - - + +
358A HIS* 1.3 60.3 + - - +
360A ARG* 3.3 11.0 + - - +
361A LYS* 2.9 28.6 + - - +
999A HEM 3.0 34.5 + - - +
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Residues in contact with HIS 358 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A THR 3.3 12.3 + - - +
355A TRP* 3.3 22.1 + + + +
356A VAL 3.2 0.4 - - - -
357A GLN* 1.3 78.5 - - - +
359A LEU* 1.3 64.1 + - + +
361A LYS* 3.3 11.4 + - - +
362A LEU* 3.0 60.1 + - + +
55B LEU* 5.0 13.5 - - + +
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Residues in contact with LEU 359 (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 THR* 4.4 21.5 - - + +
57A THR* 4.8 10.3 - - + -
58A THR* 5.4 0.9 - - - +
62A PHE* 3.9 32.1 - - + -
355A TRP* 3.4 11.6 + - + +
356A VAL* 2.9 21.8 - - - +
358A HIS* 1.3 81.2 - - + +
360A ARG* 1.3 58.7 + - - +
362A LEU* 3.1 8.6 + - + +
363A LYS* 3.0 24.5 + - + +
55B LEU* 2.9 36.8 - - + -
58B THR* 4.3 5.2 - - + -
59B LEU* 4.3 13.2 - - + -
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Residues in contact with ARG 360 (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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57A THR* 3.8 11.7 - - + -
62A PHE* 3.6 27.4 + - - +
63A ARG 3.6 17.7 - - - -
64A ARG* 3.7 16.4 - - - +
318A GLU* 3.0 29.7 + - - +
319A LYS* 4.2 7.6 + - - +
320A THR 3.3 21.8 + - - -
321A ALA* 4.1 10.9 - - - +
356A VAL 2.9 18.1 + - - +
357A GLN* 3.3 9.6 + - - +
359A LEU* 1.3 76.4 - - - +
361A LYS* 1.3 61.3 + - - +
363A LYS* 3.5 4.8 + - - +
364A ILE* 3.2 20.4 + - - +
367A LEU* 5.8 1.0 - - - +
999A HEM 2.7 40.5 + - - +
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Residues in contact with LYS 361 (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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128A SER* 5.3 13.0 + - - +
357A GLN 2.9 17.1 + - - +
358A HIS* 3.6 12.3 - - - +
360A ARG* 1.3 75.8 - - - +
362A LEU* 1.3 65.5 + - + +
364A ILE* 3.1 28.5 + - + +
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Residues in contact with LEU 362 (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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358A HIS* 3.0 50.4 + - + +
359A LEU* 3.1 10.7 + - - +
361A LYS* 1.3 77.2 - - + +
363A LYS* 1.3 63.8 + - - +
364A ILE* 3.7 4.2 + - - +
366A SER* 5.5 0.3 + - - -
55B LEU* 4.9 3.4 - - + -
59B LEU* 4.1 37.5 - - + -
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Residues in contact with LYS 363 (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 PHE* 3.4 65.4 - - + -
359A LEU* 3.0 18.1 + - + +
360A ARG 3.7 4.0 - - - +
361A LYS 3.1 0.6 - - - -
362A LEU* 1.3 81.2 - - + +
364A ILE* 1.3 66.4 + - - +
366A SER* 2.8 36.4 + - - -
367A LEU* 3.9 4.9 + - - +
58B THR 4.8 1.0 + - - -
59B LEU* 4.1 36.1 + - - +
61B GLY* 5.9 1.0 - - - +
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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
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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