Contacts of the helix formed by residues 380 - 403 (chain B) in PDB entry 1ULH
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 THR 380 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331B SER* 3.4 19.9 + - - +
333B GLY* 4.0 7.1 - - - -
334B ARG* 4.7 3.2 + - - +
373B TYR* 2.7 41.9 + - - +
379B LEU* 1.3 65.4 - - - +
381B GLY* 1.3 66.0 + - - +
382B GLU 3.0 2.2 - - - -
383B LEU* 3.1 4.3 + - - +
384B LYS* 3.0 41.6 + - + +
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Residues in contact with GLY 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B ASN* 5.2 4.0 - - - +
379B LEU 2.7 10.8 + - - -
380B THR* 1.3 78.5 - - - +
382B GLU* 1.3 54.9 + - - -
384B LYS* 4.1 6.6 - - - +
385B LYS* 3.1 27.5 + - - +
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Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ALA 4.1 4.3 - - - +
378B MET* 2.5 49.8 - - + +
379B LEU* 3.9 15.3 - - + +
380B THR 3.0 0.6 - - - -
381B GLY* 1.3 76.4 - - - +
383B LEU* 1.3 59.2 + - - +
385B LYS* 3.2 14.9 - - + +
386B ALA* 3.0 28.6 + - - +
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ASP* 3.0 37.2 - - - +
352B SER* 3.9 11.0 - - - -
353B PHE* 4.2 8.1 - - + +
356B LEU* 4.2 11.7 - - + +
369B ILE* 3.3 32.5 - - + -
373B TYR* 3.6 45.1 - - + +
378B MET* 3.9 12.3 - - - +
380B THR* 3.1 9.1 + - - +
382B GLU* 1.3 79.2 - - - +
384B LYS* 1.3 63.1 + - + +
386B ALA* 3.2 7.0 + - - +
387B LEU* 3.2 19.8 + - - +
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Residues in contact with LYS 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B VAL* 3.0 40.6 + - + +
326B ASN* 3.1 35.4 + - - +
327B LYS 5.0 1.0 + - - -
329B ALA 3.0 23.4 + - - +
331B SER* 4.4 14.0 - - - +
350B ASP* 5.1 0.9 - - - -
352B SER* 3.6 21.1 - - - +
380B THR* 3.0 37.0 + - + +
381B GLY* 4.2 4.3 - - - +
383B LEU* 1.3 75.4 - - + +
385B LYS* 1.3 61.1 + - - +
387B LEU* 3.2 3.2 + - - +
388B ILE* 2.9 35.8 + - - +
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Residues in contact with LYS 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ASN* 5.2 0.2 + - - -
381B GLY 3.1 22.6 + - - +
382B GLU* 3.2 15.3 - - + +
384B LYS* 1.3 77.5 - - - +
386B ALA* 1.3 61.3 + - - +
388B ILE* 3.4 13.1 + - - +
389B GLU* 3.2 35.4 + - + +
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Residues in contact with ALA 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B LEU* 4.5 7.0 - - + -
360B LEU* 6.1 2.0 - - + -
365B LYS* 6.0 4.0 - - - +
369B ILE* 4.7 20.2 - - + -
378B MET* 4.8 5.2 - - + -
382B GLU 3.0 12.3 + - - +
383B LEU* 3.3 12.1 - - - +
384B LYS 3.1 0.2 - - - -
385B LYS* 1.3 74.3 - - - +
387B LEU* 1.3 57.4 + - - +
389B GLU* 2.7 40.5 + - - +
390B VAL* 3.4 9.6 + - - +
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B VAL* 4.1 12.6 - - + -
329B ALA* 6.0 0.7 - - + -
352B SER* 3.5 35.0 - - - +
355B TYR* 3.5 41.3 - - + -
356B LEU* 3.7 30.6 - - + +
383B LEU 3.2 9.2 + - - +
384B LYS* 3.2 8.7 + - - +
386B ALA* 1.3 78.1 - - - +
388B ILE* 1.3 58.3 + - - +
390B VAL* 3.0 16.0 - - + +
391B LEU* 3.0 44.5 + - + +
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Residues in contact with ILE 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ILE* 5.0 2.0 - - + -
322B LYS* 3.8 30.7 - - + +
325B VAL* 3.8 25.8 - - + -
326B ASN* 3.8 35.0 - - - +
384B LYS 2.9 24.6 + - - +
385B LYS* 3.7 10.3 - - - +
386B ALA 3.1 0.4 - - - -
387B LEU* 1.3 76.9 - - - +
389B GLU* 1.3 58.5 + - + +
390B VAL 3.3 0.2 - - - -
391B LEU* 4.2 3.6 - - - +
392B GLN* 2.9 63.1 + - + +
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Residues in contact with GLU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B LYS* 5.8 1.7 + - - -
385B LYS* 3.2 27.6 - - + +
386B ALA* 2.7 17.4 + - - +
388B ILE* 1.3 79.0 - - + +
390B VAL* 1.3 59.1 + - + +
392B GLN* 4.6 4.5 - - - +
393B PRO* 2.9 21.1 - - - +
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B LEU* 4.3 5.6 - - + -
359B PHE* 4.3 25.1 - - + +
360B LEU* 3.8 30.1 - - + +
386B ALA 3.8 8.5 - - - +
387B LEU* 3.0 34.3 - - + +
389B GLU* 1.3 83.1 - - + +
391B LEU* 1.3 70.4 + - + +
393B PRO* 3.0 21.3 - - - +
394B LEU* 3.1 14.1 + - - +
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B VAL* 5.7 5.8 - - + -
293B PHE* 5.1 1.6 - - + -
312B ILE* 3.6 32.3 - - + -
321B ILE* 3.9 17.9 - - + -
325B VAL* 4.3 5.4 - - + -
355B TYR* 4.1 11.2 - - + -
359B PHE* 4.2 26.0 - - + -
387B LEU* 3.0 46.4 + - + +
388B ILE 4.8 0.2 - - - +
390B VAL* 1.3 79.4 - - + +
392B GLN* 1.3 67.5 + - - +
394B LEU* 3.6 10.9 - - + +
395B ILE* 2.9 36.9 + - + +
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Residues in contact with GLN 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B ALA* 3.0 52.2 - - + +
321B ILE* 4.1 12.2 - - + +
322B LYS* 4.0 10.8 + - - +
388B ILE* 2.9 44.3 + - + +
389B GLU* 4.6 4.4 - - - +
391B LEU* 1.3 79.2 - - - +
393B PRO* 1.4 65.5 - - + +
395B ILE* 4.1 1.4 - - - +
396B ALA* 3.1 23.2 + - - +
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Residues in contact with PRO 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B GLU 2.9 27.8 - - - +
390B VAL* 3.0 24.0 - - - +
392B GLN* 1.4 85.3 - - + +
394B LEU* 1.3 57.1 + - - +
396B ALA* 3.0 6.0 + - + -
397B GLU* 2.8 50.6 + - + +
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Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B VAL* 5.4 2.9 - - + -
127B LEU* 4.1 21.1 - - + -
131B ILE* 6.3 3.1 - - + -
359B PHE* 3.4 49.8 - - + -
390B VAL 3.1 18.9 + - - +
391B LEU* 3.3 13.7 + - + +
393B PRO* 1.3 79.6 - - - +
395B ILE* 1.3 63.7 + - + +
397B GLU* 3.6 6.7 + - - +
398B HIS* 3.2 20.3 + - - +
401B ARG* 4.8 6.0 + - - +
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Residues in contact with ILE 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B VAL* 3.6 24.0 - - + -
127B LEU* 5.6 1.1 - - + -
312B ILE* 3.5 26.2 - - + -
313B PHE 4.3 2.2 - - - +
314B LEU* 3.7 24.9 - - + +
316B ASP 3.8 11.2 - - - +
321B ILE* 3.5 24.7 - - + -
391B LEU* 2.9 23.6 + - + +
394B LEU* 1.3 78.5 - - + +
396B ALA* 1.3 65.9 + - - +
398B HIS* 3.4 6.3 + - - +
399B GLN* 3.1 44.2 + - - +
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Residues in contact with ALA 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B GLN 3.1 19.6 + - - +
393B PRO* 3.0 7.9 + - + +
395B ILE* 1.3 75.0 - - - +
397B GLU* 1.3 66.4 + - + +
399B GLN* 3.5 11.6 + - - +
400B ALA* 3.2 22.3 + - - +
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Residues in contact with GLU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B PRO* 2.8 37.2 + - + +
394B LEU* 4.0 6.6 + - - +
396B ALA* 1.3 76.0 - - + +
398B HIS* 1.3 64.0 + - - +
400B ALA* 3.4 5.8 + - - +
401B ARG* 3.1 50.1 + - + +
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Residues in contact with HIS 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LEU* 3.6 35.9 - - + +
174B ASP* 3.1 53.5 + - + -
177B ALA* 3.8 13.4 - - + +
178B CYS* 4.4 4.6 - - - -
314B LEU* 4.0 22.1 + - + +
394B LEU 3.2 14.9 + - - +
395B ILE* 3.5 13.9 - - + +
397B GLU* 1.3 78.7 - - - +
399B GLN* 1.3 59.2 + - - +
401B ARG* 3.4 23.1 + - - +
402B ARG* 2.9 27.7 + - - +
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Residues in contact with GLN 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B LEU 3.4 19.3 + - - +
315B THR* 4.8 7.3 - - - +
316B ASP 3.1 18.3 + - - -
317B THR* 5.2 1.3 - - - +
395B ILE* 3.1 39.0 + - - +
396B ALA* 3.8 8.7 - - - +
398B HIS* 1.3 79.9 - - - +
400B ALA* 1.3 63.8 + - - +
402B ARG* 3.2 11.8 + - - +
403B LYS* 3.0 29.6 + - + +
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Residues in contact with ALA 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B ALA 3.2 15.6 + - - +
397B GLU* 3.6 9.4 - - - +
398B HIS 3.2 0.2 - - - -
399B GLN* 1.3 76.2 - - - +
401B ARG* 1.3 67.6 + - + +
403B LYS* 3.2 20.3 + - - +
404B GLU* 3.4 16.8 - - - +
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Residues in contact with ARG 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ALA* 3.3 31.0 + - + +
178B CYS* 4.9 6.6 + - - +
394B LEU* 4.8 6.9 + - - +
397B GLU* 3.1 31.7 + - - +
398B HIS* 3.5 32.1 - - - +
400B ALA* 1.3 78.5 - - + +
402B ARG* 1.3 63.3 + - - +
404B GLU* 2.9 25.6 + - - +
405B VAL* 3.6 7.8 + - - +
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Residues in contact with ARG 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B GLU 5.5 1.2 + - - -
170B GLU* 3.0 47.9 + - - +
173B LYS* 3.6 33.3 - - + +
174B ASP* 2.8 37.7 + - - +
177B ALA* 3.9 10.0 - - + +
398B HIS* 2.9 20.8 + - - +
399B GLN* 3.4 11.4 - - - +
401B ARG* 1.3 76.7 - - - +
403B LYS* 1.3 57.2 + - - +
404B GLU 2.9 0.2 - - - -
405B VAL* 2.9 30.4 + - - +
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Residues in contact with LYS 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B GLN* 3.0 19.1 + - + +
400B ALA* 3.2 13.9 + - - +
402B ARG* 1.3 75.6 - - + +
404B GLU* 1.3 70.3 + - - +
405B VAL 3.4 3.1 + - - +
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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