Contacts of the helix formed by residues 317 - 334 (chain B) in PDB entry 4U1D
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 317 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B ARG 5.1 3.8 - - - +
316B ALA* 1.3 73.1 - - - +
318B GLU* 1.3 62.3 + - - +
319B GLU* 3.5 11.5 + - - +
320B GLU* 3.2 42.4 + - - +
321B PHE* 3.0 18.4 + - - -
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Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ALA 3.8 0.8 + - - -
317B THR* 1.3 73.9 - - - +
319B GLU* 1.3 57.6 + - - +
321B PHE* 3.3 12.4 + - - +
322B LYS* 3.0 26.2 + - - +
379B LYS* 3.4 39.5 + - + +
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Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B THR* 3.1 11.8 - - - +
318B GLU* 1.3 79.8 - - - +
320B GLU* 1.3 61.2 + - + +
322B LYS* 3.2 47.9 - - - +
323B THR* 3.4 13.7 + - + +
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Residues in contact with GLU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B TYR* 2.4 34.3 + - + -
315B ARG* 4.2 3.1 + - - +
316B ALA* 3.8 0.5 - - - -
317B THR* 3.2 35.7 + - - +
318B GLU 3.2 0.4 - - - -
319B GLU* 1.3 74.9 - - + +
321B PHE* 1.3 58.1 + - - +
322B LYS 3.0 1.6 - - - -
323B THR* 3.0 9.7 + - - +
324B TYR* 2.8 68.3 + - + +
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Residues in contact with PHE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B TYR* 3.1 32.1 - + - +
310B TYR* 4.1 9.6 - + - -
311B SER* 3.6 43.7 - - - -
313B ASN 5.8 0.2 - - - -
316B ALA* 3.4 36.8 - - + -
317B THR 3.0 22.1 + - - -
318B GLU* 3.3 16.3 + - - +
320B GLU* 1.3 77.6 - - + +
322B LYS* 1.3 61.9 + - - +
324B TYR* 4.8 0.9 - - - -
325B SER* 2.6 30.0 + - - -
379B LYS* 3.4 27.1 - - + +
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Residues in contact with LYS 322 (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 GLU* 3.0 13.5 + - + +
319B GLU* 3.2 40.8 - - - +
321B PHE* 1.3 80.0 - - - +
323B THR* 1.3 81.9 + - - +
326B SER* 2.8 24.4 + - - -
379B LYS* 3.2 16.9 - - - +
381B ASP* 2.7 48.2 + - - +
414B LYS* 4.1 16.9 - - - +
416B TYR* 4.5 1.8 - - - -
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Residues in contact with THR 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B GLU* 3.4 12.7 + - + +
320B GLU* 3.0 12.8 + - - +
322B LYS* 1.3 104.5 - - - +
324B TYR* 1.3 71.1 + - - +
326B SER* 3.5 5.4 + - - -
327B THR* 2.9 34.6 + - - -
415B THR* 4.3 19.5 - - + +
416B TYR* 4.3 9.6 - - + -
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Residues in contact with TYR 324 (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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284B GLU* 5.3 3.8 + - - -
303B TRP* 4.0 28.7 - + + -
306B PHE* 3.9 26.0 - + - -
307B TYR* 3.8 20.9 - + + -
310B TYR* 3.8 34.7 - + - -
320B GLU* 2.8 49.4 + - + +
321B PHE 4.8 0.4 - - - -
323B THR* 1.3 83.2 - - - +
325B SER* 1.3 57.9 + - - +
327B THR* 3.1 5.2 + - - -
328B ILE* 2.9 35.1 + - - +
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Residues in contact with SER 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B TYR* 2.9 27.1 + - - -
321B PHE 2.6 23.5 + - - -
324B TYR* 1.3 77.4 - - - +
326B SER* 1.3 62.8 + - - +
328B ILE* 3.4 4.1 + - - +
329B PHE* 3.0 24.3 + - - +
376B ILE* 3.2 35.3 + - - +
379B LYS* 3.6 12.8 - - - +
380B VAL* 3.8 5.9 - - - +
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Residues in contact with SER 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LYS 2.8 20.7 + - - -
323B THR 3.6 3.4 - - - -
324B TYR 3.2 0.4 - - - -
325B SER* 1.3 78.9 - - - +
327B THR* 1.3 53.5 + - - +
329B PHE 3.1 1.9 + - - -
330B LEU* 2.8 32.4 + - - +
380B VAL* 4.4 4.7 - - - -
381B ASP* 2.9 30.0 + - - -
384B LEU* 3.1 17.1 - - - +
416B TYR* 3.4 31.2 - - - -
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Residues in contact with THR 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TRP* 3.4 43.1 - - + +
323B THR* 2.9 21.1 + - - -
324B TYR* 3.3 9.7 - - - -
326B SER* 1.3 75.3 - - - +
328B ILE* 1.3 57.9 - - - +
330B LEU* 3.2 2.5 + - - +
331B SER* 2.8 30.1 + - - -
416B TYR* 3.2 28.7 - - - +
419B GLN* 4.8 4.3 - - - +
420B TYR* 3.9 18.4 - - + +
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Residues in contact with ILE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B THR* 3.6 11.6 - - + +
303B TRP* 3.8 32.8 - - + +
304B LYS* 3.7 26.7 - - + -
307B TYR* 3.6 39.0 - - + -
324B TYR 2.9 22.2 + - - +
325B SER* 3.6 6.3 - - - +
327B THR* 1.3 72.4 - - - +
329B PHE* 1.3 63.1 + - - +
331B SER* 2.8 22.3 + - - -
332B ALA 3.3 4.3 + - - -
370B ILE* 3.7 20.9 - - + +
376B ILE* 4.3 12.6 - - + -
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Residues in contact with PHE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B SER 3.0 17.5 + - - +
326B SER 3.5 3.6 - - - +
328B ILE* 1.3 76.2 - - - +
330B LEU* 1.3 64.0 + - - +
332B ALA* 3.0 13.0 + - - +
333B ILE* 3.1 26.5 + - + +
367B LEU* 3.6 21.1 - - + -
370B ILE* 3.6 24.9 - - + -
371B ILE* 3.8 20.0 - - + -
377B TYR* 3.9 17.0 - + - -
380B VAL* 4.0 17.5 - - + -
384B LEU* 3.4 45.5 - - + -
385B LYS* 4.2 4.7 - - - -
388B TYR* 3.6 26.9 - + + -
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Residues in contact with LEU 330 (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 SER 2.8 20.8 + - - +
327B THR* 3.7 4.3 - - - +
329B PHE* 1.3 72.4 - - - +
331B SER* 1.3 58.3 + - - +
333B ILE* 3.3 6.9 + - + +
334B SER* 2.9 31.1 + - - -
384B LEU* 3.9 15.1 - - + +
387B LEU* 4.0 26.0 - - + -
416B TYR* 3.7 22.7 - - + -
417B PHE* 3.8 23.3 - - + -
420B TYR* 3.6 35.2 - - + -
424B LEU* 4.5 15.3 - - + -
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Residues in contact with SER 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PRO* 4.9 3.3 - - - +
299B HIS* 3.9 8.2 - - - -
300B THR* 2.8 26.2 + - - +
303B TRP* 5.0 1.4 - - - -
327B THR* 2.8 11.8 + - - -
328B ILE* 2.8 18.8 + - - -
330B LEU* 1.3 76.6 - - - +
332B ALA* 1.3 55.6 + - - +
334B SER* 3.8 3.1 - - - -
335B THR* 2.8 23.0 + - - -
420B TYR* 3.3 41.5 - - - -
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Residues in contact with ALA 332 (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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300B THR* 4.2 8.1 - - + -
328B ILE 3.3 1.3 + - - +
329B PHE 3.0 9.9 + - - +
331B SER* 1.3 78.7 + - - +
333B ILE* 1.3 62.6 + - - +
334B SER 3.2 1.1 - - - -
335B THR* 3.3 19.4 + - - -
363B ARG* 3.7 12.6 + - - +
366B MET* 4.4 10.5 - - + -
367B LEU* 3.6 19.7 - - + +
370B ILE* 3.5 29.8 - - + -
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Residues in contact with ILE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B PHE* 3.1 43.7 + - + +
330B LEU* 3.3 10.7 + - + +
332B ALA* 1.3 75.4 - - - +
334B SER* 1.3 59.0 + - - +
335B THR 3.1 5.4 + - - -
363B ARG* 2.7 28.8 + - - +
367B LEU* 3.8 15.7 - - + -
384B LEU* 4.0 6.3 - - + +
387B LEU* 3.9 24.2 - - + -
388B TYR* 4.2 11.4 - - + +
391B ILE* 4.8 11.0 - - + -
392B GLU* 4.7 9.9 - - + +
424B LEU* 4.1 18.4 - - + -
427B VAL* 3.8 11.2 - - + +
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Residues in contact with SER 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PRO* 5.7 0.7 - - - +
330B LEU* 2.9 19.2 + - - -
331B SER 3.9 7.2 - - - -
332B ALA 3.2 0.4 - - - -
333B ILE* 1.3 77.0 - - - +
335B THR* 1.3 61.5 + - - +
336B GLN* 3.6 1.7 + - - +
420B TYR* 3.6 23.0 + - - -
423B PRO* 2.9 44.5 - - - +
424B LEU* 3.4 22.2 + - - +
427B VAL* 4.0 2.2 - - - +
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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