Contacts of the helix formed by residues 319 - 337 (chain B) in PDB entry 3U44
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 319 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741A ARG* 4.6 16.5 - - - +
317B ALA* 3.1 2.5 - - - +
318B ALA* 1.3 92.9 + - - +
320B ARG* 1.3 61.9 + - - +
321B ARG* 3.0 39.5 + - - +
322B ALA* 3.0 15.3 + - - +
323B GLU* 2.8 26.0 + - - +
670B PRO* 3.7 15.9 - - - -
672B ALA* 4.5 10.7 - - + +
673B ASP 4.8 10.3 - - - +
674B ALA* 6.3 0.4 - - - -
702B ASN* 5.0 1.7 + - - +
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Residues in contact with ARG 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ASN* 1.3 75.1 - - - +
321B ARG* 1.3 56.6 + - - +
323B GLU* 3.3 10.5 - - - +
324B LEU* 2.9 33.8 + - - +
354B ASP* 4.0 35.3 + - - +
355B TYR* 3.2 52.1 + - + +
358B MET* 3.7 14.8 - - + -
608B GLY* 4.9 0.4 - - - -
610B ASN* 3.4 19.6 - - - +
613B VAL* 5.8 2.6 - - - +
670B PRO* 3.7 8.1 - - + +
672B ALA 5.5 1.1 + - - +
673B ASP* 4.2 14.0 + - - -
674B ALA* 5.3 9.3 - - - +
679B LEU* 3.8 22.6 - - - +
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Residues in contact with ARG 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A TRP* 4.4 14.8 - - + -
741A ARG* 4.0 35.0 + - - +
744A TYR* 3.3 33.0 - - - -
745A ASP* 2.5 44.9 + - - -
319B ASN* 3.0 14.6 + - - +
320B ARG* 1.3 73.3 - - - +
322B ALA* 1.3 57.7 + - - +
323B GLU 3.0 0.7 + - - -
324B LEU* 3.1 2.4 + - - +
325B GLU* 2.6 46.9 + - - +
358B MET* 3.2 35.2 - - + +
362B VAL* 5.0 2.5 - - + +
674B ALA* 6.3 1.0 - - - +
702B ASN* 4.4 3.1 - - - +
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ALA* 4.0 1.8 - - - -
318B ALA* 4.0 13.7 - - + +
319B ASN* 3.0 17.6 + - - +
321B ARG* 1.3 78.7 - - - +
323B GLU* 1.3 53.3 + - - +
325B GLU* 4.0 1.3 - - - +
326B GLY* 2.7 30.5 + - - -
329B ARG* 4.7 1.0 + - - -
700B LEU* 3.6 28.0 - - - +
701B THR* 4.4 3.8 - - - +
702B ASN* 3.2 27.0 - - - +
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Residues in contact with GLU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ALA* 3.5 15.4 - - + +
319B ASN 2.8 12.3 + - - +
320B ARG* 3.3 9.6 - - - +
321B ARG 3.0 0.2 - - - -
322B ALA* 1.3 77.6 - - - +
324B LEU* 1.3 58.4 + - - +
326B GLY* 3.6 0.5 - - - -
327B ILE* 2.8 39.0 + - + +
355B TYR* 2.7 35.8 + - + -
607B LEU* 3.7 4.6 - - + -
608B GLY 3.4 10.0 + - - -
668B SER* 2.7 49.1 + - - +
670B PRO* 3.6 15.4 - - - +
700B LEU* 3.6 4.0 - - + +
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Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ARG 2.9 17.0 + - - +
321B ARG 3.8 2.0 - - - +
323B GLU* 1.3 72.8 - - - +
325B GLU* 1.3 54.2 + - - +
327B ILE* 3.2 8.8 + - + +
328B ALA* 2.7 34.8 + - - +
347B ILE* 5.3 5.4 - - + -
355B TYR* 3.9 15.0 - - + +
358B MET* 3.7 24.7 - - + -
359B VAL* 3.6 47.6 - - + +
362B VAL* 4.1 14.4 - - + +
363B PHE* 4.3 11.7 - - + -
607B LEU* 3.5 31.4 - - + -
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Residues in contact with GLU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A TRP* 6.2 0.5 - - - -
321B ARG* 2.6 30.0 + - - +
322B ALA 4.0 1.3 - - - +
324B LEU* 1.3 73.5 - - - +
326B GLY* 1.3 58.7 + - - +
328B ALA* 3.6 3.6 - - - +
329B ARG* 3.2 30.5 + - - +
362B VAL* 3.8 17.4 - - + +
366B TYR* 3.0 41.3 + - + +
702B ASN* 2.9 33.2 + - - +
721B VAL* 5.7 0.5 - - - +
725B PHE* 4.1 8.8 - - - -
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Residues in contact with GLY 326 (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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322B ALA 2.7 19.2 + - - -
323B GLU 3.6 0.9 - - - -
324B LEU 3.2 0.2 - - - -
325B GLU* 1.3 76.5 - - - +
327B ILE* 1.3 60.1 + - - +
328B ALA 3.2 0.2 - - - -
329B ARG* 2.9 38.4 - - - +
330B GLU* 3.3 8.5 + - - +
700B LEU* 3.9 24.7 - - - +
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Residues in contact with ILE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B MET* 5.0 2.7 - - - -
323B GLU* 2.8 25.3 + - + +
324B LEU* 3.6 8.7 - - + +
326B GLY* 1.3 75.1 - - - +
328B ALA* 1.3 65.0 + - - +
330B GLU* 3.2 6.5 + - - +
331B ILE* 3.0 32.7 + - + +
347B ILE* 4.4 6.3 - - + -
363B PHE* 5.2 4.7 - - + -
605B PHE* 3.5 41.3 - - + -
607B LEU* 3.5 35.4 - - + -
668B SER* 3.9 14.8 - - - +
700B LEU* 4.2 9.9 - - + -
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Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LEU 2.7 16.8 + - - +
325B GLU 3.6 9.0 - - - +
326B GLY 3.2 0.2 - - - -
327B ILE* 1.3 78.5 - - - +
329B ARG* 1.3 61.2 + - - +
331B ILE* 3.5 0.4 + - - -
332B HIS* 3.2 21.1 + - - -
362B VAL* 4.1 5.8 - - + -
363B PHE* 3.9 17.2 - - + -
366B TYR* 3.7 26.2 - - + -
368B ILE* 3.3 22.9 - - + +
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Residues in contact with ARG 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ALA 4.7 1.2 + - - -
325B GLU* 3.2 15.2 + - - +
326B GLY* 2.9 47.7 - - - +
328B ALA* 1.3 77.1 - - - +
330B GLU* 1.3 61.6 + - - +
332B HIS* 3.1 9.5 + - - +
333B ALA* 2.8 28.8 + - - +
366B TYR* 2.8 30.7 + - + -
700B LEU* 5.6 1.9 - - - +
701B THR 4.0 12.1 + - - +
702B ASN* 4.2 1.2 + - - -
714B MET* 3.2 44.8 + - + +
715B TYR* 3.2 49.3 + - - +
717B VAL* 4.2 6.6 - - + +
725B PHE* 3.5 9.1 - - - -
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Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B MET* 6.2 1.8 - - - -
326B GLY 3.8 8.7 - - - +
327B ILE* 3.2 10.2 + - - +
329B ARG* 1.3 82.7 - - - +
331B ILE* 1.3 56.9 + - - +
333B ALA* 2.9 10.8 + - - +
334B LEU* 2.8 38.5 + - + +
605B PHE* 3.4 31.0 - - + -
666B TYR* 2.6 28.4 + - + -
698B ARG* 3.1 34.7 + - - +
700B LEU* 6.4 0.4 - - + -
714B MET* 4.5 10.1 - - - +
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Residues in contact with ILE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ILE* 3.0 26.2 + - + +
328B ALA 3.7 7.9 - - - +
330B GLU* 1.3 75.8 - - - +
332B HIS* 1.3 57.9 + - - +
334B LEU* 3.3 10.1 + - - +
335B VAL* 3.0 27.9 + - + +
342B TYR* 4.0 29.4 - - + -
345B VAL* 3.7 35.7 - - + -
347B ILE* 4.7 2.5 - - + -
363B PHE* 4.2 19.5 - - + -
368B ILE* 4.0 9.2 - - + -
588B VAL* 4.0 19.5 - - + -
605B PHE* 4.0 10.3 - - + -
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Residues in contact with HIS 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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1000A TRP* 4.5 7.7 - + - -
328B ALA 3.2 22.1 + - - +
329B ARG 3.1 9.3 + - - +
331B ILE* 1.3 77.2 - - - +
333B ALA* 1.3 60.1 + - - +
335B VAL* 4.1 3.3 - - - +
336B ARG* 2.9 72.2 + - - +
342B TYR* 3.8 20.0 + - - -
366B TYR* 2.6 32.6 + + + +
367B GLU* 4.6 6.5 - - + -
368B ILE* 3.6 16.5 - - + +
717B VAL* 3.8 29.5 - - + +
718B ASN* 6.1 0.9 - - + -
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Residues in contact with ALA 333 (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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329B ARG 2.8 13.6 + - - +
330B GLU* 2.9 16.6 + - - +
332B HIS* 1.3 76.3 - - - +
334B LEU* 1.3 58.2 + - + +
336B ARG* 5.0 1.1 - - - -
337B GLU* 3.0 41.1 + - + +
338B LYS* 3.5 3.4 + - - +
714B MET* 4.5 25.1 - - + -
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Residues in contact with LEU 334 (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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330B GLU* 2.8 23.2 + - + +
331B ILE* 3.5 11.7 - - - +
332B HIS 3.2 0.2 - - - -
333B ALA* 1.3 78.5 - - + +
335B VAL* 1.3 58.5 + - + +
338B LYS* 3.2 13.2 + - + -
339B GLY 3.0 23.6 + - - -
340B TYR* 3.1 31.8 + - + -
345B VAL* 4.4 8.3 - - + -
603B CYS* 4.0 21.1 - - + -
605B PHE* 4.2 25.6 - - + -
664B ARG* 3.7 31.6 - - - +
666B TYR* 3.8 9.2 - - - +
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Residues in contact with VAL 335 (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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1000A TRP* 4.0 16.1 - - + -
1002A TYR* 3.6 30.1 - - + -
1003A PRO* 5.7 0.9 - - + -
331B ILE* 3.0 17.5 + - + +
332B HIS* 4.1 3.6 - - - +
334B LEU* 1.3 77.9 - - + +
336B ARG* 1.3 63.6 + - + +
339B GLY* 3.5 17.0 - - - -
340B TYR* 3.6 25.4 + - + +
341B ARG 4.0 1.3 - - - -
342B TYR* 3.7 42.8 - - + +
345B VAL* 5.8 1.6 - - + -
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Residues in contact with ARG 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997A GLN* 4.2 26.2 + - - +
1000A TRP* 2.8 84.1 + - + +
332B HIS* 2.9 33.3 + - - +
333B ALA* 5.0 1.6 - - - -
335B VAL* 1.3 81.6 - - + +
337B GLU* 1.3 65.4 + - + +
339B GLY* 4.4 1.0 + - - -
716B VAL 4.6 0.2 + - - -
717B VAL* 2.9 58.1 + - - +
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Residues in contact with GLU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ALA* 3.0 21.1 + - + +
336B ARG* 1.3 82.4 - - + +
338B LYS* 1.3 72.4 + - + +
339B GLY* 2.9 11.3 + - - -
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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