Contacts of the helix formed by residues 316 - 331 (chain B) in PDB entry 4WGK
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 SER 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B THR* 3.4 17.5 + - - +
136B ARG 4.0 3.5 + - - -
137B LEU* 3.9 15.9 - - - -
159B ASP* 4.0 20.2 - - - -
193B THR* 5.1 0.9 + - - -
195B THR* 3.7 13.3 - - - -
315B ASN* 1.3 74.1 - - - +
317B ASP* 1.3 72.1 + - - +
319B VAL* 4.0 5.7 - - - +
320B GLY* 3.1 32.3 + - - -
715B TRP* 3.7 4.2 + - - -
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Residues in contact with ASP 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B THR* 3.9 5.6 + - - +
196B HIS* 5.0 0.5 + - - +
197B SER* 4.5 2.3 + - - -
304B PRO* 3.1 33.8 - - + +
305B VAL* 3.6 1.6 - - - -
306B SER* 3.0 20.4 + - - -
307B MET* 3.0 34.1 + - - +
315B ASN* 2.8 16.6 + - - +
316B SER* 1.3 81.2 - - - +
318B ASN* 1.3 81.5 + - - +
321B TYR 2.8 24.4 + - - -
397B THR* 3.6 11.4 - - - -
715B TRP* 3.2 9.0 - - - -
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Residues in contact with ASN 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ILE* 4.4 2.7 - - - +
303B HIS 3.2 21.8 + - - -
304B PRO* 3.3 13.9 - - - +
306B SER* 3.2 17.6 + - - +
317B ASP* 1.3 94.5 + - - +
319B VAL* 1.3 82.3 + - - +
321B TYR* 3.1 1.6 + - - +
322B ALA* 2.9 23.9 + - - +
355B PRO* 3.6 9.9 - - - +
397B THR* 3.6 25.0 - - + +
400B ILE* 3.9 10.1 - - + +
401B GLY* 3.4 11.1 - - - +
404B MET* 3.7 15.7 - - + -
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Residues in contact with VAL 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B THR* 4.1 25.1 - - + +
300B PHE 5.5 2.2 - - - +
302B ILE* 3.7 24.9 - - + +
304B PRO* 3.9 24.0 - - + -
316B SER 4.0 7.6 - - - +
318B ASN* 1.3 92.3 + - - +
320B GLY* 1.3 61.3 + - - +
322B ALA* 3.4 4.8 + - - +
323B SER* 2.9 32.2 + - - -
345B PHE* 3.9 23.5 - - + +
346B ALA 6.5 0.7 - - - -
404B MET* 3.9 12.6 - - + -
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Residues in contact with GLY 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ARG* 5.5 1.7 + - - -
159B ASP* 4.8 6.1 - - - -
316B SER* 3.1 44.8 + - - -
317B ASP 3.6 0.2 - - - -
319B VAL* 1.3 77.8 - - - +
321B TYR* 1.3 59.1 + - - +
323B SER* 3.4 7.7 + - - -
324B TYR* 2.9 27.4 + - - +
715B TRP* 4.0 1.3 - - - -
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Residues in contact with TYR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ASP 2.8 8.7 + - - +
318B ASN* 3.1 10.5 + - - +
320B GLY* 1.3 74.1 - - - +
322B ALA* 1.3 59.9 + - - +
324B TYR* 3.2 20.1 + + - +
325B LEU* 2.9 58.4 + - + +
397B THR 4.5 1.8 - - - +
398B GLN* 3.3 60.6 + - + +
401B GLY* 3.8 10.1 - - - -
402B ARG* 3.8 12.4 + - + -
715B TRP* 3.5 49.5 - + + -
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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
----------------------------------------------------------
318B ASN 2.9 10.4 + - - +
319B VAL* 3.6 9.0 - - - +
320B GLY 3.2 0.2 - - - -
321B TYR* 1.3 74.6 - - - +
323B SER* 1.3 63.7 + - - +
325B LEU 3.4 0.5 + - - -
326B LEU* 3.1 28.4 + - - +
345B PHE* 3.5 30.7 - - + -
401B GLY 3.2 24.6 + - - +
404B MET* 4.2 5.2 - - + -
405B TYR* 3.9 10.9 - - - +
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Residues in contact with SER 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ARG* 4.1 18.4 + - - -
159B ASP* 5.8 0.2 + - - -
319B VAL 2.9 19.3 + - - -
320B GLY* 3.6 6.9 - - - -
322B ALA* 1.3 74.0 - - - +
324B TYR* 1.3 62.6 + - - +
326B LEU* 3.4 4.8 + - - +
327B GLU* 3.0 31.0 + - - +
343B ALA 3.3 18.4 - - - -
344B ALA* 4.1 0.5 - - - -
345B PHE* 3.3 30.6 + - - +
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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
----------------------------------------------------------
135B THR* 4.9 1.3 - - - -
138B TYR* 6.3 2.9 - + - -
140B ARG* 5.0 2.2 - - - +
320B GLY 2.9 15.2 + - - +
321B TYR* 3.2 25.3 + + - +
323B SER* 1.3 77.1 - - - +
325B LEU* 1.3 69.2 + - + +
327B GLU* 3.5 7.7 + - - +
328B GLN* 3.1 50.3 + - + +
336B PRO* 3.7 34.4 - - + +
337B GLY 5.9 0.7 - - - -
713B ALA* 3.7 8.3 - - + -
714B SER* 3.6 10.0 - - - -
715B TRP* 3.4 41.7 - + + +
716B GLU* 3.1 24.2 + - - -
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Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B TYR* 2.9 58.0 + - + +
322B ALA 3.4 0.9 + - - +
324B TYR* 1.3 88.1 - - + +
326B LEU* 1.3 66.1 + - - +
328B GLN* 3.4 4.5 + - + +
329B GLU* 3.0 25.6 + - - +
402B ARG* 3.8 32.8 - - - +
405B TYR* 3.5 43.4 - - + -
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LEU* 4.0 30.7 - - + -
322B ALA 3.1 15.5 + - - +
323B SER* 3.7 4.3 - - - +
324B TYR 3.4 0.2 - - - -
325B LEU* 1.3 77.9 - - - +
327B GLU* 1.3 61.3 + - - +
329B GLU* 3.5 4.2 + - - +
330B LYS* 3.2 32.3 + - - +
341B PHE* 4.8 1.6 - - + -
343B ALA* 3.7 15.0 - - + -
345B PHE* 3.5 33.0 - - + -
405B TYR* 3.5 33.2 - - + +
408B ALA* 3.9 9.4 - - + -
409B LYS* 4.0 19.5 - - + +
412B TYR* 6.0 0.2 - - + -
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Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ARG* 3.0 30.8 + - - -
138B TYR* 5.4 0.9 - - - -
140B ARG* 2.8 44.8 + - - -
323B SER 3.0 17.6 + - - +
324B TYR* 4.0 4.9 - - - +
326B LEU* 1.3 74.1 - - - +
328B GLN* 1.3 60.5 + - - +
331B ASN* 2.7 51.0 + - - +
337B GLY* 5.1 6.1 + - - -
338B GLN 5.8 0.7 - - - +
341B PHE* 4.0 10.1 - - + +
342B VAL* 3.7 0.5 - - - -
343B ALA* 3.1 26.6 + - + +
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Residues in contact with GLN 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B TYR* 3.1 45.7 + - + +
325B LEU* 4.0 6.7 - - + +
327B GLU* 1.3 80.0 - - + +
329B GLU* 1.3 62.2 + - - +
331B ASN* 3.9 14.8 - - - +
332B LYS* 4.1 4.5 + - - +
334B TYR 3.4 21.7 + - - +
335B LEU 3.6 2.9 - - - +
336B PRO* 3.4 40.6 - - - +
337B GLY 4.6 0.9 + - - -
338B GLN 4.6 4.2 - - - +
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Residues in contact with GLU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU 3.0 17.5 + - - +
326B LEU* 3.8 6.3 - - - +
327B GLU 3.2 0.2 - - - -
328B GLN* 1.3 78.8 - - - +
330B LYS* 1.3 74.9 + - - +
332B LYS* 3.3 39.8 + - - +
405B TYR* 3.4 19.4 + - - +
409B LYS* 3.1 47.1 + - - +
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Residues in contact with LYS 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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293B ASP* 3.4 33.9 - - + +
296B LEU* 5.6 1.6 - - - +
326B LEU* 3.2 16.5 + - + +
327B GLU 4.0 0.2 - - - +
329B GLU* 1.3 92.7 + - - +
331B ASN* 1.3 58.7 + - - +
332B LYS* 2.9 18.3 + - - +
341B PHE* 3.6 38.3 - - + -
409B LYS* 5.3 6.7 - - - +
412B TYR* 3.7 29.6 - - - +
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Residues in contact with ASN 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ARG* 4.4 1.4 - - - +
327B GLU* 2.7 33.3 + - - +
328B GLN* 3.9 11.2 - - - +
330B LYS* 1.3 67.4 - - - +
332B LYS* 1.3 66.4 + - - +
333B GLY 3.3 0.2 + - - -
334B TYR* 3.0 30.2 + - + +
338B GLN 3.5 22.4 + - - +
339B GLY* 3.4 11.3 + - - -
340B PRO* 3.2 10.5 - - - +
341B PHE* 2.8 51.8 + - - +
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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