Contacts of the helix formed by residues 310 - 330 (chain B) in PDB entry 5LDH
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 ASP 310 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B LYS 3.2 7.3 + - - -
309B ASP* 1.3 76.0 - - - +
311B GLU* 1.3 51.6 + - - +
312B VAL* 3.0 2.9 - - - +
313B ALA* 2.7 18.6 + - - +
314B GLN* 2.4 59.5 + - - +
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B VAL* 3.8 17.2 - - + +
201B ALA 3.9 2.1 - - - +
202B VAL* 5.1 1.0 - - - +
203B TRP* 1.6 63.0 + - + +
204B SER* 4.9 5.4 + - - -
307B LEU* 5.6 2.0 - - + +
309B ASP* 2.6 34.9 + - - +
310B ASP* 1.3 71.4 + - - +
312B VAL* 1.3 66.5 + - - +
314B GLN* 3.0 25.1 + - - +
315B LEU* 2.7 26.7 + - - +
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LYS* 3.2 31.0 - - + +
307B LEU 2.7 32.0 - - - +
308B LYS* 2.5 58.3 - - + +
309B ASP 3.3 0.9 - - - +
310B ASP 3.4 5.4 - - - +
311B GLU* 1.3 80.1 - - - +
313B ALA* 1.3 57.7 + - + +
315B LEU* 3.1 8.0 - - - +
316B LYS* 2.7 35.7 + - + +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ASP* 2.7 25.1 + - - +
312B VAL* 1.3 75.7 - - + +
314B GLN* 1.3 73.7 + - - +
316B LYS* 2.8 25.1 - - + +
317B ASN* 2.7 31.0 + - - +
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Residues in contact with GLN 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER* 5.7 2.6 - - - -
200B VAL* 3.4 23.5 - - + +
203B TRP* 5.4 1.9 - - - -
226B LYS* 5.8 4.4 - - - +
310B ASP* 2.4 43.5 + - - +
311B GLU* 3.0 35.1 - - - +
313B ALA* 1.3 71.6 - - - +
315B LEU* 1.3 65.7 + - - +
317B ASN* 4.1 2.2 - - - +
318B SER* 3.5 16.8 + - - -
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LEU* 2.4 54.5 - - + -
193B GLY* 4.2 12.3 - - - +
200B VAL* 4.0 13.9 - - + +
279B TYR* 3.0 16.8 - - - +
281B ILE* 5.8 1.8 - - + -
287B LEU* 4.4 17.4 - - + +
289B LEU* 4.5 1.6 - - + -
306B LYS* 2.5 40.2 - - + +
311B GLU 2.7 14.0 + - - +
312B VAL 3.1 11.7 - - - +
314B GLN* 1.3 75.1 - - - +
316B LYS* 1.3 71.3 + - + +
318B SER* 3.5 12.9 + - - -
319B ALA* 4.1 2.3 + - - +
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Residues in contact with LYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR* 5.2 2.0 - - - +
281B ILE* 5.4 10.6 - - + +
306B LYS* 5.4 0.4 - - - +
312B VAL* 2.7 15.2 + - + +
313B ALA* 2.8 34.1 + - + +
315B LEU* 1.3 86.5 - - + +
317B ASN* 1.3 94.9 + - + +
318B SER 3.2 0.5 + - - -
319B ALA* 3.5 16.8 + - - +
320B ASP* 3.7 4.8 + - - +
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Residues in contact with ASN 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ALA* 2.7 18.5 + - - +
314B GLN* 4.1 2.7 - - - +
316B LYS* 1.3 92.1 + - - +
318B SER* 1.3 65.8 + - - +
320B ASP* 3.1 29.8 + - - +
321B THR* 2.9 25.5 + - - -
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Residues in contact with SER 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLY* 6.5 0.7 - - - -
194B GLU* 2.5 34.3 + - - -
197B ASP 4.7 0.3 + - - -
198B SER* 3.5 16.5 + - - -
287B LEU* 5.4 1.8 - - - -
314B GLN 3.5 8.2 + - - -
315B LEU* 3.5 11.1 + - - -
316B LYS 3.2 1.4 + - - -
317B ASN* 1.3 76.4 - - - +
319B ALA* 1.3 73.2 + - - +
320B ASP 3.1 0.2 + - - -
321B THR* 3.1 23.2 + - - +
322B LEU* 3.5 3.6 + - - +
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Residues in contact with ALA 319 (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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281B ILE* 5.6 11.7 - - + -
285B VAL 4.2 1.8 - - - +
286B PHE* 3.7 31.5 - - + +
287B LEU* 3.7 29.6 - - + +
315B LEU 4.1 2.1 + - - +
316B LYS 3.5 10.2 + - - +
317B ASN 3.4 0.2 - - - -
318B SER* 1.3 79.7 - - - +
320B ASP* 1.3 68.5 + - - +
322B LEU* 3.3 9.6 + - - +
323B TRP 3.4 8.5 + - - -
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Residues in contact with ASP 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLU* 2.8 38.9 - - + +
286B PHE* 5.6 0.2 - - - -
316B LYS 3.7 3.4 + - - +
317B ASN* 3.1 32.9 + - - +
318B SER 3.1 0.6 + - - -
319B ALA* 1.3 81.7 - - - +
321B THR* 1.3 71.2 + - - +
322B LEU 2.9 1.0 + - - -
323B TRP* 3.1 10.5 + - - -
324B GLY* 2.8 29.6 + - - -
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Residues in contact with THR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ASN* 2.9 14.1 + - - +
318B SER* 3.1 15.0 + - - +
320B ASP* 1.3 85.1 + - - +
322B LEU* 1.3 70.7 + - + +
324B GLY* 3.7 2.2 + - - -
325B ILE* 3.3 30.3 + - - +
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ASN* 4.7 26.7 - - + +
141B PRO* 5.6 6.5 - - + -
144B ILE* 4.8 16.4 - - + -
286B PHE* 5.6 2.2 - - + -
318B SER 4.2 4.0 - - - +
319B ALA* 3.3 8.9 + - - +
320B ASP 2.9 2.8 + - - -
321B THR* 1.3 80.0 - - + +
323B TRP* 1.3 57.9 + - - +
324B GLY 3.0 1.3 - - - -
325B ILE* 2.9 12.1 + - + -
326B GLN* 2.3 48.2 + - + +
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Residues in contact with TRP 323 (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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147B TYR* 6.5 0.4 - + - -
282B GLU* 3.7 25.0 + - - -
283B ASN* 2.7 38.6 - - + +
284B GLU* 4.7 20.2 - - + -
285B VAL 6.4 0.2 - - - -
286B PHE* 3.2 31.6 - + + -
319B ALA 3.4 2.1 + - - +
320B ASP* 3.1 16.8 + - - +
322B LEU* 1.3 76.5 - - - +
324B GLY* 1.3 74.7 + - - +
326B GLN* 2.7 21.3 + - - +
327B LYS* 2.4 80.5 + - + +
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Residues in contact with GLY 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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320B ASP* 2.8 18.9 + - - -
321B THR* 3.8 4.7 - - - -
323B TRP* 1.3 90.2 - - - +
325B ILE* 1.3 64.0 + - - +
327B LYS* 3.3 16.7 - - - +
328B ASP* 4.5 0.3 + - - +
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Residues in contact with ILE 325 (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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321B THR* 3.3 17.7 + - - +
322B LEU* 2.9 16.6 + - + +
324B GLY* 1.3 72.0 - - - -
326B GLN* 1.3 70.2 + - - +
327B LYS 3.1 1.8 - - - -
328B ASP* 3.1 31.1 + - - +
329B LEU* 4.4 11.2 - - + -
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Residues in contact with GLN 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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113B VAL* 6.2 1.3 - - + -
144B ILE* 2.9 37.0 - - + +
147B TYR* 4.4 18.7 + - - -
286B PHE* 3.3 22.3 - - - -
322B LEU* 2.3 41.8 + - + +
323B TRP* 2.7 25.3 + - + +
325B ILE* 1.3 66.0 - - - +
327B LYS* 1.3 74.8 - - - +
329B LEU* 2.6 13.9 + - + -
330B LYS* 2.6 38.4 + - + +
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Residues in contact with LYS 327 (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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323B TRP* 2.4 62.7 + - + +
324B GLY* 3.3 16.2 - - - +
326B GLN* 1.3 81.6 - - - +
328B ASP* 1.3 62.9 + - - +
330B LYS* 3.1 18.5 + - - +
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Residues in contact with ASP 328 (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 ILE* 3.1 13.8 + - + +
326B GLN 2.7 2.4 + - - -
327B LYS* 1.3 79.5 - - - +
329B LEU* 1.3 94.7 + - - +
330B LYS* 2.9 14.9 + - - +
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Residues in contact with LEU 329 (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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113B VAL* 4.5 13.3 - - + +
114B GLN* 2.9 40.7 - - + +
325B ILE* 3.4 13.6 + - + -
326B GLN* 2.6 20.5 + - + +
328B ASP* 1.3 103.9 + - - +
330B LYS* 1.3 68.0 + - - +
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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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113B VAL* 5.1 9.4 - - + -
144B ILE* 6.0 0.4 - - + -
147B TYR* 3.2 33.4 - - + +
151B LYS* 5.2 14.2 - - - +
152B LEU* 5.8 3.4 - - - +
326B GLN* 2.6 37.8 + - + +
327B LYS* 3.3 13.5 - - - +
328B ASP 2.9 2.9 + - - +
329B LEU* 1.3 72.5 - - - +
330B ASP* 1.3 83.3 + - - +
331B LEU* 4.1 13.8 - - - +
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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
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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