Contacts of the helix formed by residues 309 - 325 (chain A) in PDB entry 3LDH
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 PRO 309 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU 3.3 1.0 - - - +
308A LYS* 1.3 88.0 - - + +
310A ASP* 1.3 77.6 + - + +
312A GLU* 3.1 13.2 - - + -
313A GLN* 2.7 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TRP* 6.2 1.8 - - - +
221A GLU* 4.9 13.2 - - - +
222A VAL* 5.6 4.2 - - - +
308A LYS* 3.3 5.6 - - + -
309A PRO* 1.3 89.0 - - + +
311A GLU* 1.3 64.5 + - - +
313A GLN* 4.1 7.2 + - - +
314A GLN* 3.6 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ILE* 5.1 1.8 - - + +
200A PRO* 2.7 20.4 - - - +
201A SER* 1.8 60.1 + - - +
202A VAL* 3.3 19.2 - - + +
203A TRP* 3.5 17.4 + - + +
204A SER* 5.1 2.0 - - - +
307A LEU* 4.3 8.3 - - + -
308A LYS* 3.0 19.7 + - + +
310A ASP* 1.3 80.2 - - - +
312A GLU* 1.3 69.5 + - - +
314A GLN* 2.7 27.1 + - - +
315A LEU* 3.2 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR* 4.2 25.2 - - - +
306A LYS* 5.3 0.7 - - - -
307A LEU* 2.8 48.6 + - - +
308A LYS 1.9 32.2 + - - +
309A PRO* 2.9 15.7 + - + -
311A GLU* 1.3 69.6 - - - +
313A GLN* 1.3 69.2 - - + +
315A LEU* 3.2 13.9 + - - +
316A GLN* 3.4 9.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A PRO* 2.7 32.4 + - + +
310A ASP* 4.1 6.8 + - - +
312A GLU* 1.3 78.8 - - + +
314A GLN* 1.3 51.5 + - - +
316A GLN* 2.6 25.8 + - - +
317A LYS* 2.3 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A SER* 3.3 25.5 + - - +
200A PRO* 3.2 24.4 - - + +
310A ASP 3.6 10.5 + - - +
311A GLU* 2.7 31.1 + - - +
313A GLN* 1.3 73.7 - - - +
315A LEU* 1.3 55.3 + - - +
317A LYS* 3.0 20.2 - - - +
318A SER* 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ILE* 4.4 20.0 - - + -
193A GLY* 5.7 0.7 - - - -
200A PRO* 3.7 16.1 - - + +
275A VAL* 5.5 2.0 - - + -
279A TYR* 2.7 43.5 - - + +
281A ILE* 3.9 4.7 - - + +
287A LEU* 4.2 29.6 - - + -
289A LEU* 4.9 17.7 - - + -
305A MET* 5.8 0.9 - - + -
307A LEU* 3.1 14.8 - - + -
311A GLU* 3.2 2.2 + - - +
312A GLU 3.2 8.1 + - - +
313A GLN 3.0 0.6 - - - -
314A GLN* 1.3 76.1 - - - +
316A GLN* 1.3 74.4 + - - +
318A SER* 3.2 10.8 + - - -
319A ALA 3.4 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR* 4.4 9.4 - - + +
280A GLY* 3.6 32.3 + - - +
281A ILE* 3.0 18.1 - - + +
312A GLU* 3.4 4.7 + - + +
313A GLN* 2.6 29.2 + - - +
315A LEU* 1.3 79.5 - - - +
317A LYS* 1.3 75.1 + - - +
319A ALA* 2.8 18.7 + - - +
320A THR* 3.2 5.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A GLN* 2.3 29.2 + - + +
314A GLN* 3.0 32.1 - - - +
316A GLN* 1.3 69.7 - - - +
318A SER* 1.3 68.1 + - - +
320A THR* 2.6 47.2 + - + +
321A THR* 3.0 16.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLY* 5.4 2.7 - - - -
194A GLN* 3.3 24.0 + - - -
198A SER* 4.5 5.7 + - - -
200A PRO* 3.2 25.0 - - - +
287A LEU* 4.8 7.4 - - - -
314A GLN* 2.9 15.1 + - - +
315A LEU* 3.2 9.6 + - - -
316A GLN 3.0 0.8 + - - -
317A LYS* 1.3 76.3 - - - +
319A ALA* 1.3 56.8 + - - +
321A THR* 3.0 8.6 + - - -
322A LEU* 2.5 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ILE* 2.2 52.0 - - + -
285A VAL* 3.8 12.3 - - + +
287A LEU* 4.2 12.6 - - + +
315A LEU 3.4 1.6 + - - +
316A GLN 2.8 9.8 + - - +
318A SER* 1.3 74.7 - - - +
320A THR* 1.3 64.7 + - - +
322A LEU* 3.4 6.4 - - - +
323A TRP* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ILE* 4.7 0.2 - - - +
316A GLN* 3.2 5.9 + - - +
317A LYS* 2.6 49.9 + - - +
319A ALA* 1.3 78.1 - - - +
321A THR* 1.3 82.7 + - + +
323A TRP* 3.5 10.1 + - - +
324A ASP* 3.8 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 5.9 0.9 - - - +
194A GLN* 4.8 5.0 + - - -
198A SER* 5.4 4.4 + - - -
317A LYS* 3.0 34.7 + - + +
318A SER* 3.2 8.0 + - - +
320A THR* 1.3 83.4 - - + +
322A LEU* 1.3 66.6 + - - +
324A ASP* 3.3 21.3 - - - +
325A ILE* 4.6 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 4.8 16.4 - - + -
143A THR* 3.5 21.8 - - - +
144A ASP* 4.6 15.7 - - + +
194A GLN* 2.2 41.1 - - + +
285A VAL* 5.4 7.6 - - + -
286A PHE 4.5 9.6 - - - +
287A LEU* 5.1 5.8 - - + -
318A SER 2.5 22.7 + - - +
319A ALA* 3.4 8.3 - - - +
321A THR* 1.3 74.4 + - - +
323A TRP* 1.3 66.4 + - - +
325A ILE* 3.0 26.9 - - + +
326A GLN* 4.4 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ILE* 5.3 0.2 - - + -
283A ASP* 2.2 56.5 + - + +
284A ASN* 2.9 29.9 + - - -
285A VAL* 2.3 34.9 - - + +
319A ALA 2.9 14.6 + - - +
320A THR* 3.5 5.3 + - - +
322A LEU* 1.3 73.0 - - - +
324A ASP* 1.3 71.0 + - - +
325A ILE 3.2 0.2 - - - -
326A GLN* 3.0 42.8 + - + +
327A LYS* 3.2 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A THR 3.8 5.0 + - - +
321A THR* 3.3 18.9 + - - +
322A LEU 3.0 0.6 + - - -
323A TRP* 1.3 80.4 - - - +
325A ILE* 1.3 74.3 + - + +
327A LYS* 3.2 21.6 - - - +
328A ASP* 4.0 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 2.5 55.4 - - + +
113A VAL* 3.3 47.9 - - + +
144A ASP* 5.0 8.5 - - - +
321A THR 4.6 3.4 - - - +
322A LEU* 3.0 19.7 - - + +
324A ASP* 1.3 85.4 - - + +
326A GLN* 1.3 67.5 + - - +
328A ASP* 3.8 13.6 - - - +
329A LEU 4.4 0.2 + - - -
330A LYS* 5.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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