Contacts of the helix formed by residues 307 - 323 (chain A) in PDB entry 8LDH
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 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A LEU 4.6 1.3 - - - +
306A LYS* 1.3 88.4 - - + +
308A ASN* 1.3 60.6 + - + +
309A GLU 3.0 2.2 - - - -
310A GLU* 3.5 20.6 - - + +
311A GLN* 2.6 44.5 + - - +
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Residues in contact with ASN 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LYS* 4.2 21.0 + - - -
306A LYS* 4.3 10.7 - - + +
307A PRO* 1.3 82.7 - - + +
309A GLU* 1.3 72.7 + - - +
311A GLN* 3.8 7.0 - - - +
312A GLN* 3.6 31.0 + - - +
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Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A PRO* 4.8 9.6 - - + +
199A SER 4.2 5.4 - - - +
200A VAL* 4.1 24.9 - - - +
201A TRP* 4.5 8.3 + - - +
202A SER* 4.7 9.2 + - - -
219A LYS* 5.4 3.6 - - - -
304A LYS 4.8 0.5 - - - +
305A LEU* 3.4 27.9 - - + +
306A LYS* 2.9 43.3 + - + +
308A ASN* 1.3 86.7 - - - +
310A GLU* 1.3 60.0 + - - +
311A GLN 3.1 1.6 - - - -
312A GLN* 3.0 33.1 - - - +
313A LEU* 3.1 10.1 + - - +
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Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 4.1 34.5 - - + +
305A LEU* 4.7 12.2 - - + +
306A LYS 2.9 20.7 + - - +
307A PRO* 3.5 23.9 - - + +
309A GLU* 1.3 70.7 - - - +
311A GLN* 1.3 65.9 + - - +
313A LEU* 3.3 21.9 - - + +
314A GLN* 3.0 33.3 + - - +
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Residues in contact with GLN 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A PRO* 2.6 30.9 + - - +
308A ASN* 3.8 7.8 - - - +
310A GLU* 1.3 74.8 - - - +
312A GLN* 1.3 51.6 + - - +
314A GLN* 3.0 21.4 + - + +
315A LYS* 2.9 43.6 + - + +
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Residues in contact with GLN 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A SER 5.2 5.4 - - - +
197A VAL 6.2 0.4 - - - -
198A PRO* 3.9 29.6 - - + +
308A ASN* 3.6 25.1 + - - +
309A GLU* 3.0 19.0 + - - +
311A GLN* 1.3 79.3 - - - +
313A LEU* 1.3 56.9 + - - -
315A LYS* 3.4 19.2 + - + +
316A SER* 3.4 23.0 + - - -
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ILE* 3.7 33.4 - - + -
191A GLY* 3.8 17.9 - - - -
198A PRO* 4.7 3.8 - - + -
278A TYR* 3.8 30.1 - - + -
280A ILE* 4.4 12.1 - - + -
286A LEU* 3.7 13.8 - - + +
288A LEU* 4.9 8.5 - - + -
305A LEU* 3.3 28.0 - - + -
309A GLU 3.1 6.2 + - - +
310A GLU* 3.3 16.6 - - - +
312A GLN* 1.3 77.5 - - - +
314A GLN* 1.3 58.8 - - - +
316A SER* 3.2 11.1 + - - -
317A ALA* 3.1 21.8 + - - +
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Residues in contact with GLN 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A TYR 2.4 37.7 + - - +
279A GLY* 3.8 15.0 + - - +
280A ILE* 4.2 15.9 - - + -
310A GLU* 3.0 23.9 + - - +
311A GLN* 3.1 24.6 - - + +
313A LEU* 1.3 74.4 - - - +
315A LYS* 1.3 61.3 + - - +
316A SER 3.1 0.2 - - - -
317A ALA* 3.1 13.2 + - - +
318A THR* 3.2 14.3 + - - -
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Residues in contact with LYS 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A GLN* 2.9 22.6 + - + +
312A GLN* 3.5 22.6 - - - +
313A LEU 3.3 0.4 - - - -
314A GLN* 1.3 74.9 - - - +
316A SER* 1.3 54.6 + - - +
318A THR* 2.9 18.0 - - + +
319A THR* 2.7 29.6 + - - +
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Residues in contact with SER 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLY* 5.5 0.2 - - - -
192A GLU* 3.3 31.1 + - - +
196A SER* 4.2 10.9 + - - -
286A LEU* 3.6 22.7 - - - -
312A GLN 3.4 10.5 + - - -
313A LEU* 3.2 12.7 + - - -
314A GLN 3.1 0.4 - - - -
315A LYS* 1.3 75.4 - - - +
317A ALA* 1.3 67.9 + - - +
318A THR 3.1 0.6 + - - -
319A THR* 3.3 5.8 + - - -
320A LEU* 2.9 29.7 + - - +
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ILE* 3.5 48.2 - - + -
282A ASP* 3.9 3.3 - - - +
284A VAL* 3.3 25.5 - - + +
286A LEU* 4.5 1.3 - - + +
313A LEU 3.1 2.0 + - - -
314A GLN* 3.1 7.0 + - - +
316A SER* 1.3 82.1 - - - +
318A THR* 1.3 55.2 - - - +
321A TRP* 3.2 26.5 + - - +
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Residues in contact with THR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ASP* 5.3 1.1 - - - -
314A GLN 3.2 7.9 + - - -
315A LYS* 2.9 33.7 - - + +
316A SER 3.1 0.2 - - - -
317A ALA* 1.3 74.9 - - - +
319A THR* 1.3 71.4 - - - +
320A LEU 3.1 1.1 - - - -
321A TRP* 3.1 6.5 + - - +
322A ASP* 2.9 41.0 + - - +
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Residues in contact with THR 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ARG* 3.3 33.7 - - - +
192A GLU* 5.2 4.3 - - - +
315A LYS* 2.7 23.4 + - - +
316A SER* 3.6 6.7 - - - -
318A THR* 1.3 86.6 - - - +
320A LEU* 1.3 55.4 + - + -
322A ASP* 3.5 13.8 - - - +
323A ILE* 3.2 20.8 - - + +
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ARG* 4.0 14.1 - - - +
141A ASP* 4.2 9.0 - - + -
142A VAL* 3.0 42.0 - - + +
192A GLU* 4.1 16.6 - - + +
284A VAL* 3.6 19.5 - - + -
285A PHE 4.0 7.0 - - - +
286A LEU* 3.5 32.8 - - + -
316A SER 2.9 17.2 + - - +
319A THR* 1.3 74.3 - - - +
321A TRP* 1.3 64.2 + - - +
322A ASP 3.0 2.0 - - - -
323A ILE* 3.3 5.9 + - - +
324A GLN* 2.9 36.8 + - - +
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Residues in contact with TRP 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A TYR* 4.2 13.0 - - - -
149A LYS* 6.1 0.2 - - - -
282A ASP* 3.3 35.9 + - + +
283A ASN* 3.5 35.9 - - + -
284A VAL* 4.2 1.1 - - + +
317A ALA 3.2 17.9 + - - +
318A THR* 3.1 7.5 + - - +
320A LEU* 1.3 80.9 - - - +
322A ASP* 1.3 65.9 + - - +
324A GLN* 3.3 50.6 + - + +
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Residues in contact with ASP 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A THR* 2.9 21.7 + - - +
319A THR* 3.5 12.3 - - - +
321A TRP* 1.3 80.5 - - - +
323A ILE* 1.3 67.8 + - + +
324A GLN 3.0 2.0 + - - +
325A LYS* 3.3 26.9 + - - +
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Residues in contact with ILE 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ARG* 4.3 27.4 - - + +
107A LEU* 3.9 37.8 - - + +
110A VAL* 3.7 39.0 - - + -
142A VAL* 4.4 9.4 - - + -
319A THR* 3.2 20.2 - - + +
320A LEU* 3.3 11.2 + - - +
322A ASP* 1.3 73.8 - - + +
324A GLN* 1.3 53.3 + - + +
325A LYS* 2.3 27.0 + - - +
326A ASP* 3.2 17.7 - - - +
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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