Contacts of the helix formed by residues 308 - 326 (chain D) in PDB entry 2LDX
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 THR 308 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D SER* 4.9 5.3 - - - -
221D LYS* 5.1 0.4 - - - +
306D ASN 3.5 3.0 + - - -
307D MET* 1.3 73.7 - - - +
309D ALA* 1.3 85.0 + - - +
310D GLU* 2.9 29.6 + - - +
311D GLU* 2.6 51.0 + - + +
312D GLU* 2.9 5.2 + - - -
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Residues in contact with ALA 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D MET 4.0 0.4 + - - -
308D THR* 1.3 80.6 + - - +
310D GLU* 1.3 57.8 + - - +
312D GLU* 3.0 16.2 - - - +
313D GLY* 2.9 15.5 + - - -
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Residues in contact with GLU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D LYS* 2.6 31.6 + - - +
308D THR* 2.7 28.4 + - - +
309D ALA* 1.3 72.5 - - + +
311D GLU* 1.3 62.8 + - - +
312D GLU 2.8 2.2 - - - -
313D GLY* 2.5 23.8 + - - +
314D LEU* 2.5 43.2 + - + +
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Residues in contact with GLU 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D VAL* 4.3 17.0 - - + +
199D ILE* 4.0 24.7 - - + +
200D TRP* 3.9 9.5 + - - +
201D SER* 2.9 45.3 + - - -
221D LYS* 4.8 8.6 + - - +
307D MET* 3.1 28.6 - - + -
308D THR* 2.6 37.9 + - + +
310D GLU* 1.3 85.5 + - - +
312D GLU* 1.3 51.7 + - - -
314D LEU* 3.8 2.3 - - - +
315D LEU* 2.9 26.5 + - - +
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Residues in contact with GLU 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D HIS* 3.6 42.5 + - + +
307D MET* 3.2 24.2 - - + +
308D THR 2.9 7.7 + - - +
309D ALA* 3.0 17.4 - - - +
311D GLU* 1.3 74.3 - - - +
313D GLY* 1.3 53.6 + - - +
315D LEU* 4.5 2.9 - - - -
316D LYS* 2.7 59.0 + - + +
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Residues in contact with GLY 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D ALA 2.9 6.0 + - - -
310D GLU* 2.5 25.6 + - - -
312D GLU* 1.3 67.7 - - - +
314D LEU* 1.3 55.9 + - - -
316D LYS* 2.8 30.9 + - - +
317D LYS* 2.8 13.5 + - - +
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Residues in contact with LEU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D SER 6.0 0.4 - - - +
196D SER 5.7 1.1 - - - +
197D VAL* 3.9 32.1 - - + -
198D PRO* 6.0 0.9 - - + -
221D LYS* 5.6 8.5 - - - +
310D GLU* 2.5 54.0 + - + +
311D GLU* 3.8 3.6 - - - +
313D GLY* 1.3 68.0 - - - -
315D LEU* 1.3 55.8 + - - +
317D LYS* 2.6 46.0 + - + +
318D SER* 2.8 8.2 + - - -
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Residues in contact with LEU 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D LEU* 3.4 32.5 - - + -
190D GLY* 3.8 9.4 - - - +
197D VAL* 3.8 16.9 - - + +
199D ILE* 4.9 0.2 - - + -
280D HIS* 3.6 28.3 - - + +
288D LEU* 3.3 36.1 - - + -
290D ILE* 4.1 6.3 - - + -
305D VAL* 5.9 0.2 - - + -
307D MET* 4.3 21.5 - - + -
311D GLU 2.9 19.3 + - - +
312D GLU* 4.1 1.3 - - - +
314D LEU* 1.3 72.5 - - - +
316D LYS* 1.3 66.3 + - - +
317D LYS 2.8 1.7 + - - -
318D SER* 3.0 13.1 + - - +
319D ALA* 3.1 13.3 + - - +
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Residues in contact with LYS 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D HIS* 3.2 34.7 - - + +
281D GLY* 3.6 18.9 - - - -
282D ILE* 4.3 7.0 - - + +
312D GLU* 2.7 45.9 + - - +
313D GLY* 2.8 12.2 + - - +
315D LEU* 1.3 71.4 - - - +
317D LYS* 1.3 54.3 + - - +
319D ALA* 3.1 18.0 - - - +
320D ASP* 3.6 16.1 + - - +
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Residues in contact with LYS 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D SER* 6.1 6.7 - - - +
313D GLY 2.8 9.4 + - - +
314D LEU* 2.6 29.9 + - + +
316D LYS* 1.3 69.3 - - - +
318D SER* 1.3 71.1 + - - +
320D ASP* 3.2 8.0 + - - +
321D THR* 3.0 25.1 + - - +
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Residues in contact with SER 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D GLY* 4.1 8.9 - - - -
191D GLU* 3.7 16.6 + - - -
195D SER* 3.0 42.2 + - - -
197D VAL* 5.6 0.2 - - - +
288D LEU* 5.0 1.1 - - - -
314D LEU 2.8 13.2 + - - -
315D LEU* 3.7 6.6 - - - -
317D LYS* 1.3 73.4 - - - +
319D ALA* 1.3 70.3 + - - +
321D THR* 2.5 26.1 + - - -
322D LEU* 2.9 17.9 + - - -
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Residues in contact with ALA 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D ILE* 3.1 48.7 - - + -
286D VAL* 3.1 30.3 - - - +
288D LEU* 4.7 4.6 - - - +
315D LEU 3.1 2.9 + - - +
316D LYS 3.1 14.6 - - - +
318D SER* 1.3 77.2 - - - +
320D ASP* 1.3 54.0 + - - +
322D LEU* 3.2 2.6 - - - +
323D TRP 2.8 26.7 + - - -
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Residues in contact with ASP 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D ILE* 5.3 3.0 - - - +
284D GLU* 5.8 1.7 - - - +
286D VAL* 5.1 1.6 - - - +
316D LYS 3.6 12.8 - - - +
317D LYS* 3.2 9.8 + - - +
318D SER 2.6 3.6 + - - -
319D ALA* 1.3 77.5 - - - +
321D THR* 1.3 69.8 + - - +
323D TRP* 2.5 35.0 + - - +
324D ASN* 3.1 4.7 + - - +
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Residues in contact with THR 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LEU* 5.4 6.7 - - + -
191D GLU* 5.4 2.7 - - - +
195D SER* 5.0 11.9 + - - +
317D LYS* 3.0 24.6 + - - +
318D SER* 2.5 18.0 + - - -
320D ASP* 1.3 75.1 - - - +
322D LEU* 1.3 56.4 + - - +
323D TRP 2.7 7.3 + - - -
324D ASN* 3.3 9.0 + - - +
325D MET* 3.6 26.9 + - + +
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Residues in contact with LEU 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU* 5.1 0.4 - - + -
140D ASP* 3.6 21.5 - - + +
141D ILE* 3.3 38.9 - - + +
191D GLU* 4.4 24.9 - - + +
286D VAL* 4.1 7.0 - - + -
287D PHE 3.5 10.8 - - - +
288D LEU* 3.4 35.2 - - + -
318D SER* 2.9 10.0 + - - +
319D ALA 3.2 11.9 - - - +
321D THR* 1.3 82.9 - - - +
323D TRP* 1.3 55.1 + - - +
325D MET* 3.4 13.3 - - - +
326D GLN* 2.9 30.1 + - - +
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Residues in contact with TRP 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D TYR* 4.8 7.2 - - - -
284D GLU* 3.3 42.1 + - + +
285D GLU* 4.2 19.7 - - + -
286D VAL* 3.5 21.5 - - + -
319D ALA 2.8 14.4 + - - +
320D ASP* 2.5 35.3 + - - +
322D LEU* 1.3 67.9 - - - +
324D ASN* 1.3 85.0 + - + +
325D MET 3.0 1.6 - - - -
326D GLN* 2.9 43.6 + - + +
327D LYS* 5.9 1.3 - - + -
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Residues in contact with ASN 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D ASP 3.1 9.5 + - - -
321D THR 3.3 1.3 + - - +
323D TRP* 1.3 88.0 + - + +
325D MET* 1.3 55.0 - - - +
326D GLN 2.4 0.9 + - - -
327D LYS* 2.4 72.2 + - + +
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Residues in contact with MET 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU* 3.3 48.2 - - + +
109D LEU* 4.3 18.8 - - + +
110D GLN* 5.8 0.2 - - - +
141D ILE* 3.9 18.5 - - + +
321D THR* 3.6 25.2 + - + +
322D LEU* 3.4 14.4 - - - +
324D ASN* 1.3 75.9 - - - +
326D GLN* 1.3 55.1 + - - +
327D LYS* 3.2 18.8 + - - +
328D ASN* 3.0 21.5 + - - -
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Residues in contact with GLN 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D ILE* 4.3 11.9 - - + +
144D TYR* 3.1 59.3 + - + +
285D GLU 3.1 9.7 - - - +
286D VAL* 3.9 17.4 - - - +
287D PHE 4.1 7.7 + - - +
322D LEU* 2.9 35.5 + - - +
323D TRP* 3.2 31.4 - - + +
324D ASN 2.4 6.8 + - - -
325D MET* 1.3 67.0 - - - +
327D LYS* 1.3 48.8 + - - -
328D ASN* 2.7 29.9 + - - +
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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