Contacts of the helix formed by residues 308 - 326 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A SER* 4.9 4.9 - - - -
221A LYS* 5.1 0.4 - - - +
306A ASN 3.5 3.0 + - - -
307A MET* 1.3 74.4 - - - +
309A ALA* 1.3 85.3 + - - +
310A GLU* 2.9 31.0 + - - +
311A GLU* 2.6 51.2 + - + +
312A GLU 2.9 4.9 + - - -
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Residues in contact with ALA 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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307A MET 4.0 1.0 + - - -
308A THR* 1.3 79.5 + - - +
310A GLU* 1.3 56.9 + - - +
312A GLU* 3.0 17.7 - - - +
313A GLY* 2.9 15.7 + - - -
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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
----------------------------------------------------------
221A LYS* 2.6 32.4 + - - +
308A THR* 2.7 29.4 + - - +
309A ALA* 1.3 72.5 - - + +
311A GLU* 1.3 63.3 + - - +
312A GLU 2.8 1.8 - - - -
313A GLY* 2.5 10.6 + - - +
314A LEU* 2.5 56.5 + - + +
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A VAL* 4.3 16.6 - - + +
198A PRO 4.9 0.2 - - - +
199A ILE* 4.0 23.7 - - + +
200A TRP* 3.9 9.2 + - - +
201A SER* 2.9 45.0 + - - -
221A LYS* 4.8 8.4 + - - +
307A MET* 3.1 29.4 - - + -
308A THR* 2.6 37.2 + - + +
310A GLU* 1.3 85.3 + - - +
312A GLU* 1.3 52.7 + - - -
314A LEU* 3.8 2.0 - - - +
315A LEU* 2.8 27.4 + - - +
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Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A HIS* 3.6 40.9 + - + +
307A MET* 3.2 24.2 - - + +
308A THR 2.9 7.4 + - - +
309A ALA* 3.0 17.7 - - - +
310A GLU 2.8 0.2 - - - -
311A GLU* 1.3 74.3 - - - +
313A GLY* 1.3 54.1 + - - +
315A LEU* 4.5 2.9 - - - -
316A LYS* 2.7 58.7 + - + +
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Residues in contact with GLY 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ALA 2.9 5.6 + - - -
310A GLU* 2.5 26.4 + - - -
312A GLU* 1.3 68.0 - - - +
314A LEU* 1.3 56.3 + - - -
316A LYS* 2.8 31.2 + - - +
317A LYS* 2.8 13.7 + - - +
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A SER 6.0 0.9 - - - +
196A SER 5.7 1.1 - - - +
197A VAL* 3.9 31.6 - - + -
198A PRO* 6.0 0.7 - - + -
221A LYS* 5.6 9.2 - - - +
310A GLU* 2.5 53.3 + - + +
311A GLU* 3.8 4.3 - - - +
313A GLY* 1.3 67.9 - - - -
315A LEU* 1.3 56.3 + - - +
317A LYS* 2.6 46.6 + - + +
318A SER* 2.8 8.2 + - - -
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 3.4 33.7 - - + -
190A GLY* 3.8 7.6 - - - +
197A VAL* 3.8 16.7 - - + +
199A ILE* 4.9 0.2 - - + -
280A HIS* 3.6 28.7 - - + +
288A LEU* 3.3 36.1 - - + -
290A ILE* 4.1 6.5 - - + -
305A VAL* 5.9 0.2 - - + -
307A MET* 4.3 21.1 - - + -
311A GLU 2.8 19.3 + - - +
312A GLU* 4.1 1.6 - - - +
314A LEU* 1.3 71.7 - - - +
316A LYS* 1.3 64.8 + - - +
317A LYS 2.8 1.6 + - - -
318A SER* 3.0 13.3 + - - +
319A ALA* 3.1 13.2 + - - +
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Residues in contact with LYS 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A HIS* 3.2 34.9 - - + +
281A GLY* 3.6 17.5 - - - -
282A ILE* 4.3 7.1 - - + +
312A GLU* 2.7 48.1 + - - +
313A GLY* 2.8 11.1 + - - +
315A LEU* 1.3 71.4 - - - +
317A LYS* 1.3 54.7 + - - +
319A ALA* 3.1 18.2 - - - +
320A ASP* 3.6 15.6 + - - +
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Residues in contact with LYS 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A SER* 6.1 5.6 - - - +
313A GLY 2.8 10.5 + - - +
314A LEU* 2.6 30.5 + - + +
316A LYS* 1.3 67.8 - - - +
318A SER* 1.3 72.0 + - - +
320A ASP* 3.2 7.8 + - - +
321A THR* 3.0 24.4 + - - +
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Residues in contact with SER 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A GLY* 4.1 8.8 - - - -
191A GLU* 3.7 16.4 + - - -
195A SER* 3.0 41.4 + - - -
288A LEU* 5.0 1.3 - - - -
314A LEU 2.8 13.2 + - - -
315A LEU* 3.7 6.6 - - - -
317A LYS* 1.3 71.9 - - - +
319A ALA* 1.3 70.3 + - - +
321A THR* 2.5 26.7 + - - -
322A LEU* 2.9 17.6 + - - -
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Residues in contact with ALA 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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282A ILE* 3.1 48.0 - - + -
286A VAL* 3.1 31.5 - - + +
288A LEU* 4.7 4.6 - - - +
315A LEU 3.1 2.9 + - - +
316A LYS 3.1 15.5 - - - +
318A SER* 1.3 77.2 - - - +
320A ASP* 1.3 53.6 + - - +
322A LEU* 3.2 2.3 - - - +
323A TRP 2.8 26.7 + - - -
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Residues in contact with ASP 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ILE* 5.3 3.5 - - - +
284A GLU* 5.8 1.9 - - - +
286A VAL* 5.1 1.4 - - - +
316A LYS 3.6 12.5 - - - +
317A LYS* 3.2 9.5 + - - +
318A SER 2.6 3.8 + - - -
319A ALA* 1.3 77.8 - - - +
321A THR* 1.3 71.4 + - - +
323A TRP* 2.5 35.7 + - + +
324A ASN 3.1 4.7 + - - -
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Residues in contact with THR 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 5.4 7.2 - - + -
191A GLU* 5.4 2.5 - - - +
195A SER* 5.0 11.8 + - - +
317A LYS* 3.0 25.0 + - - +
318A SER* 2.5 19.5 + - - -
320A ASP* 1.3 75.3 - - - +
322A LEU* 1.3 57.3 + - - +
323A TRP 2.7 7.8 + - - -
324A ASN* 3.3 9.0 + - - +
325A MET* 3.6 26.3 + - + +
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Residues in contact with LEU 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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106A LEU* 5.2 0.4 - - + -
140A ASP* 3.6 22.9 - - + +
141A ILE* 3.3 38.3 - - + +
191A GLU* 4.4 23.1 - - + +
286A VAL* 4.1 5.8 - - + -
287A PHE 3.5 10.1 - - - +
288A LEU* 3.4 35.7 - - + -
318A SER* 2.9 9.8 + - - +
319A ALA 3.2 12.6 - - - +
321A THR* 1.3 81.7 - - - +
323A TRP* 1.3 55.9 + - - +
325A MET* 3.4 13.7 - - - +
326A GLN* 2.9 29.8 + - - +
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Residues in contact with TRP 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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144A TYR* 4.8 7.4 - - - -
284A GLU* 3.3 41.3 + - + +
285A GLU* 4.2 19.5 - - + -
286A VAL* 3.5 22.2 - - + -
319A ALA 2.8 13.9 + - - +
320A ASP* 2.5 35.9 + - - +
322A LEU* 1.3 66.7 - - - +
324A ASN* 1.3 84.9 + - + +
325A MET 3.0 1.1 - - - -
326A GLN* 2.9 42.6 + - + +
327A LYS* 5.9 2.2 - - + -
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Residues in contact with ASN 324 (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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320A ASP 3.1 9.5 + - - -
321A THR 3.3 1.1 + - - +
323A TRP* 1.3 88.6 + - + +
325A MET* 1.3 54.5 - - - +
326A GLN 2.4 1.0 + - - -
327A LYS* 2.4 70.5 + - + +
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Residues in contact with MET 325 (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 LEU* 3.3 47.6 - - + +
109A LEU* 4.3 18.9 - - + +
110A GLN* 5.8 0.2 - - - +
141A ILE* 3.9 17.7 - - + +
321A THR* 3.6 26.1 + - + +
322A LEU 3.4 13.9 - - - +
324A ASN* 1.3 75.9 - - - +
326A GLN* 1.3 56.4 + - - +
327A LYS* 3.2 19.3 + - - +
328A ASN* 3.0 22.1 + - - +
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Residues in contact with GLN 326 (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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141A ILE* 4.3 11.5 - - + +
144A TYR* 3.1 59.6 + - + +
285A GLU 3.1 9.9 - - - +
286A VAL* 3.9 17.0 - - - +
287A PHE 4.1 7.9 + - - +
322A LEU* 2.9 36.4 + - - +
323A TRP* 3.2 30.2 - - + +
324A ASN 2.4 7.0 + - - -
325A MET* 1.3 68.0 - - - +
327A LYS* 1.3 50.2 + - - -
328A ASN* 2.7 30.4 + - - +
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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