Contacts of the helix formed by residues 248 - 264 (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 SER 248 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B ASP* 2.7 7.3 + - - -
29D ASP* 4.4 8.1 - - - -
30D VAL* 4.2 5.7 - - - +
33D ALA* 3.8 9.1 - - - +
244D LYS* 2.5 31.6 + - - -
246D TYR* 3.1 26.6 - - - -
247D THR* 1.3 71.5 - - - +
249D TRP* 1.3 82.7 + - - +
250D ALA 3.6 1.8 - - - -
251D ILE* 2.7 26.5 - - - +
252D GLY 3.4 1.9 + - - -
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Residues in contact with TRP 249 (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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29B ASP 5.6 1.1 - - - -
32B MET* 3.2 54.8 + - + +
33B ALA 5.3 0.2 - - - -
36B ILE* 4.8 21.7 - - + +
60B GLU* 3.6 11.4 + - - -
63B ASP* 3.5 10.0 + - + +
64B LEU* 2.8 45.0 - - + +
249B TRP* 4.7 26.0 - + - -
29D ASP* 5.1 3.1 - - + -
33D ALA* 3.6 24.9 - - + +
36D ILE* 5.9 2.7 - - + -
244D LYS* 4.1 7.0 - - - -
246D TYR* 5.2 7.2 - + - -
248D SER* 1.3 89.7 + - - +
250D ALA* 1.3 53.3 + - - +
252D GLY* 2.6 26.7 + - - -
253D LEU* 3.0 23.1 + - + +
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Residues in contact with ALA 250 (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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63B ASP* 3.5 30.2 + - - +
66B HIS* 4.6 9.2 - - + +
67B GLY* 4.4 14.8 - - - +
164D LEU* 4.1 9.5 - - + +
168D ARG* 4.8 9.0 - - - +
248D SER 3.6 0.6 - - - -
249D TRP* 1.3 76.7 - - - +
251D ILE* 1.3 61.0 + - - +
253D LEU* 4.1 11.6 - - - +
254D SER* 3.3 20.6 + - - -
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Residues in contact with ILE 251 (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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30D VAL* 3.2 25.6 - - + -
135D VAL* 3.4 35.0 - - + +
160D SER* 4.4 9.4 - - - -
164D LEU* 3.7 36.5 - - + +
247D THR* 3.5 25.0 + - + +
248D SER 2.7 26.4 + - - +
249D TRP 3.0 1.4 + - - -
250D ALA* 1.3 75.9 - - - +
252D GLY* 1.3 62.1 - - - +
254D SER* 3.3 3.8 - - - +
255D VAL* 3.0 36.5 + - + +
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Residues in contact with GLY 252 (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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33D ALA 4.1 3.6 - - - -
34D CYS* 3.6 34.1 - - - +
248D SER 4.2 1.8 - - - -
249D TRP 2.6 16.4 + - - -
251D ILE* 1.3 73.5 - - - +
253D LEU* 1.3 58.0 + - - -
255D VAL* 2.9 15.1 + - - +
256D THR* 2.8 27.6 + - - +
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Residues in contact with LEU 253 (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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36B ILE* 4.0 22.7 - - + -
40B LEU* 3.9 16.8 - - + -
64B LEU* 5.6 2.9 - - + -
67B GLY* 5.1 10.1 - - - +
70B PHE* 3.3 57.4 - - + -
71B LEU* 4.6 10.5 - - + -
33D ALA 4.9 0.8 + - - -
37D SER* 4.0 7.2 + - - +
249D TRP* 3.0 27.0 + - + +
250D ALA* 4.3 8.1 - - - +
252D GLY* 1.3 71.6 - - - +
254D SER* 1.3 69.3 + - - +
256D THR* 3.0 21.1 - - - +
257D ASP* 3.0 12.7 + - - +
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Residues in contact with SER 254 (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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160D SER* 4.8 4.5 + - - -
163D ASN* 2.9 24.9 + - - +
164D LEU* 4.0 22.2 + - - +
250D ALA 3.3 14.5 + - - -
251D ILE* 3.3 14.4 + - - +
252D GLY 3.1 0.6 - - - -
253D LEU* 1.3 76.9 - - - +
255D VAL* 1.3 60.5 + - - +
257D ASP* 2.9 27.5 + - - +
258D LEU* 3.1 14.0 + - - +
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Residues in contact with VAL 255 (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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34D CYS* 3.7 28.9 - - - -
38D ILE* 5.3 4.3 - - + -
92D ILE* 4.1 11.4 - - + -
133D ILE* 4.1 28.0 - - + +
135D VAL* 4.0 13.7 - - + -
160D SER* 5.3 4.0 - - - -
251D ILE* 3.0 33.0 - - + +
252D GLY 2.9 8.6 + - - +
254D SER* 1.3 70.1 - - - +
256D THR* 1.3 56.1 + - - +
257D ASP 2.9 6.5 - - - -
258D LEU* 2.8 26.5 + - - +
259D ALA* 2.8 16.8 + - - +
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Residues in contact with THR 256 (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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70B PHE* 4.7 9.9 - - + -
34D CYS* 5.1 2.9 - - - +
37D SER* 3.7 28.4 + - - +
38D ILE* 3.8 22.4 - - + +
41D LYS* 5.4 3.1 - - - +
43D LEU* 3.6 12.6 - - - +
252D GLY 2.8 28.3 - - - +
253D LEU* 3.0 20.4 - - - +
255D VAL* 1.3 79.1 - - - +
257D ASP* 1.3 53.5 + - - +
259D ALA* 3.5 9.6 - - - +
260D ARG* 2.8 33.4 + - - +
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Residues in contact with ASP 257 (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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69B LEU 5.5 3.2 - - - +
70B PHE* 4.7 17.7 - - + -
163D ASN* 3.9 9.6 + - - +
253D LEU 3.0 11.4 + - - +
254D SER* 2.9 15.9 - - - +
256D THR* 1.3 79.4 - - - +
258D LEU* 1.3 57.5 + - - +
260D ARG* 4.1 7.1 + - - -
261D SER* 3.7 17.8 + - - -
268D ARG* 3.8 20.4 + - - +
270D HIS* 3.3 23.8 - - - -
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Residues in contact with LEU 258 (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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133D ILE* 4.3 14.4 - - + -
158D ILE* 5.8 3.4 - - + -
159D GLY 5.9 0.9 - - - +
160D SER* 5.4 6.7 - - - +
163D ASN* 3.1 40.8 - - + +
254D SER* 3.1 20.3 + - - +
255D VAL* 2.8 15.3 + - - +
257D ASP* 1.3 78.2 - - - +
259D ALA* 1.3 56.6 + - - +
260D ARG 3.3 0.2 - - - -
261D SER* 3.2 5.9 + - - -
262D ILE* 2.8 42.5 + - + +
270D HIS* 3.9 7.6 - - + +
272D VAL* 3.4 19.5 - - + -
294D LEU* 3.1 35.2 - - + -
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Residues in contact with ALA 259 (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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38D ILE* 4.5 9.0 - - + -
43D LEU* 4.1 7.6 - - + -
90D LEU* 4.1 14.4 - - + -
133D ILE* 4.2 0.6 - - + +
255D VAL 2.8 11.3 + - - +
256D THR* 3.5 14.6 - - - +
258D LEU* 1.3 76.4 - - - +
260D ARG* 1.3 55.6 + - - +
262D ILE* 2.9 13.7 + - - +
263D LEU* 2.6 56.1 + - + +
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Residues in contact with ARG 260 (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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71A LEU 5.3 0.8 + - - -
72A SER* 2.3 30.7 + - - +
41D LYS* 4.2 17.4 - - + +
43D LEU* 3.9 16.3 - - + +
256D THR* 2.8 22.4 + - - +
257D ASP* 3.8 10.1 - - - +
259D ALA* 1.3 72.4 - - - +
261D SER* 1.3 56.0 + - - +
263D LEU* 4.9 0.4 - - - -
264D LYS* 2.8 64.2 + - + +
266D LEU* 3.0 13.8 - - - +
268D ARG* 2.6 55.4 - - - +
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Residues in contact with SER 261 (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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257D ASP 3.7 11.6 + - - -
258D LEU 3.2 10.5 + - - -
259D ALA 3.0 0.4 - - - -
260D ARG* 1.3 80.2 - - - +
262D ILE* 1.3 68.9 + - - +
265D ASN* 3.4 1.6 + - - -
266D LEU* 2.9 44.1 + - - +
268D ARG* 4.4 7.2 - - - -
270D HIS* 3.8 17.9 - - - -
294D LEU* 3.3 30.5 + - - +
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Residues in contact with ILE 262 (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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90D LEU* 3.7 6.7 - - + -
131D LYS* 3.0 57.9 - - + +
133D ILE* 3.6 20.9 - - + -
158D ILE* 5.1 1.6 - - + -
258D LEU* 2.8 36.8 - - + +
259D ALA* 2.9 11.1 + - - +
261D SER* 1.3 84.8 + - - +
263D LEU* 1.3 71.3 + - + +
265D ASN* 2.9 18.2 + - - -
294D LEU* 4.7 9.0 - - + -
295D GLY* 3.3 17.0 - - - +
296D GLU* 3.3 17.7 + - - +
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Residues in contact with LEU 263 (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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45A ASP* 4.2 10.0 - - - +
22D ILE* 4.2 27.8 - - + -
43D LEU* 4.8 19.1 - - + +
89D LYS* 4.7 15.0 - - + +
90D LEU* 4.4 17.5 - - + -
259D ALA* 2.6 51.3 + - + +
260D ARG* 4.5 2.0 - - - +
262D ILE* 1.3 82.4 - - + +
264D LYS* 1.3 60.5 + - + +
265D ASN* 3.2 5.2 + - - +
296D GLU* 5.1 7.3 - - - +
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Residues in contact with LYS 264 (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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42A GLY* 5.1 12.3 - - - -
45A ASP* 3.7 13.0 - - + +
72A SER* 2.6 44.9 + - - +
74A PRO* 3.3 22.0 - - - +
41D LYS* 2.9 25.4 - - - +
42D GLY 5.9 1.8 - - - -
43D LEU* 5.3 9.4 - - + -
260D ARG* 2.8 46.8 + - + +
263D LEU* 1.3 77.6 - - + +
265D ASN* 1.3 66.3 + - - +
266D LEU* 3.0 15.8 + - + +
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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