Contacts of the helix formed by residues 248 - 264 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ASP* 2.7 7.0 + - - -
29C ASP* 4.4 8.1 - - - -
30C VAL* 4.2 6.0 - - - +
33C ALA* 3.8 9.4 - - - +
244C LYS* 2.5 32.1 + - - -
246C TYR* 3.1 27.1 - - - -
247C THR* 1.3 71.5 - - - +
249C TRP* 1.3 82.3 + - - +
250C ALA 3.6 1.6 - - - -
251C ILE* 2.7 26.7 - - - +
252C GLY 3.4 1.9 + - - -
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Residues in contact with TRP 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASP 5.6 1.3 - - - -
32A MET* 3.2 55.4 + - + +
36A ILE* 4.8 21.2 - - + +
60A GLU* 3.6 9.9 + - - -
63A ASP* 3.5 9.5 + - + +
64A LEU* 2.8 44.8 - - + +
249A TRP* 4.7 25.1 - + - -
29C ASP* 5.1 3.1 - - + -
33C ALA* 3.6 24.1 - - + +
36C ILE* 5.9 2.5 - - + -
244C LYS* 4.1 7.4 - - - -
246C TYR* 5.2 7.6 - - - -
248C SER* 1.3 90.4 + - - +
250C ALA* 1.3 56.1 + - + +
252C GLY* 2.6 27.0 + - - -
253C LEU* 3.0 23.5 + - + +
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Residues in contact with ALA 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASP* 3.5 29.5 + - - +
66A HIS* 4.5 9.9 - - + +
67A GLY* 4.4 14.4 - - - +
164C LEU* 4.1 10.2 - - + +
168C ARG* 4.8 8.7 - - - +
248C SER 3.6 0.8 - - - -
249C TRP* 1.3 77.0 - - - +
251C ILE* 1.3 61.0 + - - +
253C LEU* 4.1 12.1 - - - +
254C SER* 3.3 20.4 + - - -
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Residues in contact with ILE 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASP* 5.3 0.2 + - - -
30C VAL* 3.2 25.8 - - + -
135C VAL* 3.4 34.5 - - + +
160C SER* 4.4 9.9 - - - -
164C LEU* 3.7 36.7 - - + +
247C THR* 3.5 24.3 + - + +
248C SER 2.7 26.8 + - - +
249C TRP 3.0 1.4 + - - -
250C ALA* 1.3 76.6 - - - +
252C GLY* 1.3 62.6 - - - +
254C SER* 3.3 4.0 - - - +
255C VAL* 3.0 36.9 + - + +
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Residues in contact with GLY 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ALA 4.1 4.3 - - - -
34C CYS* 3.6 33.4 - - - +
248C SER 3.4 1.8 + - - -
249C TRP 2.6 17.3 + - - -
251C ILE* 1.3 73.2 - - - +
253C LEU* 1.3 57.0 - - - -
255C VAL* 2.9 14.4 + - - +
256C THR* 2.8 28.0 + - - +
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ILE* 4.0 22.9 - - + -
40A LEU* 3.9 16.4 - - + -
64A LEU* 5.6 2.7 - - + -
67A GLY* 5.1 9.9 - - - +
70A PHE* 3.3 56.5 - - + -
71A LEU* 4.6 12.1 - - + -
33C ALA 4.9 1.0 + - - -
37C SER* 4.0 6.9 + - - +
249C TRP* 3.0 24.9 + - + +
250C ALA* 4.3 9.2 - - - +
252C GLY* 1.3 71.6 - - - +
254C SER* 1.3 66.8 + - - +
256C THR* 3.0 20.3 - - - +
257C ASP* 3.0 13.2 + - - +
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Residues in contact with SER 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C SER* 4.8 4.0 + - - -
163C ASN* 2.9 24.9 + - - +
164C LEU* 4.0 22.8 + - - +
167C ALA* 6.3 1.3 - - - -
250C ALA 3.3 14.5 + - - -
251C ILE* 3.3 14.5 + - - +
252C GLY 3.1 0.6 - - - -
253C LEU* 1.3 76.1 - - - +
255C VAL* 1.3 60.7 + - - +
257C ASP* 2.9 28.0 + - - +
258C LEU* 3.1 14.6 + - - +
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Residues in contact with VAL 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C CYS* 3.7 28.5 - - - -
38C ILE* 5.3 4.0 - - + -
92C ILE* 4.1 11.7 - - + -
133C ILE* 4.1 28.6 - - + +
135C VAL* 4.0 13.0 - - + -
160C SER* 5.3 4.0 - - - -
251C ILE* 3.0 33.0 - - + +
252C GLY 2.9 8.7 + - - +
254C SER* 1.3 70.4 - - - +
256C THR* 1.3 55.4 + - - +
257C ASP 2.9 7.0 - - - -
258C LEU* 2.8 26.6 + - - +
259C ALA* 2.8 16.3 + - - +
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Residues in contact with THR 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A PHE* 4.7 9.9 - - + -
34C CYS 5.1 2.9 - - - +
37C SER* 3.7 28.9 + - - +
38C ILE* 3.8 22.4 - - + -
41C LYS* 5.4 3.1 - - - +
43C LEU* 3.6 12.6 - - - +
252C GLY 2.8 27.4 - - - +
253C LEU* 3.0 20.9 - - - +
255C VAL* 1.3 79.5 - - - +
257C ASP* 1.3 53.1 - - - +
259C ALA* 3.5 9.8 - - - +
260C ARG* 2.8 33.8 + - - +
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Residues in contact with ASP 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU 5.5 2.9 - - - +
70A PHE* 4.7 17.8 - - + -
163C ASN* 3.9 9.6 + - - +
253C LEU 3.0 11.6 + - - +
254C SER* 2.9 15.6 - - - +
256C THR* 1.3 80.0 - - - +
258C LEU* 1.3 57.4 + - - +
260C ARG* 4.1 6.8 + - - -
261C SER* 3.7 18.5 + - - -
268C ARG* 3.8 20.4 + - - +
270C HIS* 3.3 24.1 - - - -
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Residues in contact with LEU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ILE* 4.3 14.6 - - + -
158C ILE* 5.8 2.7 - - + -
159C GLY 6.2 0.7 - - - -
160C SER* 5.4 7.2 - - - +
163C ASN* 3.0 41.3 - - + +
254C SER* 3.1 20.1 + - - +
255C VAL* 2.8 16.0 + - - +
257C ASP* 1.3 78.2 - - - +
259C ALA* 1.3 57.0 + - - +
260C ARG 3.3 0.2 - - - -
261C SER* 3.2 5.7 + - - -
262C ILE* 2.8 41.5 + - + +
270C HIS* 3.9 7.2 - - + +
272C VAL* 3.4 19.7 - - + -
294C LEU* 3.1 35.9 - - + -
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Residues in contact with ALA 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE* 4.5 9.0 - - + -
43C LEU* 4.1 7.9 - - + -
90C LEU* 4.1 14.4 - - + -
133C ILE* 4.2 0.9 - - + +
255C VAL 2.8 11.5 + - - +
256C THR* 3.5 13.9 - - - +
258C LEU* 1.3 76.4 - - - +
260C ARG* 1.3 56.3 + - - +
262C ILE* 2.9 14.0 + - - +
263C LEU* 2.6 56.0 + - + +
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Residues in contact with ARG 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU 5.3 0.8 + - - -
72B SER* 2.3 31.1 + - - +
41C LYS* 4.2 17.2 - - + +
43C LEU* 3.9 15.2 - - + +
256C THR* 2.8 22.8 + - - +
257C ASP* 3.8 10.5 + - - +
259C ALA* 1.3 71.8 - - - +
261C SER* 1.3 55.9 + - - +
263C LEU* 4.9 0.2 - - - -
264C LYS* 2.8 64.6 + - + +
266C LEU* 3.0 13.6 - - - +
268C ARG* 2.6 54.3 - - - +
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Residues in contact with SER 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C ASP 3.7 10.7 + - - -
258C LEU 3.2 10.4 + - - -
259C ALA 3.0 0.4 - - - -
260C ARG* 1.3 78.7 - - - +
262C ILE* 1.3 68.1 + - - +
265C ASN* 3.4 1.6 + - - -
266C LEU* 2.9 43.7 + - - -
268C ARG* 4.4 8.5 - - - -
270C HIS* 3.8 17.9 - - - -
294C LEU* 3.3 31.0 + - - +
295C GLY* 4.2 0.2 - - - -
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Residues in contact with ILE 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C LEU* 3.7 7.2 - - + -
131C LYS* 3.0 56.8 - - + +
133C ILE* 3.6 20.4 - - + -
158C ILE* 5.1 0.9 - - + -
258C LEU* 2.8 37.7 - - + +
259C ALA* 2.9 10.9 + - - +
261C SER* 1.3 84.0 + - - +
263C LEU* 1.3 71.2 + - + +
265C ASN* 2.9 18.2 + - - -
294C LEU* 4.7 8.7 - - + -
295C GLY* 3.3 18.8 - - - +
296C GLU* 3.3 17.6 + - - +
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Residues in contact with LEU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ASP* 4.2 9.9 - - - +
22C ILE* 4.2 27.8 - - + -
43C LEU* 4.8 19.3 - - + +
89C LYS* 4.7 14.8 - - + -
90C LEU* 4.4 18.2 - - + -
259C ALA* 2.6 52.2 + - + +
260C ARG* 4.5 2.0 - - - +
262C ILE* 1.3 83.5 - - + +
264C LYS* 1.3 61.3 + - + +
265C ASN* 3.2 4.7 + - - +
296C GLU* 5.1 7.1 - - - +
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Residues in contact with LYS 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLY* 5.1 12.5 - - - -
45B ASP* 3.7 13.0 - - + +
72B SER* 2.6 42.8 + - - +
74B PRO* 3.3 21.8 - - - +
41C LYS* 2.9 25.8 - - - +
42C GLY 5.9 1.8 - - - -
43C LEU* 5.3 9.2 - - + -
260C ARG* 2.8 48.2 + - + +
263C LEU* 1.3 77.7 - - + +
265C ASN* 1.3 66.3 + - - +
266C LEU* 3.0 16.0 + - + +
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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