Contacts of the helix formed by residues 241 - 259 (chain B) in PDB entry 4MDH
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 241 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLU* 2.9 22.3 + - - +
15B ILE* 5.5 2.1 - - - +
157B LEU* 5.3 1.3 - - - -
161B ARG* 3.0 30.0 + - - -
230B GLY* 5.2 5.6 - - - -
233B VAL* 3.6 21.3 - - - +
234B ILE* 4.8 5.3 - - - +
239B LEU 3.6 0.2 + - - -
240B SER* 1.3 69.1 - - - +
242B ALA* 1.3 53.6 + - - +
244B SER* 3.3 9.0 + - - -
245B ALA* 2.9 28.6 + - - +
335B NAD 5.5 8.3 - - - -
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Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR* 3.0 14.2 + - + +
14B GLN* 3.5 32.5 - - + +
15B ILE* 4.0 11.7 - - - +
18B SER* 3.7 10.6 - - - +
237B ARG* 4.3 0.7 - - - +
240B SER* 2.8 16.8 + - - +
241B SER* 1.3 73.1 - - - +
243B MET* 1.3 65.8 + - - +
245B ALA 4.5 0.4 - - - +
246B ALA* 2.9 27.5 + - - +
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Residues in contact with MET 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR* 2.6 59.3 + - + +
20A LEU* 4.7 7.2 - - + -
21A TYR* 3.9 24.9 - - + +
52A VAL* 4.2 13.5 - - + -
55A GLU* 4.0 10.3 - - + +
56A LEU* 3.2 37.0 - - + -
59A CYS* 3.8 17.0 - - - -
18B SER* 4.4 9.4 - - - +
242B ALA* 1.3 76.4 - - - +
244B SER* 1.4 61.7 + - - +
246B ALA* 3.8 2.4 - - - +
247B LYS* 3.2 20.3 + - - +
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Residues in contact with SER 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU* 2.7 35.3 + - - +
58A ASP* 4.1 20.1 + - - +
59A CYS* 3.5 21.1 - - - -
157B LEU* 4.0 9.9 - - - +
160B ASN* 5.5 0.5 + - - -
161B ARG* 4.5 3.6 + - - -
233B VAL* 5.7 0.3 - - - +
241B SER* 3.2 15.2 + - - -
243B MET* 1.4 75.2 - - - +
245B ALA* 1.3 62.3 + - - +
247B LYS* 3.3 4.3 + - - +
248B ALA* 3.2 21.7 + - - +
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Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.7 27.6 - - + -
154B LEU* 5.0 1.3 - - + +
157B LEU* 3.7 27.3 - - + +
241B SER 2.9 19.8 + - - +
244B SER* 1.3 76.3 + - - +
246B ALA* 1.3 64.1 + - - +
248B ALA* 3.2 5.3 + - - +
249B ILE* 3.0 29.8 + - + +
335B NAD 4.4 6.1 - - + -
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Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 4.1 11.0 - - - +
18B SER* 3.8 22.7 - - - +
19B LEU* 3.9 21.4 - - + +
22B SER* 6.2 0.2 - - - -
242B ALA 2.9 20.6 + - - +
243B MET 3.8 3.4 - - - +
245B ALA* 1.3 79.3 - - - +
247B LYS* 1.3 55.3 + - - +
249B ILE* 3.4 6.8 + - - +
250B CYS* 3.0 35.1 + - - -
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Residues in contact with LYS 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.7 37.5 - - + +
58A ASP 4.5 3.4 - - - +
59A CYS* 3.7 35.9 - - - +
60A ALA* 4.6 10.7 - - - +
156B ARG* 5.4 0.6 - - - +
160B ASN* 3.9 14.0 + - - +
243B MET 3.2 11.8 + - - +
244B SER 3.4 10.5 - - - +
245B ALA 3.2 0.6 - - - -
246B ALA* 1.3 78.9 - - - +
248B ALA* 1.3 56.7 + - - +
250B CYS* 3.4 10.9 + - + +
251B ASP* 2.9 51.0 + - - +
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Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 3.5 7.6 - - + +
156B ARG* 3.7 3.2 - - + +
157B LEU* 3.6 41.3 - - + +
160B ASN* 3.8 19.0 - - - +
244B SER 3.2 9.8 + - - +
245B ALA 3.2 8.0 + - - +
247B LYS* 1.3 74.2 - - - +
249B ILE* 1.3 61.4 + - - +
251B ASP* 3.4 3.8 + - - +
252B HIS* 2.9 27.4 + - - +
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Residues in contact with ILE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.9 25.1 - - + -
19B LEU* 3.7 34.1 - - + -
84B ILE* 4.5 16.8 - - + -
86B VAL* 5.1 1.6 - - + -
126B ILE* 5.3 2.7 - - + -
128B VAL* 3.6 40.2 - - + -
154B LEU* 3.8 18.4 - - + -
245B ALA* 3.0 23.8 + - + +
246B ALA* 3.6 3.1 - - - +
248B ALA* 1.3 77.8 - - - +
250B CYS* 1.3 65.8 + - - +
252B HIS* 2.9 13.6 + - - +
253B VAL* 3.1 16.3 + - + +
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Residues in contact with CYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 4.1 11.0 - - - -
22B SER* 3.7 27.6 - - - -
27B SER* 5.2 5.8 - - - +
28B VAL* 3.6 30.4 - - + +
246B ALA 3.0 22.9 + - - -
247B LYS* 3.4 14.1 - - + +
249B ILE* 1.3 77.3 - - - +
251B ASP* 1.4 52.6 + - - +
253B VAL* 3.6 2.4 + - - +
254B ARG* 2.8 37.4 + - - +
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Residues in contact with ASP 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ARG* 3.5 30.0 + - + +
160B ASN* 3.0 18.4 + - - -
247B LYS* 2.9 43.1 + - - +
248B ALA 3.5 8.3 - - - +
250B CYS* 1.4 75.4 - - - +
252B HIS* 1.3 67.3 + - - +
253B VAL 3.3 0.2 - - - -
254B ARG* 4.5 4.7 - - - +
255B ASP* 2.9 34.2 + - - +
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Residues in contact with HIS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ILE* 3.7 15.0 - - + +
152B SER* 2.9 25.3 + - - -
153B CYS 2.5 31.8 + - - -
154B LEU* 3.4 27.4 - - + -
155B THR 4.5 3.4 - - - -
156B ARG* 4.4 11.7 - - + +
248B ALA 2.9 16.7 + - - +
249B ILE* 2.9 6.1 + - - +
251B ASP* 1.3 80.0 - - - +
253B VAL* 1.3 59.9 + - + +
255B ASP* 3.6 3.2 + - - +
256B ILE* 3.4 28.2 + - + +
267B SER 5.2 2.0 - - - -
268B MET* 3.3 30.6 - - + +
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 3.9 13.2 - - + -
29B PHE* 3.5 33.9 - - + -
82B VAL* 4.9 3.1 - - + -
84B ILE* 4.1 21.8 - - + -
126B ILE* 3.4 33.7 - - + -
249B ILE* 3.1 16.4 + - + +
250B CYS* 5.2 0.2 - - - -
252B HIS* 1.3 72.0 - - - +
254B ARG* 1.3 67.0 + - - +
255B ASP 3.1 1.6 - - - -
256B ILE* 2.8 10.7 + - + -
257B TRP* 2.8 28.7 + - + +
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Residues in contact with ARG 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLY 5.3 3.3 + - - -
27B SER* 3.6 24.8 + - - +
28B VAL* 3.4 24.4 + - - +
30B GLY* 5.4 4.2 - - - +
250B CYS 2.8 25.9 + - - +
251B ASP* 4.5 3.1 - - - +
253B VAL* 1.3 71.2 - - - +
255B ASP* 1.3 65.8 + - - +
257B TRP* 3.7 1.0 - - - +
258B PHE* 2.9 65.4 + - + +
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Residues in contact with ASP 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ARG* 2.3 35.6 + - - +
251B ASP* 2.9 19.6 + - - +
252B HIS* 3.9 3.8 - - - +
254B ARG* 1.3 87.5 - - - +
256B ILE* 1.3 54.5 + - - +
259B GLY* 2.7 45.8 + - - +
260B THR* 4.2 7.2 - - + +
261B PRO* 5.2 4.2 - - - +
266B VAL* 3.7 13.4 - - + +
291B ILE* 3.6 18.9 - - + +
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Residues in contact with ILE 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LYS* 4.4 18.2 - - + -
126B ILE* 3.8 20.6 - - + -
152B SER* 4.5 2.2 - - - +
252B HIS* 3.4 43.2 + - + +
253B VAL* 2.8 8.2 + - + +
255B ASP* 1.3 77.9 - - - +
257B TRP* 1.4 68.4 + - + +
258B PHE 3.7 0.2 + - - -
259B GLY 4.2 0.7 + - - -
268B MET* 4.2 19.5 - - + -
291B ILE* 3.9 12.7 - - + +
294B LYS* 3.2 48.7 + - + +
296B TRP* 6.3 0.7 - - + -
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Residues in contact with TRP 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 3.8 29.1 - - + +
28B VAL 4.4 11.7 - - - +
29B PHE* 3.6 48.7 + + + +
33B GLN* 5.0 2.6 + - - -
81B ASP* 4.7 9.6 - - + -
82B VAL* 3.7 29.6 - - + -
124B LYS* 4.5 15.3 - - + -
253B VAL* 2.8 18.6 + - + +
254B ARG 4.0 2.7 - - - +
256B ILE* 1.4 84.7 - - + +
258B PHE* 1.3 77.1 + + + +
292B LYS 5.5 0.9 - - - +
294B LYS* 3.5 49.5 + - + +
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Residues in contact with PHE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL 3.9 15.9 - - - -
29B PHE* 3.7 25.8 - - - -
30B GLY* 4.2 6.1 - - - -
32B ASP* 6.1 0.9 - - - -
254B ARG* 2.9 53.1 + - + +
257B TRP* 1.3 92.7 - + - +
259B GLY* 1.3 64.4 + - - +
292B LYS 4.3 7.9 - - - +
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Residues in contact with GLY 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B ASP* 2.7 36.2 + - - +
256B ILE 4.2 1.4 + - - -
257B TRP 3.8 1.0 - - - -
258B PHE* 1.3 78.2 - - - +
260B THR* 1.3 64.5 + - - -
261B PRO* 3.9 4.3 - - - +
291B ILE* 3.2 22.4 - - - -
292B LYS 4.1 4.0 - - - -
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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
------------------------------------------------------------
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