Contacts of the helix formed by residues 241 - 259 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLN* 4.2 0.5 + - - -
15A ILE* 3.4 16.3 - - - +
157A LEU* 3.3 14.1 - - - +
161A ARG* 2.8 31.0 + - - -
230A GLY* 5.0 0.4 + - - -
233A VAL* 4.3 8.9 - - - +
240A SER* 1.3 76.1 - - - +
242A ALA* 1.3 58.4 + - - +
244A SER* 4.1 3.1 + - - -
245A ALA* 3.7 4.9 - - - -
334A SO4 2.9 8.7 + - - -
335A NAD 3.4 27.2 + - - -
55B GLU* 3.7 11.7 - - - -
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Residues in contact with ALA 242 (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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14A GLN* 3.1 49.8 - - + +
15A ILE* 3.8 8.2 - - + +
18A SER* 4.3 3.8 - - - +
240A SER 3.5 0.4 + - - -
241A SER* 1.3 71.6 - - - +
243A MET* 1.3 58.2 + - - +
244A SER 3.3 0.4 - - - -
246A ALA* 2.7 39.8 + - - +
17B TYR* 3.0 17.6 + - + +
55B GLU* 3.0 5.1 + - - -
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Residues in contact with MET 243 (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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18A SER* 4.1 11.6 + - - +
242A ALA* 1.3 72.9 - - - +
244A SER* 1.3 61.2 - - - +
246A ALA* 3.5 2.1 + - - +
247A LYS* 3.2 23.9 + - - +
17B TYR* 2.8 59.0 + - + +
20B LEU* 4.1 18.8 - - + -
21B TYR* 4.3 25.8 - - + +
52B VAL* 4.4 13.5 - - + +
55B GLU* 3.6 14.6 - - + +
56B LEU* 4.0 24.5 - - + -
59B CYS* 4.1 15.9 - - - -
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Residues in contact with SER 244 (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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157A LEU* 3.8 21.3 - - - +
161A ARG* 5.0 1.4 + - - -
233A VAL* 5.8 0.2 - - - +
241A SER* 4.1 8.0 + - - -
243A MET* 1.3 71.3 - - - +
245A ALA* 1.3 65.0 + - - +
247A LYS* 3.4 4.3 + - - +
248A ALA* 3.1 23.4 + - - +
55B GLU* 2.3 56.5 + - - +
58B ASP* 3.8 15.5 + - - +
59B CYS* 3.8 9.0 - - - -
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Residues in contact with ALA 245 (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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15A ILE* 3.9 10.8 - - + -
128A VAL* 5.5 0.2 - - + -
154A LEU* 4.4 3.4 - - + +
157A LEU* 3.5 24.5 - - + +
241A SER* 3.7 20.0 - - - +
242A ALA 3.3 2.8 + - - +
244A SER* 1.3 80.1 + - - +
246A ALA* 1.3 63.9 + - - +
248A ALA* 3.2 4.8 + - - +
249A ILE* 3.0 29.6 + - + +
335A NAD 3.7 19.3 - - + +
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Residues in contact with ALA 246 (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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15A ILE* 3.9 14.2 - - + +
18A SER* 3.7 35.2 - - - +
19A LEU* 3.5 19.1 - - + +
242A ALA 2.7 21.7 + - - +
243A MET 3.7 3.1 - - - +
245A ALA* 1.3 75.2 - - - +
247A LYS* 1.3 61.6 + - - +
248A ALA 3.1 0.9 + - - -
249A ILE* 3.2 13.6 + - - -
250A CYS* 3.2 12.2 + - - -
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Residues in contact with LYS 247 (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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160A ASN* 4.2 5.1 - - - +
243A MET 3.2 15.5 + - - +
244A SER 3.5 5.2 - - - +
246A ALA* 1.3 80.1 - - - +
248A ALA* 1.3 56.8 + - - +
250A CYS* 3.3 11.2 - - + +
251A ASP* 3.2 46.5 + - - +
21B TYR* 3.5 33.7 - - + +
59B CYS* 2.6 54.9 + - + -
60B ALA* 4.3 4.6 + - - +
61B LEU* 4.2 10.5 - - - -
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Residues in contact with ALA 248 (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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154A LEU* 3.6 7.4 - - + +
156A ARG* 3.7 6.6 - - + +
157A LEU* 3.6 36.8 - - + +
160A ASN* 4.0 6.5 - - - +
244A SER 3.1 16.2 + - - +
245A ALA 3.6 4.0 - - - +
246A ALA 3.1 0.6 - - - -
247A LYS* 1.3 74.7 - - - +
249A ILE* 1.3 59.6 + - - +
250A CYS 3.2 1.1 - - - -
251A ASP* 3.3 10.6 + - - +
252A HIS* 2.9 30.0 + - - +
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Residues in contact with ILE 249 (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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15A ILE* 3.8 24.9 - - + -
19A LEU* 3.9 22.0 - - + -
84A ILE* 3.8 27.4 - - + -
86A VAL* 4.9 2.5 - - + -
126A ILE* 4.9 2.9 - - + -
128A VAL* 3.9 31.2 - - + -
154A LEU* 3.7 16.4 - - + -
245A ALA 3.0 17.0 + - - +
246A ALA* 3.2 8.0 + - - +
248A ALA* 1.3 74.5 - - - +
250A CYS* 1.3 64.7 + - - +
252A HIS* 3.1 1.9 + - - +
253A VAL* 2.9 39.1 + - + +
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Residues in contact with CYS 250 (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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19A LEU* 3.6 18.2 - - - -
22A SER* 4.1 18.8 - - - -
27A SER* 5.5 1.1 - - - +
28A VAL* 3.5 33.1 - - + +
246A ALA 3.2 14.2 + - - -
247A LYS* 3.3 15.3 - - + +
249A ILE* 1.3 77.8 - - - +
251A ASP* 1.3 57.5 + - - +
253A VAL* 3.7 3.4 - - - +
254A ARG* 2.8 33.7 + - - +
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Residues in contact with ASP 251 (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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156A ARG* 3.5 29.4 + - + +
160A ASN* 3.2 27.5 + - - +
247A LYS* 3.2 34.7 + - - +
248A ALA* 3.4 7.3 - - - +
249A ILE 3.2 0.6 - - - -
250A CYS* 1.3 78.1 - - - +
252A HIS* 1.3 57.8 - - - +
254A ARG* 3.1 7.1 + - - +
255A ASP* 2.9 34.5 + - - -
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Residues in contact with HIS 252 (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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126A ILE* 3.8 19.2 - - + +
152A SER* 3.0 30.0 + - - -
153A CYS 3.3 23.0 + - - -
154A LEU* 3.5 28.3 - - + -
155A THR 4.7 2.7 - - - -
156A ARG* 4.4 15.7 - - + +
248A ALA 2.9 16.5 + - - +
249A ILE* 3.5 2.7 - - - +
251A ASP* 1.3 78.3 - - - +
253A VAL* 1.3 62.8 + - + +
255A ASP* 3.3 10.1 + - - +
256A ILE* 3.3 30.8 + - + +
266A VAL* 6.5 0.4 - - - -
267A SER 5.1 1.8 - - - -
268A MET* 3.8 18.4 - - + +
291A ILE* 5.5 0.2 - - - +
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Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A VAL* 3.9 11.7 - - + -
29A PHE* 3.5 36.3 - - + -
82A VAL* 4.6 10.3 - - + -
84A ILE* 4.4 8.5 - - + -
126A ILE* 4.2 24.2 - - + -
249A ILE* 2.9 33.3 + - + +
250A CYS* 3.9 2.5 - - - +
252A HIS* 1.3 76.1 - - - +
254A ARG* 1.3 61.2 + - - +
256A ILE* 3.2 9.4 + - + +
257A TRP* 3.1 23.7 + - + +
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Residues in contact with ARG 254 (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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26A GLY 3.9 3.8 + - - -
27A SER* 2.9 48.1 + - - +
28A VAL* 3.7 14.8 + - - +
30A GLY* 4.2 2.4 - - - +
250A CYS* 2.8 22.6 + - - +
251A ASP* 3.1 6.7 + - - +
253A VAL* 1.3 71.1 - - - +
255A ASP* 1.4 68.8 + - - +
257A TRP 4.5 0.2 - - - +
258A PHE* 3.0 69.9 + - + +
259A GLY 4.5 0.3 - - - +
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Residues in contact with ASP 255 (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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156A ARG* 2.7 39.4 + - - +
251A ASP 2.9 14.2 + - - +
252A HIS* 3.3 4.7 + - - +
254A ARG* 1.4 79.7 - - - +
256A ILE* 1.3 56.9 + - - +
259A GLY* 2.6 44.5 + - - +
260A THR* 3.9 15.7 - - + -
261A PRO* 4.5 6.8 - - - +
266A VAL* 3.2 10.9 - - + +
291A ILE* 3.6 22.1 - - + +
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Residues in contact with ILE 256 (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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124A LYS* 5.1 13.0 - - + -
126A ILE* 4.6 10.3 - - + -
152A SER* 4.5 2.7 - - - +
252A HIS* 3.3 45.9 + - + +
253A VAL* 3.2 10.7 + - + +
254A ARG 3.1 0.4 - - - -
255A ASP* 1.3 82.8 - - - +
257A TRP* 1.3 72.0 + - + +
259A GLY 3.9 0.9 + - - -
268A MET* 4.1 20.0 - - + -
291A ILE* 3.8 14.1 - - + +
294A LYS* 3.1 52.8 + - + +
296A TRP* 5.9 1.6 - - + -
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Residues in contact with TRP 257 (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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4A ILE* 4.1 24.7 - - + -
28A VAL 4.5 1.8 - - - +
29A PHE* 3.5 44.1 - + + +
33A GLN* 4.0 16.1 + - - -
81A ASP* 4.6 9.0 - - + -
82A VAL* 3.5 30.1 - - + -
124A LYS* 4.7 15.5 - - + -
253A VAL* 3.1 16.3 + - + +
254A ARG 3.4 0.4 + - - -
256A ILE* 1.3 84.4 - - + +
258A PHE* 1.4 76.1 + + + +
294A LYS* 3.8 51.0 + - + +
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Residues in contact with PHE 258 (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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28A VAL 3.2 24.2 - - - -
29A PHE 3.6 28.5 - - - -
30A GLY* 3.6 9.2 - - - -
254A ARG* 3.0 52.6 + - + +
257A TRP* 1.4 86.9 - + + +
259A GLY* 1.3 64.8 + - - +
293A ASP 6.2 0.2 - - - -
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Residues in contact with GLY 259 (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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254A ARG 4.5 0.2 - - - +
255A ASP* 2.6 34.0 + - - +
256A ILE 3.9 1.6 + - - -
257A TRP 3.7 1.6 - - - -
258A PHE* 1.3 79.6 - - - +
260A THR* 1.3 65.2 + - - -
261A PRO* 3.9 1.6 - - - +
291A ILE* 3.3 21.8 - - - -
292A LYS* 4.7 2.7 - - - -
293A ASP 5.5 1.7 - - - +
294A LYS 5.7 0.8 - - - +
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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