Contacts of the helix formed by residues 237 - 252 (chain A) in PDB entry 1DRK
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 PRO 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A PHE* 3.4 55.8 - - + +
18A SER* 3.7 16.8 - - - +
19A LEU* 3.5 15.3 - - + +
215A ASP 4.9 2.7 - - - +
217A THR* 6.4 0.9 - - + -
235A GLN* 3.3 13.5 - - + +
236A LEU* 1.3 85.7 - - - +
238A ASP* 1.4 61.7 + - - +
240A ILE* 2.9 12.5 + - + +
241A GLY 2.9 25.1 + - - -
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Residues in contact with ASP 238 (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* 3.5 24.1 + - - +
21A ASP* 6.3 0.2 - - + -
22A GLY* 3.3 17.0 - - - -
236A LEU* 3.7 19.1 - - - +
237A PRO* 1.4 79.7 - - - +
239A GLN* 1.3 79.2 + - - +
242A ALA* 3.0 24.8 + - - +
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Residues in contact with GLN 239 (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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236A LEU* 3.0 43.8 + - + +
238A ASP* 1.3 93.1 + - - +
240A ILE* 1.3 58.9 + - - +
242A ALA* 3.8 8.0 - - + +
243A LYS* 3.0 30.1 + - - +
263A VAL* 4.6 10.0 - - + +
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Residues in contact with ILE 240 (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 PHE* 4.3 16.8 - - + -
19A LEU* 4.3 8.5 - - + -
88A LEU* 3.9 23.0 - - + +
89A ASP* 4.2 8.7 - - + +
101A ILE* 3.7 30.3 - - + +
102A ALA* 4.6 10.3 - - - -
103A SER* 4.4 8.5 - - - +
235A GLN* 4.3 11.9 - - - +
236A LEU 3.0 19.8 + - - +
237A PRO* 2.9 16.3 + - + +
239A GLN* 1.3 74.5 - - - +
241A GLY* 1.3 65.2 + - - +
243A LYS* 4.0 1.6 - - - +
244A GLY* 3.1 19.1 + - - -
263A VAL* 3.7 20.6 - - + -
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Residues in contact with GLY 241 (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* 3.5 31.8 - - - +
23A ALA* 3.6 23.2 - - - +
62A LEU* 4.9 1.2 - - - +
88A LEU* 4.6 3.6 - - - -
237A PRO 2.9 11.1 + - - -
238A ASP 3.9 0.9 - - - -
240A ILE* 1.3 78.2 - - - +
242A ALA* 1.3 60.5 + - - +
244A GLY* 3.2 9.2 + - - -
245A VAL* 3.2 10.0 + - - +
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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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22A GLY 3.8 14.3 - - - +
26A GLU* 3.6 25.9 - - - +
238A ASP 3.0 18.5 + - - +
239A GLN* 4.1 8.1 - - + +
240A ILE 3.4 0.2 - - - -
241A GLY* 1.3 72.4 - - - +
243A LYS* 1.3 61.8 + - - +
245A VAL 3.2 1.9 + - - -
246A GLU* 2.9 33.3 + - - +
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Residues in contact with LYS 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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101A ILE* 3.7 26.2 - - + -
239A GLN 3.0 20.9 + - - +
240A ILE 4.0 3.4 - - - +
242A ALA* 1.3 77.5 - - - +
244A GLY* 1.3 53.7 + - - +
246A GLU* 3.7 26.6 + - - +
247A THR* 2.7 42.0 + - - +
250A LYS* 5.2 6.2 - - - +
261A TYR* 3.4 45.2 - - + -
263A VAL* 5.6 2.7 - - + -
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Residues in contact with GLY 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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62A LEU* 3.6 16.6 - - - +
86A ILE* 4.0 1.1 - - - +
88A LEU* 3.8 12.3 - - - -
101A ILE* 3.6 17.2 - - - +
240A ILE 3.1 13.9 + - - -
241A GLY 3.2 4.2 + - - -
242A ALA 3.1 0.4 - - - -
243A LYS* 1.3 77.2 - - - +
245A VAL* 1.3 54.5 + - - +
247A THR* 3.5 2.6 + - - -
248A ALA* 2.9 27.0 + - - +
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Residues in contact with VAL 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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4A ILE* 4.3 16.9 - - + +
23A ALA* 3.4 30.3 - - + +
26A GLU* 3.7 26.2 - - + -
27A ALA* 3.7 21.5 - - + +
30A LEU* 3.9 7.4 - - + -
32A TYR* 4.7 2.0 - - + -
34A LEU* 4.9 4.3 - - + -
62A LEU* 3.9 11.9 - - + -
241A GLY 3.2 10.6 + - - +
242A ALA 3.2 2.7 + - - +
244A GLY* 1.3 73.8 - - - +
246A GLU* 1.3 65.2 + - - +
248A ALA* 3.4 7.6 + - - +
249A ASP* 3.1 21.8 + - - +
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Residues in contact with GLU 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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26A GLU* 4.1 17.2 - - - +
29A LYS* 5.7 1.1 + - - -
30A LEU* 4.1 11.2 - - + -
242A ALA* 2.9 20.3 + - - +
243A LYS* 3.7 29.8 + - - +
245A VAL* 1.3 78.3 - - - +
247A THR* 1.3 61.8 + - - +
249A ASP* 3.3 6.8 + - - +
250A LYS* 3.2 34.2 + - + +
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Residues in contact with THR 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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86A ILE* 3.8 16.2 - - + -
99A SER* 4.0 16.8 - - - -
101A ILE* 3.9 7.4 - - + +
243A LYS* 2.7 29.2 + - - +
244A GLY 3.7 3.8 - - - -
246A GLU* 1.3 74.3 - - - +
248A ALA* 1.3 64.1 + - - +
250A LYS* 3.4 11.9 + - - +
251A VAL* 3.1 22.0 + - - +
257A VAL* 3.9 25.4 - - + -
261A TYR* 3.6 19.8 - - + -
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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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4A ILE* 3.9 20.4 - - + -
60A ILE* 3.6 28.9 - - + +
62A LEU* 4.2 5.6 - - + -
86A ILE* 3.7 9.8 - - - +
244A GLY 2.9 18.5 + - - +
245A VAL* 3.5 8.5 - - - +
246A GLU 3.3 0.2 - - - -
247A THR* 1.3 76.1 - - - +
249A ASP* 1.3 61.2 + - - +
251A VAL* 3.4 0.7 + - - -
252A LEU* 3.0 30.3 + - - +
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Residues in contact with ASP 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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30A LEU* 3.8 23.4 - - + +
32A TYR* 2.6 40.5 + - + +
245A VAL 3.1 13.0 + - - +
246A GLU* 3.3 10.3 - - - +
247A THR 3.2 0.2 - - - -
248A ALA* 1.3 72.8 - - - +
250A LYS* 1.3 67.8 + - - +
252A LEU* 3.1 4.5 + - - +
253A LYS* 2.9 64.7 + - - +
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Residues in contact with LYS 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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243A LYS* 5.2 5.9 - - - +
246A GLU* 3.2 24.6 + - + +
247A THR* 3.4 8.7 + - - +
249A ASP* 1.3 79.0 - - - +
251A VAL* 1.3 63.3 + - - +
253A LYS* 3.1 2.9 + - - +
254A GLY 3.0 4.5 + - - -
255A GLU* 2.9 60.4 + - + +
256A LYS 4.7 7.7 + - - +
257A VAL* 3.6 24.0 - - + -
261A TYR* 3.4 25.6 + - - +
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Residues in contact with VAL 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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60A ILE* 3.8 18.6 - - + -
84A PRO* 4.1 19.1 - - + -
86A ILE* 4.6 8.3 - - + -
98A VAL* 3.8 29.2 - - + -
247A THR 3.1 15.7 + - - +
248A ALA 3.7 7.4 - - - +
250A LYS* 1.3 77.3 - - - +
252A LEU* 1.3 60.3 + - + +
254A GLY* 3.0 18.7 + - - -
255A GLU 3.9 7.2 + - - +
257A VAL* 3.9 14.8 - - + -
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Residues in contact with LEU 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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2A ASP* 4.4 9.6 - - + +
4A ILE* 5.1 3.8 - - + -
32A TYR* 3.6 38.1 - - + +
59A LYS* 4.0 29.6 - - + +
60A ILE* 3.6 28.7 - - + -
84A PRO* 5.9 1.8 - - + -
248A ALA 3.0 16.1 + - - +
249A ASP 3.1 8.0 + - - +
251A VAL* 1.3 76.4 - - + +
253A LYS* 1.3 61.6 + - + +
254A GLY 3.2 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