Contacts of the helix formed by residues 237 - 254 (chain A) in PDB entry 3DUF
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 ASP 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLN* 3.4 3.1 - - - +
25A ILE 3.0 11.3 + - - -
26A LEU* 2.7 46.2 + - - +
83A ALA* 3.9 2.5 - - - -
234A ASP* 3.3 24.9 + - + +
235A GLY 3.4 0.8 - - - -
236A MET* 1.3 79.0 - - - +
238A PRO* 1.3 67.9 - - - +
239A LEU* 3.2 6.6 + - - +
240A ALA* 3.0 25.7 + - + -
241A VAL* 3.2 23.7 + - - +
298A ARG* 4.0 4.0 - - - +
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Residues in contact with PRO 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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26A LEU* 4.8 1.8 - - + -
49A LEU* 4.7 5.4 - - + -
53A MET* 4.0 22.9 - - + -
83A ALA* 3.7 17.5 - - + -
87A ALA* 3.3 17.9 - - + +
236A MET 3.3 10.3 - - - +
237A ASP* 1.3 85.4 - - - +
239A LEU* 1.3 63.8 + - - +
242A TYR* 3.2 20.1 + - - +
295A PRO* 4.2 7.9 - - + +
298A ARG* 4.4 11.9 - - + -
299A PHE* 4.0 36.8 - - + -
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Residues in contact with LEU 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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25A ILE* 4.1 14.0 - - + +
26A LEU* 3.7 27.1 - - + -
38A MET* 3.9 26.7 - - + -
39A PRO* 4.1 23.5 - - + +
41A LEU* 4.2 7.0 - - + -
46A LEU* 4.1 19.5 - - + -
49A LEU* 5.0 2.7 - - + -
237A ASP* 3.2 6.5 + - - +
238A PRO* 1.3 76.8 - - - +
240A ALA* 1.3 58.0 + - - +
242A TYR* 3.4 5.1 + - + +
243A ALA* 3.0 28.8 + - - +
299A PHE* 3.8 23.3 - - + -
302A PHE* 3.9 16.6 - - + -
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Residues in contact with ALA 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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23A PHE* 3.9 15.2 - - + +
25A ILE* 3.7 21.0 - - + +
233A VAL* 3.5 21.3 - - + +
237A ASP* 3.0 33.0 + - + +
239A LEU* 1.3 74.7 - - - +
241A VAL* 1.3 65.2 + - - +
243A ALA* 3.2 2.8 + - - +
244A ALA* 3.0 24.8 + - - +
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Residues in contact with VAL 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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83A ALA 3.9 13.9 - - - +
84A SER* 4.0 23.1 - - - +
87A ALA* 4.4 0.4 - - + -
88A SER* 3.8 27.8 - - - +
233A VAL* 4.3 13.5 - - + -
234A ASP 3.6 16.4 - - - +
235A GLY* 4.4 5.4 - - - -
237A ASP 3.2 17.5 + - - +
238A PRO 4.1 2.0 - - - +
240A ALA* 1.3 77.3 - - - +
242A TYR* 1.3 63.9 + - - +
244A ALA* 4.0 3.4 - - + +
245A VAL* 3.3 27.0 + - + +
261A ILE* 6.0 1.6 - - + -
263A THR* 4.5 8.7 - - + -
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Residues in contact with TYR 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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39A PRO* 3.7 25.6 - - + -
40A GLU 4.8 2.8 + - - -
41A LEU* 3.7 33.3 - - + +
45A GLN* 5.2 3.5 + - - -
49A LEU* 5.4 4.5 - - + -
87A ALA* 3.6 22.4 + - + +
90A PHE* 3.7 30.0 + + + -
91A ALA* 3.7 27.2 - - + +
238A PRO 3.2 14.4 + - - +
239A LEU* 3.5 10.3 - - - +
240A ALA 3.1 0.4 - - - -
241A VAL* 1.3 80.0 - - - +
243A ALA* 1.3 58.3 + - - +
246A LYS* 3.1 53.4 + - + +
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Residues in contact with ALA 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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23A PHE* 4.3 15.5 - - + -
25A ILE* 5.3 1.1 - - + -
37A ALA 4.5 16.4 - - - +
39A PRO* 4.6 9.6 - - + -
239A LEU 3.0 17.2 + - - +
240A ALA* 3.2 4.0 + - - +
242A TYR* 1.3 80.3 - - - +
244A ALA* 1.3 59.8 + - - +
246A LYS* 3.7 6.0 - - - +
247A ALA* 3.0 31.4 + - - +
5C PHE* 5.6 3.1 - - + -
7C PHE* 4.2 5.5 - - + -
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Residues in contact with ALA 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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23A PHE* 4.9 0.7 - - + -
231A ILE* 4.8 6.8 - - + +
233A VAL* 4.7 9.9 - - + -
240A ALA 3.0 17.2 + - - +
241A VAL* 4.0 6.1 - - + +
242A TYR 3.4 0.2 - - - -
243A ALA* 1.3 76.5 - - - +
245A VAL* 1.3 62.7 + - - +
247A ALA* 3.6 2.3 + - - +
248A ALA* 3.1 24.1 + - - +
261A ILE* 3.9 33.9 - - + +
7C PHE* 4.4 18.3 - - + -
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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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88A SER* 3.8 37.2 - - - +
91A ALA* 3.9 14.8 - - + +
92A LEU* 4.1 10.1 - - + -
168A ILE* 4.4 6.5 - - + -
196A ILE* 4.1 26.8 - - + +
198A VAL* 5.2 5.2 - - + -
241A VAL* 3.3 21.7 + - + +
244A ALA* 1.3 75.9 - - + +
246A LYS* 1.3 56.0 + - - +
248A ALA* 3.2 7.0 + - - +
249A ARG* 2.7 32.7 + - + +
261A ILE* 5.2 8.1 - - + -
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Residues in contact with LYS 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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39A PRO* 5.4 3.0 - - + +
40A GLU* 3.1 47.7 + - - +
91A ALA* 4.1 11.6 - - + +
242A TYR* 3.1 43.2 + - + +
243A ALA* 3.7 7.2 - - - +
244A ALA 3.3 0.2 - - - -
245A VAL* 1.3 73.4 - - - +
247A ALA* 1.3 66.6 + - - +
249A ARG* 3.0 8.7 + - - +
250A GLU* 3.0 44.0 + - + +
4C THR* 4.8 8.2 + - - +
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Residues in contact with ALA 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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243A ALA 3.0 17.5 + - - +
244A ALA 3.9 2.7 - - - +
246A LYS* 1.3 76.5 - - - +
248A ALA* 1.3 62.1 + - - +
250A GLU* 3.5 12.4 + - - +
251A ARG* 3.1 25.1 + - - +
5C PHE* 5.1 7.6 - - + +
6C GLN* 5.6 3.1 - - - +
7C PHE* 3.7 30.7 - - + -
9C PHE* 5.1 9.6 - - + -
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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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196A ILE* 4.4 21.4 - - + +
231A ILE* 5.9 0.7 - - + -
244A ALA 3.1 19.9 + - - +
245A VAL* 3.4 8.1 - - - +
247A ALA* 1.3 76.7 - - - +
249A ARG* 1.3 63.9 + - - +
251A ARG* 3.9 3.5 - - - +
252A ALA* 3.2 23.4 + - - +
257A GLY 5.1 0.5 - - - +
259A THR* 4.0 34.9 + - + -
261A ILE* 4.6 2.2 - - + -
9C PHE* 5.6 2.0 - - - -
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Residues in contact with ARG 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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91A ALA 3.4 22.6 + - - +
92A LEU* 4.5 2.2 - - - +
93A GLU* 3.5 27.9 - - - +
95A GLU* 4.5 4.0 + - - +
96A ASP* 2.8 41.9 + - - -
164A LYS 3.8 14.5 + - - -
165A ALA* 4.3 0.6 - - - +
166A VAL* 3.9 16.4 - - + -
196A ILE* 4.3 9.0 - - + -
245A VAL* 2.7 17.2 + - + +
246A LYS* 3.0 12.1 + - + +
248A ALA* 1.3 72.2 - - - +
250A GLU* 1.3 66.9 + - + +
252A ALA* 3.1 2.8 + - - +
253A ILE* 2.9 58.7 + - - +
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Residues in contact with GLU 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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246A LYS* 3.0 37.2 + - + +
247A ALA* 3.8 12.3 - - - +
249A ARG* 1.3 75.9 - - + +
251A ARG* 1.3 62.5 + - - +
253A ILE* 3.2 20.5 - - + +
254A ASN* 2.9 28.5 + - - +
4C THR* 3.7 35.7 + - - +
5C PHE 5.4 0.9 - - - +
6C GLN* 5.2 4.2 - - - +
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Residues in contact with ARG 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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229A PRO* 3.4 36.9 - - - +
247A ALA 3.1 14.5 + - - +
248A ALA* 3.9 4.7 - - - +
250A GLU* 1.3 80.1 - - - +
252A ALA* 1.3 63.6 + - - +
254A ASN* 3.5 3.8 + - - +
256A GLU* 3.1 83.8 + - + +
257A GLY 4.4 3.7 + - - +
258A PRO 4.5 2.4 + - - -
259A THR* 3.7 12.7 + - - -
9C PHE* 3.6 42.4 - - + +
13C LEU* 5.0 8.5 - - - +
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Residues in contact with ALA 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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166A VAL* 3.9 11.7 - - + -
194A PRO* 3.7 40.7 - - + +
195A ALA 4.4 3.8 - - - +
196A ILE* 5.3 1.8 - - + -
248A ALA 3.2 15.2 + - - +
249A ARG 3.1 4.9 + - - +
251A ARG* 1.3 80.2 - - - +
253A ILE* 1.3 56.5 - - - +
255A GLY* 2.8 23.7 + - - -
256A GLU 3.9 0.2 + - - -
257A GLY 3.6 16.4 + - - +
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Residues in contact with ILE 253 (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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164A LYS* 3.7 51.8 + - + +
165A ALA 4.5 1.6 - - - +
166A VAL* 3.6 17.5 - - + -
194A PRO* 5.2 2.5 - - - -
249A ARG* 2.9 45.4 + - - +
250A GLU* 3.2 29.6 - - + +
252A ALA* 1.3 70.0 - - - +
254A ASN* 1.3 63.8 + - - +
255A GLY 3.2 2.1 + - - -
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Residues in contact with ASN 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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250A GLU* 2.9 24.3 + - - +
251A ARG 3.8 5.4 - - - +
252A ALA 2.9 1.6 + - - -
253A ILE* 1.3 88.3 - - - +
255A GLY* 1.3 61.9 + - - +
256A GLU* 3.5 22.2 + - + +
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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