Contacts of the helix formed by residues 241 - 250 (chain A) in PDB entry 5TSQ
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 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 ASP* 3.0 21.1 + - - +
15A ASP* 2.8 17.9 + - - +
18A ALA* 3.8 8.5 - - + +
126A THR* 3.4 23.1 - - + +
152A MET* 3.4 18.2 - - - +
240A HIS* 1.3 78.8 - - - +
242A PRO* 1.3 68.7 - - + +
243A CYS 3.1 1.2 + - - -
244A ALA* 3.1 18.5 + - - +
245A VAL 3.9 2.3 + - - -
401A CA 2.4 25.8 - - - -
402A BDR 2.6 23.9 + - - -
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Residues in contact with PRO 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 ASP 3.5 9.4 - - - +
17A VAL* 3.5 32.8 - - + -
18A ALA* 3.5 21.3 - - + +
21A LEU* 3.6 20.4 - - + +
239A VAL* 3.7 9.9 - - + +
240A HIS 3.4 4.0 - - - -
241A ASP* 1.3 89.5 - - - +
243A CYS* 1.3 55.1 + - - -
244A ALA 3.1 0.4 - - - -
245A VAL* 3.2 3.2 + - + +
246A ALA* 2.8 30.0 + - - +
299A TYR* 3.2 23.8 - - + +
303A VAL* 4.5 2.5 - - + -
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Residues in contact with CYS 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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189A VAL* 3.7 20.4 - - + -
193A LEU* 3.8 19.3 - - + -
194A THR* 4.1 4.7 - - + -
197A ALA* 3.6 30.1 - - - -
239A VAL 3.9 0.2 - - - -
240A HIS 2.9 18.5 + - - +
242A PRO* 1.3 78.0 - - - +
244A ALA* 1.3 60.0 + - - +
246A ALA* 3.4 2.1 + - - +
247A TYR* 3.1 18.9 + - - +
254A MET* 3.4 15.6 - - + +
294A LEU* 4.6 4.0 - - - -
299A TYR* 3.6 20.4 + - - -
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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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124A VAL* 4.0 19.3 - - + -
126A THR* 4.3 1.8 - - + -
150A VAL* 3.5 25.0 - - + +
151A LEU 4.1 3.6 - - - +
152A MET* 3.9 30.2 - - + +
189A VAL* 4.2 6.6 - - + +
240A HIS 4.2 0.2 + - - -
241A ASP 3.1 12.0 + - - +
243A CYS* 1.3 76.3 - - - +
245A VAL* 1.3 65.0 + - - +
247A TYR 3.3 8.0 + - - -
248A VAL* 3.4 11.1 + - - +
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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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5A ILE* 4.6 4.7 - - + -
7A LEU* 4.0 24.5 - - + -
18A ALA* 4.0 25.1 - - + +
21A LEU* 3.9 17.9 - - + -
22A ALA* 3.8 30.7 - - + +
28A ILE* 4.3 9.4 - - + -
124A VAL* 4.1 9.2 - - + -
241A ASP 4.5 1.8 - - - +
242A PRO* 3.2 7.2 + - + +
244A ALA* 1.3 75.2 - - - +
246A ALA* 1.3 62.9 + - - +
248A VAL* 3.0 9.3 + - - +
249A ILE* 3.0 25.8 + - + +
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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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21A LEU* 4.0 4.9 - - + +
242A PRO 2.8 16.8 + - - +
243A CYS* 3.6 5.4 - - - +
244A ALA 3.2 0.2 - - - -
245A VAL* 1.3 77.6 - - - +
247A TYR* 1.3 62.0 + - - +
249A ILE* 3.2 14.0 + - - +
250A ASP* 2.9 25.1 + - - +
253A VAL* 3.8 13.9 - - + +
254A MET* 5.2 0.2 - - + -
299A TYR* 3.9 23.3 - - + -
302A LEU* 4.2 14.1 - - + +
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Residues in contact with TYR 247 (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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148A GLU* 4.3 10.2 + - - -
150A VAL* 3.8 29.8 - - + -
187A THR* 3.9 16.2 - - + -
189A VAL* 4.8 0.4 - - + -
243A CYS 3.1 13.1 + - - +
244A ALA* 3.6 9.6 - - - +
245A VAL 3.3 0.4 - - - -
246A ALA* 1.3 75.0 - - - +
248A VAL* 1.3 66.2 + - - +
250A ASP 4.1 0.4 - - - -
251A PRO* 3.1 61.2 - - + +
253A VAL* 4.0 8.6 - - - +
254A MET* 3.8 28.5 - - + -
256A THR* 4.0 19.3 + - + +
289A GLN* 2.8 23.9 + - - -
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Residues in contact with VAL 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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3A ARG* 3.9 37.5 + - + +
5A ILE* 4.0 10.8 - - + -
27A GLU* 5.7 0.2 - - - +
28A ILE* 3.6 20.6 - - + -
122A THR* 4.1 10.5 - - + +
124A VAL* 4.1 19.7 - - + -
148A GLU* 6.4 0.2 - - - -
150A VAL* 4.0 23.8 - - + -
244A ALA 3.4 14.1 + - - +
245A VAL* 3.0 8.4 + - - +
247A TYR* 1.3 80.2 - - - +
249A ILE* 1.3 63.2 + - - +
250A ASP* 4.5 0.2 - - - -
251A PRO* 4.6 3.5 - - - +
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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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21A LEU* 3.8 29.4 - - + -
25A ASN* 3.5 50.0 - - + +
27A GLU* 4.2 21.1 - - + +
28A ILE* 3.6 16.2 - - + -
245A VAL* 3.0 24.1 + - + +
246A ALA* 3.2 8.9 + - - +
248A VAL* 1.3 78.1 - - - +
250A ASP* 1.3 63.4 + - + +
251A PRO* 4.4 1.7 - - - +
302A LEU* 4.0 18.8 - - + -
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Residues in contact with ASP 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 ALA 2.9 6.9 + - - +
247A TYR 3.4 2.5 - - - -
248A VAL 3.3 0.2 - - - -
249A ILE* 1.3 87.0 - - + +
251A PRO* 1.3 71.2 - - - +
252A THR* 2.7 26.4 + - - +
253A VAL* 2.9 25.5 + - + +
298A LYS* 2.7 36.1 + - + +
302A LEU* 4.9 5.2 - - + -
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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