Contacts of the helix formed by residues 240 - 250 (chain A) in PDB entry 2ATW
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 GLY 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A ILE* 3.1 29.8 - - - -
237A GLY 2.9 6.0 + - - -
238A PRO 2.9 2.8 + - - -
239A MET* 1.3 78.1 - - - +
241A GLN* 1.3 60.3 + - - +
243A VAL* 3.3 5.2 - - - +
244A ARG* 2.9 35.0 + - - +
1B G 4.0 3.2 - - - -
2B A 4.2 8.1 - - - -
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Residues in contact with GLN 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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236A ILE 3.5 0.8 + - - -
237A GLY 4.2 0.2 - - - -
238A PRO* 3.0 27.4 + - + +
239A MET* 3.7 33.5 - - + +
240A GLY* 1.3 78.2 - - - +
242A ARG* 1.3 58.7 + - + +
244A ARG* 3.7 7.1 - - + +
245A ASN* 2.8 43.4 + - - +
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Residues in contact with ARG 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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193A PHE* 5.2 0.4 - - - -
196A GLU* 3.8 24.6 + - + +
197A VAL* 3.8 7.6 - - + +
198A PRO* 3.6 28.4 - - - +
199A GLU* 2.9 27.5 + - - -
234A ALA 3.0 25.3 + - - -
235A CYS 3.6 8.5 - - - +
236A ILE 3.1 8.6 + - - +
237A GLY* 3.7 14.5 - - - -
238A PRO* 4.8 3.7 - - + +
241A GLN* 1.3 76.7 - - + +
243A VAL* 1.3 63.8 + - - +
245A ASN* 3.1 18.5 + - - +
246A VAL* 3.3 15.8 + - - +
0B A 3.4 30.9 + - - -
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Residues in contact with VAL 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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193A PHE* 3.9 17.5 - - + -
235A CYS 3.5 13.2 + - - +
236A ILE* 3.3 15.9 + - + +
240A GLY* 3.3 17.3 - - - +
242A ARG* 1.3 79.7 - - - +
244A ARG* 1.3 60.2 + - - +
246A VAL* 3.2 3.0 + - - +
247A MET* 3.0 32.0 + - + +
255A ILE* 4.0 20.0 - - + +
257A ILE* 3.6 19.7 - - + -
2B A 3.8 30.1 - - + +
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Residues in contact with ARG 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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239A MET* 3.4 24.7 + - - +
240A GLY 2.9 22.3 + - - +
241A GLN* 3.7 8.3 - - + +
242A ARG 3.1 0.2 - - - -
243A VAL* 1.3 76.9 - - - +
245A ASN* 1.3 68.3 + - - +
247A MET* 3.2 18.2 + - + +
248A SER* 2.9 24.6 + - - -
2B A 3.4 45.8 + - - -
3B A 4.6 2.8 + - - -
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Residues in contact with ASN 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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196A GLU* 3.3 35.0 + - - +
241A GLN* 2.8 32.3 + - - +
242A ARG* 3.1 5.2 + - - +
244A ARG* 1.3 75.8 - - - +
246A VAL* 1.3 60.5 + - - +
248A SER* 3.4 7.6 + - - -
249A GLU* 3.2 21.8 + - - +
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Residues in contact with VAL 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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189A VAL* 5.0 2.0 - - + +
192A LEU* 4.1 21.3 - - + -
193A PHE* 3.8 37.7 - - + -
196A GLU* 3.9 18.2 - - + -
242A ARG 3.3 12.5 + - - +
243A VAL 3.2 7.3 + - - +
244A ARG 3.1 0.8 - - - -
245A ASN* 1.3 73.4 - - - +
247A MET* 1.3 66.4 + - - +
249A GLU* 3.4 6.9 + - - +
250A LEU* 3.1 35.6 + - + +
255A ILE* 3.4 22.4 - - + -
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Residues in contact with MET 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 VAL* 3.0 19.2 + - + +
244A ARG* 3.5 39.0 - - + +
246A VAL* 1.3 78.6 - - - +
248A SER* 1.3 60.5 + - - +
250A LEU* 3.0 9.9 + - - +
252A GLY* 2.8 30.6 + - - +
253A GLU 3.2 26.5 - - - +
254A LYS* 4.2 11.9 - - - -
255A ILE* 3.6 26.7 - - + +
2B A 3.8 17.5 - - + +
3B A 5.2 9.2 - - - +
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Residues in contact with SER 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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244A ARG 2.9 17.4 + - - -
245A ASN* 3.5 9.9 - - - -
246A VAL 3.2 0.2 - - - -
247A MET* 1.3 76.5 - - - +
249A GLU* 1.3 62.4 + - - +
251A SER* 3.0 15.6 + - - -
252A GLY* 4.6 2.7 - - - +
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Residues in contact with GLU 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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162A ARG* 4.9 4.6 + - - +
163A LEU* 3.3 9.8 - - - +
164A ARG* 2.6 58.4 + - + +
183A ARG* 2.7 45.0 + - - +
192A LEU* 3.6 33.9 - - + -
245A ASN 3.2 9.5 + - - +
246A VAL* 3.8 8.1 - - - +
248A SER* 1.3 79.1 - - - +
250A LEU* 1.3 50.3 + - - +
251A SER* 3.1 2.8 + - - -
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Residues in contact with LEU 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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155A GLU* 4.0 3.8 - - - +
183A ARG* 3.7 9.0 - - - +
188A LEU* 3.8 17.9 - - + -
189A VAL* 3.9 22.4 - - + -
192A LEU* 3.5 23.1 - - + -
212A ARG* 3.7 17.7 - - - +
215A GLY* 5.5 2.9 - - - -
246A VAL* 3.1 34.7 + - + +
247A MET 3.0 6.0 + - - +
249A GLU* 1.3 76.9 - - - +
251A SER* 1.3 72.8 + - - +
252A GLY 3.2 2.8 + - - -
253A GLU* 3.3 35.9 + - + +
255A ILE* 4.5 7.9 - - + -
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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