Contacts of the helix formed by residues 241 - 252 (chain A) in PDB entry 2XK3
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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110A GLU* 2.7 33.5 + - - -
235A ARG* 3.5 2.3 + - - -
239A ARG 4.0 1.4 + - - -
240A TYR* 1.3 77.1 - - - +
242A ASP* 1.3 64.0 + - - +
243A GLU* 3.5 15.9 + - - +
244A LEU* 3.2 13.0 + - - +
245A ASN* 3.0 18.5 + - - +
270A LEU* 4.4 3.8 - - - +
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Residues in contact with ASP 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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235A ARG* 3.0 26.2 + - - +
241A SER* 1.3 72.8 - - - +
243A GLU* 1.3 65.8 + - - +
245A ASN* 3.8 4.9 + - - +
246A GLU* 2.8 32.3 + - - +
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Residues in contact with GLU 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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241A SER* 3.5 16.2 - - - +
242A ASP* 1.3 82.6 + - - +
244A LEU* 1.3 60.7 + - - +
246A GLU* 3.7 15.2 - - - +
247A ILE* 3.2 23.4 + - - +
250A ARG* 5.8 0.2 + - - -
268A ASN* 5.1 5.7 + - - +
270A LEU* 3.7 27.8 - - + +
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Residues in contact with LEU 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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110A GLU* 3.6 29.6 - - + +
113A VAL* 3.9 25.4 - - + -
114A LEU* 4.0 20.2 - - + -
117A MET* 4.3 6.7 - - + -
210A CYS* 4.0 5.2 - - - -
236A ILE* 4.2 3.4 - - + -
240A TYR* 4.0 19.3 - - + -
241A SER* 3.2 22.7 + - - +
243A GLU* 1.3 73.4 - - - +
245A ASN* 1.3 66.9 + - - +
247A ILE* 3.2 16.2 - - + +
248A ILE* 3.2 39.8 + - + +
270A LEU* 3.5 6.6 - - + +
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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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207A TYR* 5.9 0.3 - - - -
233A PHE* 5.5 1.6 - - - -
235A ARG* 3.4 44.9 - - - +
236A ILE* 3.5 33.9 + - + +
241A SER 3.0 14.9 + - - +
242A ASP* 3.8 5.1 + - - +
244A LEU* 1.3 77.4 - - - +
246A GLU* 1.3 58.7 + - - +
248A ILE* 3.5 2.5 + - - +
249A THR* 2.7 49.7 + - - -
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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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242A ASP 2.8 22.1 + - - +
243A GLU* 3.7 14.2 - - - +
244A LEU 3.3 0.2 - - - -
245A ASN* 1.3 77.2 - - - +
247A ILE* 1.3 57.2 + - - +
249A THR* 3.2 7.7 + - - +
250A ARG* 2.9 54.0 + - + +
268A ASN* 5.5 1.4 + - - -
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Residues in contact with ILE 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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117A MET* 3.9 34.5 - - + -
243A GLU 3.2 11.4 + - - +
244A LEU* 3.2 19.7 - - + +
246A GLU* 1.3 79.1 - - - +
248A ILE* 1.3 68.5 + - + +
250A ARG* 3.2 23.4 + - - +
251A MET* 3.0 37.0 + - + +
260A PRO* 4.9 4.5 - - + -
265A ILE* 4.1 20.2 - - + +
268A ASN* 3.8 35.0 - - + +
270A LEU* 4.7 2.9 - - + -
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Residues in contact with ILE 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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113A VAL* 4.9 0.2 - - + -
203A GLY 3.7 21.3 - - - +
206A LEU* 3.8 39.9 - - + -
207A TYR* 3.8 24.7 - - + +
210A CYS* 4.0 15.5 - - - -
233A PHE* 6.1 0.2 - - + -
236A ILE* 4.5 9.4 - - + -
244A LEU* 3.2 35.3 + - + +
245A ASN* 3.9 3.8 - - - +
247A ILE* 1.3 81.0 - - + +
249A THR* 1.3 63.8 + - - +
251A MET* 3.3 9.9 + - - +
252A LEU* 3.1 24.6 + - + +
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Residues in contact with THR 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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233A PHE* 4.0 30.7 - - + -
245A ASN* 2.7 42.4 + - - +
246A GLU* 3.5 7.9 - - - -
248A ILE* 1.3 78.5 - - - +
250A ARG* 1.3 62.8 + - - +
252A LEU* 3.1 20.4 + - - +
253A ASN* 3.5 2.6 + - - +
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Residues in contact with ARG 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 GLU 5.8 0.2 + - - -
246A GLU* 2.9 45.9 + - + +
247A ILE* 3.2 22.7 + - - +
249A THR* 1.3 74.0 - - - +
251A MET* 1.3 58.5 + - - +
253A ASN* 2.9 34.2 + - - +
258A HIS 4.8 8.5 - - - +
259A ARG* 3.6 9.4 - - - +
260A PRO* 3.8 37.0 - - + +
264A GLU* 5.1 8.7 + - - +
268A ASN* 3.5 25.5 - - - +
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Residues in contact with MET 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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117A MET* 3.9 10.8 - - - -
199A ILE* 3.6 28.0 - - + +
200A TRP* 3.5 12.0 - - - -
202A LEU* 4.0 15.7 - - + -
203A GLY* 3.8 26.2 - - - -
206A LEU* 3.9 21.3 - - + -
247A ILE* 3.0 41.7 + - + +
248A ILE* 3.3 9.6 + - - +
250A ARG* 1.3 76.0 - - - +
252A LEU* 1.3 58.5 + - - +
253A ASN 3.2 0.2 - - - -
259A ARG* 3.2 23.6 + - - -
260A PRO* 3.8 13.9 - - + +
265A ILE* 4.1 15.3 - - + -
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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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200A TRP* 3.3 49.6 - - + +
203A GLY 3.9 3.1 - - - -
204A CYS* 3.7 23.3 - - - +
207A TYR* 4.0 21.3 - - + -
215A PRO* 4.0 24.9 - - + -
216A PHE* 5.1 0.9 - - + -
231A GLY* 5.1 3.1 - - - +
233A PHE* 3.9 30.4 - - + -
248A ILE* 3.1 17.8 + - + +
249A THR 3.1 12.4 + - - +
250A ARG 3.1 1.2 - - - -
251A MET* 1.3 76.2 - - - +
253A ASN* 1.3 64.1 + - - -
254A LEU* 3.5 2.9 + - - +
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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