Contacts of the helix formed by residues 237 - 250 (chain A) in PDB entry 3KXM
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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195A ARG* 3.5 16.9 - - - +
236A HIS* 1.3 79.2 + - + +
238A ASN* 1.3 65.7 + - - +
239A HIS* 3.3 14.1 + - - +
240A ASP* 2.8 25.2 + - - +
241A GLN 3.0 15.9 + - - -
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Residues in contact with ASN 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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191A ARG* 5.9 5.5 - - - +
195A ARG* 3.1 23.0 + - - -
198A LYS* 3.6 27.5 - - - +
203A LEU* 3.6 15.4 - - + +
237A ASP* 1.3 70.9 - - - +
239A HIS* 1.3 63.2 + - + +
241A GLN* 2.7 34.1 + - - +
242A LEU* 3.2 5.5 + - - +
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Residues in contact with HIS 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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237A ASP* 3.3 12.6 + - - +
238A ASN* 1.3 79.9 - - + +
240A ASP* 1.3 62.7 + - - +
241A GLN 3.1 0.5 + - - -
242A LEU* 3.3 11.5 + - - +
243A VAL* 3.3 16.9 + - - +
266A ASP* 5.2 3.1 - - - -
268A GLN* 3.5 34.9 + - - -
269A LEU* 3.5 47.3 - - + +
272A LEU* 3.9 26.7 - - + -
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Residues in contact with ASP 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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235A GLY* 3.5 2.3 - - - -
236A HIS* 3.1 42.2 + - + +
237A ASP* 2.8 22.9 + - - +
239A HIS* 1.3 73.4 - - - +
241A GLN* 1.3 62.7 + - - +
243A VAL* 3.3 14.9 + - - +
244A LYS* 3.0 53.7 + - - +
247A LYS* 5.8 0.2 + - - -
272A LEU* 6.1 1.8 - - - +
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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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195A ARG* 3.3 38.6 + - + +
196A TYR* 3.5 10.1 + - - -
198A LYS 4.8 2.7 + - - +
203A LEU* 3.6 25.8 - - + -
233A PHE* 3.2 38.2 + - - +
235A GLY* 3.2 24.2 + - - -
237A ASP 3.0 10.7 + - - +
238A ASN* 2.7 16.6 + - - +
240A ASP* 1.3 77.8 - - - +
242A LEU* 1.3 58.6 + - - +
244A LYS* 3.5 4.6 + - - +
245A ILE* 3.3 30.3 + - - +
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Residues in contact with LEU 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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200A PRO* 4.6 11.7 - - + -
203A LEU* 3.8 27.3 - - + +
204A VAL* 3.8 32.3 - - + -
238A ASN 3.2 4.7 + - - +
239A HIS 3.3 6.2 + - - +
241A GLN* 1.3 79.5 - - - +
243A VAL* 1.3 55.1 + - - +
245A ILE* 3.2 8.2 + - + +
246A ALA* 2.9 27.8 + - - +
254A LEU* 4.5 18.2 - - + -
265A LEU* 4.3 7.0 - - + -
269A LEU* 4.1 22.4 - - + -
273A VAL* 4.1 21.8 - - + -
307A TYR* 4.9 7.0 - - + -
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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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239A HIS 3.3 15.8 + - - +
240A ASP* 3.3 19.3 + - - +
242A LEU* 1.3 74.8 - - - +
244A LYS* 1.3 57.6 + - - +
246A ALA* 3.3 7.2 + - - +
247A LYS* 2.9 61.2 + - + +
272A LEU* 3.7 46.9 - - + +
273A VAL* 4.1 13.4 - - + +
276A HIS* 4.9 0.4 - - - +
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Residues in contact with LYS 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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233A PHE* 3.8 12.1 - - + -
234A TYR* 3.4 30.5 + - + +
235A GLY* 3.7 15.7 - - - +
236A HIS* 6.2 0.2 - - - -
240A ASP* 3.0 39.3 + - - +
241A GLN* 3.7 7.0 - - - +
242A LEU 3.4 0.2 - - - -
243A VAL* 1.3 76.3 - - - +
245A ILE* 1.3 63.9 + - - +
247A LYS* 3.8 23.9 + - + +
248A VAL* 3.7 17.8 + - - +
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Residues in contact with ILE 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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198A LYS 4.2 7.4 - - - +
200A PRO* 4.7 6.5 - - + -
203A LEU* 3.7 24.7 - - + -
216A TRP* 3.6 42.8 - - + +
233A PHE* 3.9 24.0 - - + -
241A GLN* 3.3 19.7 + - - +
242A LEU* 3.2 9.5 + - + +
243A VAL 3.2 0.4 - - - -
244A LYS* 1.3 75.8 - - - +
246A ALA* 1.4 53.5 - - - +
248A VAL* 2.6 29.8 + - - +
249A LEU* 3.0 18.3 + - + -
307A TYR* 3.9 22.4 - - + -
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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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242A LEU 2.9 17.3 + - - +
243A VAL* 3.5 6.5 - - - +
245A ILE* 1.4 75.7 - - - +
247A LYS* 1.3 54.8 + - - +
248A VAL 3.1 0.4 - - - -
250A GLY* 2.8 33.8 + - - -
251A THR* 4.2 8.5 - - + -
254A LEU* 4.4 5.4 - - + -
273A VAL* 3.7 29.4 - - + -
276A HIS* 3.6 8.8 - - + +
307A TYR* 3.3 18.1 + - + +
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Residues in contact with LYS 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* 2.9 39.9 + - - +
244A LYS* 4.0 23.8 - - + +
245A ILE 2.9 0.4 + - - -
246A ALA* 1.3 73.6 - - - +
248A VAL* 1.3 65.0 + - + +
250A GLY 4.6 0.7 - - - -
276A HIS* 3.4 43.7 - - + +
277A SER 4.5 4.9 - - - +
279A LYS* 4.0 16.1 - - - +
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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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232A PHE* 4.7 1.8 - - + -
233A PHE* 4.0 18.2 - - + -
244A LYS 3.7 13.2 - - - +
245A ILE 2.6 13.4 + - - +
247A LYS* 1.3 77.6 - - + +
249A LEU* 1.3 61.3 + - + +
250A GLY 3.2 3.7 + - - -
278A ARG* 3.5 1.9 - - - +
279A LYS* 2.8 38.5 + - + +
281A TRP* 4.0 25.6 - - + -
284A PHE* 3.6 41.5 - - + -
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Residues in contact with LEU 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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216A TRP* 3.9 17.3 - - + -
233A PHE* 5.2 2.2 - - + -
245A ILE* 3.0 16.1 + - + +
248A VAL* 1.3 80.0 - - + +
250A GLY* 1.3 62.2 + - - +
253A GLY* 4.8 5.0 + - - -
278A ARG* 3.8 24.1 - - + +
281A TRP* 3.7 29.2 - - + -
305A LEU* 3.4 28.0 - - + +
306A ARG* 4.3 0.7 - - - -
307A TYR* 3.4 53.4 - - + +
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Residues in contact with GLY 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 2.8 23.1 + - - -
248A VAL 3.2 4.6 + - - -
249A LEU* 1.3 76.1 - - - +
251A THR* 1.3 61.9 + - - -
252A ASP 3.4 2.9 - - - -
253A GLY 4.0 1.0 + - - -
254A LEU 4.0 0.5 + - - -
276A HIS 3.2 14.4 - - - -
277A SER 3.6 9.4 + - - -
278A ARG* 3.7 5.6 - - - +
307A TYR* 2.6 28.6 + - - -
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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