Contacts of the helix formed by residues 243 - 256 (chain A) in PDB entry 2QDM
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 ALA 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A SER* 1.3 74.6 - - - +
244A GLY* 1.3 65.9 + - - +
245A PRO 3.5 1.3 - - - -
246A LEU* 3.4 8.0 + - - +
247A LEU* 3.2 22.7 + - - +
321A PHE* 3.8 7.3 - - + -
324A HIS* 3.8 24.2 - - + +
325A THR* 3.5 30.5 - - + +
328A LEU* 3.8 18.1 - - + +
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Residues in contact with GLY 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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242A SER* 4.2 2.2 + - - -
243A ALA* 1.3 75.8 - - - +
245A PRO* 1.3 70.0 - - - +
247A LEU* 3.2 6.7 + - - +
248A ARG* 3.1 27.3 + - - +
328A LEU* 3.8 15.1 - - - +
332A GLN* 5.3 4.7 + - - -
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Residues in contact with PRO 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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209A GLU* 3.9 22.4 - - + -
210A TYR* 4.7 1.2 - - - -
231A PHE* 3.8 12.1 - - + -
240A PRO* 6.6 0.4 - - + -
242A SER* 3.6 22.9 - - - +
243A ALA 3.9 1.8 - - - -
244A GLY* 1.3 87.6 - - - +
246A LEU* 1.3 56.6 + - - +
248A ARG* 3.1 34.4 + - - +
249A LEU* 2.9 28.2 + - - +
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Residues in contact with LEU 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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231A PHE* 3.8 15.2 - - + -
234A TRP* 3.9 32.8 - - + -
240A PRO* 5.4 3.1 - - + -
242A SER 5.2 2.2 + - - +
243A ALA* 3.4 13.3 + - - +
244A GLY 3.4 0.6 - - - -
245A PRO* 1.3 77.7 - - - +
247A LEU* 1.3 58.3 + - - +
249A LEU* 3.3 12.1 + - + +
250A VAL* 2.9 32.7 + - + +
280A PHE* 4.0 24.5 - - + -
283A THR* 4.0 16.8 - - + +
321A PHE* 3.9 22.9 - - + -
325A THR* 3.9 25.6 - - + +
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Residues in contact with LEU 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 3.2 11.8 + - - +
244A GLY* 3.2 7.2 + - - +
246A LEU* 1.3 71.8 - - - +
248A ARG* 1.3 61.2 + - - +
250A VAL* 3.3 7.0 + - + +
251A ALA* 2.9 27.9 + - - +
283A THR* 4.3 5.6 - - + -
287A CYS* 4.1 25.8 - - - -
325A THR* 3.6 26.7 - - + +
328A LEU* 3.7 21.3 - - + -
329A TYR* 3.5 36.1 - - + +
332A GLN* 3.6 25.6 - - - +
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Residues in contact with ARG 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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207A CYS* 4.4 1.2 - - - +
208A PRO* 2.6 60.1 + - - +
210A TYR* 3.5 25.5 + - + +
244A GLY 3.1 15.0 + - - +
245A PRO* 3.1 33.2 + - - +
247A LEU* 1.3 74.8 - - - +
249A LEU* 1.3 53.0 + - - +
251A ALA* 3.3 8.3 + - - +
252A GLU* 2.8 34.1 + - - +
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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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171A VAL* 4.2 6.1 - - + -
173A LEU* 3.8 18.8 - - + -
210A TYR* 3.9 14.2 - - + -
229A ILE* 3.5 41.5 - - + -
231A PHE* 3.8 26.7 - - + -
245A PRO 2.9 12.7 + - - +
246A LEU* 3.3 14.4 - - + +
248A ARG* 1.3 76.6 - - - +
250A VAL* 1.3 57.2 + - - +
252A GLU* 3.2 4.5 + - + +
253A VAL* 2.9 32.7 + - + +
280A PHE* 3.7 29.8 - - + -
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Residues in contact with VAL 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 LEU* 2.9 21.1 + - + +
247A LEU* 3.3 12.5 + - + +
249A LEU* 1.3 75.3 - - - +
251A ALA* 1.3 56.8 + - - +
253A VAL* 3.3 8.5 + - - +
254A GLU* 2.9 47.7 + - - +
280A PHE* 4.0 20.4 - - + -
283A THR* 3.9 26.9 - - + -
284A ARG* 4.6 14.8 - - - +
287A CYS* 4.4 18.6 - - + -
329A TYR* 5.6 3.6 - - + -
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Residues in contact with ALA 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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247A LEU 2.9 16.3 + - - +
248A ARG* 3.6 11.2 - - - +
250A VAL* 1.3 70.8 - - - +
252A GLU* 1.3 66.2 + - - +
254A GLU* 3.4 9.0 + - - +
255A GLU* 2.9 26.0 + - - +
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Residues in contact with GLU 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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205A LYS* 4.8 11.9 + - - -
207A CYS* 4.9 2.8 - - - -
210A TYR* 2.7 48.5 + - + +
212A VAL* 4.1 9.0 - - + +
227A LYS* 2.8 27.4 + - - +
229A ILE* 3.7 22.0 - - + -
248A ARG 2.8 11.5 + - - +
249A LEU* 3.2 9.8 + - + +
251A ALA* 1.3 71.3 - - - +
253A VAL* 1.3 60.5 + - - +
255A GLU* 3.3 9.0 + - - +
256A SER* 2.8 26.9 + - - -
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Residues in contact with VAL 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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169A LEU* 3.9 16.3 - - + +
171A VAL* 3.7 28.5 - - + -
229A ILE* 4.0 11.0 - - + -
249A LEU* 2.9 19.2 + - + +
250A VAL 3.5 8.1 - - - +
252A GLU* 1.3 74.6 - - - +
254A GLU* 1.3 62.6 + - - +
256A SER* 3.2 23.6 + - - +
266A ILE* 4.2 14.5 - - + +
280A PHE* 3.7 17.3 - - + -
284A ARG* 4.2 26.3 + - - +
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Residues in contact with GLU 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 VAL* 2.9 29.1 + - - +
251A ALA* 3.4 8.6 + - - +
253A VAL* 1.3 76.2 - - - +
255A GLU* 1.3 59.7 + - - +
256A SER 3.5 4.7 + - - +
284A ARG* 2.8 47.7 + - - +
287A CYS* 5.3 3.6 - - - +
288A GLN* 4.2 11.4 + - - +
291A LYS* 6.0 1.7 - - - +
329A TYR* 5.0 10.7 + - - -
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Residues in contact with GLU 255 (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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227A LYS* 5.2 1.3 - - - +
251A ALA 2.9 17.9 + - - +
252A GLU* 3.7 9.6 - - - +
253A VAL 3.2 0.2 - - - -
254A GLU* 1.3 75.5 - - - +
256A SER* 1.3 61.2 + - - +
257A PRO* 3.4 9.7 - - - +
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Residues in contact with SER 256 (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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169A LEU* 4.2 16.5 - - - +
227A LYS* 2.8 40.1 + - - +
252A GLU 2.8 13.7 + - - -
253A VAL* 3.2 16.8 + - - +
254A GLU 3.3 4.4 - - - +
255A GLU* 1.3 76.1 - - - +
257A PRO* 1.4 74.2 - - - +
258A GLU 3.8 0.7 + - - -
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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