Contacts of the helix formed by residues 245 - 264 (chain A) in PDB entry 2QFZ
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 ARG 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A PRO* 3.8 29.7 - - + +
242A ASN* 3.1 32.3 + - - +
244A ASP* 1.3 79.7 - - + +
246A ARG* 1.3 62.7 + - - +
247A PRO* 3.5 1.2 - - - -
248A ALA* 3.5 8.2 + - - +
249A THR* 3.0 30.1 + - - +
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Residues in contact with ARG 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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205A LEU* 3.0 21.0 + - - +
210A THR* 2.9 29.5 + - - -
230A MET* 4.4 25.1 - - + +
234A LEU* 3.8 19.8 - - - +
239A LEU* 3.9 12.2 - - + +
240A PRO* 2.9 37.6 + - + +
241A ALA 2.9 17.4 + - - -
242A ASN 3.5 5.4 - - - +
243A VAL* 3.2 27.5 + - - +
245A ARG* 1.3 77.6 - - - +
247A PRO* 1.4 65.5 - - + +
249A THR* 3.3 2.3 + - - -
250A LEU* 2.9 32.8 + - - +
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Residues in contact with PRO 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A VAL 3.6 7.2 - - - +
244A ASP* 3.6 13.9 - - - +
245A ARG 3.5 4.7 - - - -
246A ARG* 1.4 95.8 - - + +
248A ALA* 1.3 56.5 + - - +
250A LEU* 3.7 7.2 - - + +
251A GLN* 3.0 30.0 + - - +
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Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ASP 5.6 1.1 - - - +
245A ARG* 3.5 9.1 + - - +
246A ARG 3.4 0.4 - - - -
247A PRO* 1.3 76.7 - - - +
249A THR* 1.3 60.8 + - - +
251A GLN* 3.5 5.8 + - - +
252A ARG* 2.9 63.2 + - - +
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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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238A TYR 4.1 4.3 - - - +
239A LEU* 4.5 1.3 - - + -
240A PRO* 3.7 29.1 - - + +
245A ARG* 3.0 26.0 + - - +
246A ARG 3.7 3.6 - - - -
248A ALA* 1.3 77.8 - - - +
250A LEU* 1.3 56.7 + - - +
252A ARG* 3.3 5.6 + - - +
253A LYS* 2.9 57.1 + - + +
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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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230A MET* 5.7 2.9 - - + -
233A LYS* 5.0 6.3 - - - +
238A TYR* 3.6 37.2 - - + +
239A LEU* 3.7 25.5 - - + +
246A ARG 2.9 18.1 + - - +
247A PRO* 3.7 7.0 - - + +
249A THR* 1.3 74.1 - - - +
251A GLN* 1.3 67.5 + - - +
253A LYS* 4.1 2.4 - - - +
254A GLN* 2.9 44.6 + - - +
362A ASP* 3.6 14.6 - - - +
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Residues in contact with GLN 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 PRO 3.0 18.6 + - - +
248A ALA* 4.0 5.4 - - - +
250A LEU* 1.3 76.2 - - - +
252A ARG* 1.3 67.0 + - - +
254A GLN* 3.4 11.8 + - + +
255A LYS* 3.0 54.5 + - + +
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Residues in contact with ARG 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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248A ALA* 2.9 44.1 + - - +
249A THR* 4.0 4.1 - - - +
251A GLN* 1.3 83.3 - - + +
253A LYS* 1.3 59.7 + - + +
255A LYS* 3.4 11.0 + - + +
256A GLU* 3.0 27.7 + - - +
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Residues in contact with LYS 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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237A GLY 3.8 9.1 + - - -
238A TYR* 2.7 64.1 + - + +
249A THR* 2.9 34.6 + - + +
250A LEU* 4.1 2.0 - - - +
252A ARG* 1.3 72.6 - - + +
254A GLN* 1.3 65.7 + - - +
256A GLU* 3.3 7.3 + - - +
257A TYR 3.2 10.9 + - - -
365A TRP* 2.9 32.2 + - + +
369A LYS* 5.1 7.3 - - - +
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Residues in contact with GLN 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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238A TYR* 4.0 1.8 - - - +
250A LEU* 2.9 39.7 + - - +
251A GLN* 3.8 13.8 + - + +
253A LYS* 1.3 76.6 - - - +
255A LYS* 1.3 62.4 + - + +
257A TYR* 3.1 5.7 + - - +
258A PHE* 3.0 37.9 + - + -
358A ASN* 3.6 37.6 + - - +
361A ALA* 3.6 26.0 - - + -
362A ASP* 3.0 27.2 + - - +
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Residues in contact with LYS 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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251A GLN* 3.0 56.2 + - + +
252A ARG* 3.7 9.4 - - + +
254A GLN* 1.3 75.7 - - + +
256A GLU* 1.3 63.3 + - - +
258A PHE* 3.3 16.6 + - + +
259A ALA* 3.0 23.0 + - - +
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Residues in contact with GLU 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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252A ARG 3.0 14.0 + - - +
253A LYS* 3.6 11.2 - - - +
254A GLN 3.2 0.4 - - - -
255A LYS* 1.3 76.6 - - - +
257A TYR* 1.3 60.8 + - - +
259A ALA* 3.4 9.8 - - + +
260A PHE* 3.2 38.2 + - + -
365A TRP* 3.8 20.9 - - + -
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Residues in contact with TYR 257 (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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253A LYS 3.2 2.0 + - - -
254A GLN 3.1 8.4 + - - +
256A GLU* 1.3 74.7 - - - +
258A PHE* 1.3 72.7 + + - +
260A PHE* 2.8 31.7 + + - +
261A ILE* 3.1 21.9 + - + +
305A ILE* 3.6 18.0 + - - +
308A ILE* 3.8 25.1 - - + +
360A GLU* 2.6 47.5 + - + +
361A ALA* 3.7 23.1 - - + -
364A TYR* 3.5 44.0 - + + -
365A TRP* 3.8 17.4 - - - +
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Residues in contact with PHE 258 (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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254A GLN* 3.0 32.1 + - + -
255A LYS* 3.6 17.0 - - + +
257A TYR* 1.3 85.9 - + - +
259A ALA* 1.3 60.1 + - - +
261A ILE* 3.3 17.3 + - + +
262A GLU* 3.1 24.9 + - - +
357A CYS* 3.4 38.8 - - + -
358A ASN* 3.5 25.1 - - - -
361A ALA* 4.1 6.7 - - + -
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Residues in contact with ALA 259 (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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255A LYS 3.0 13.5 + - - +
256A GLU* 3.4 13.5 - - - +
257A TYR 3.2 0.2 - - - -
258A PHE* 1.3 73.9 - - - +
260A PHE* 1.3 66.4 + - + +
262A GLU* 3.6 6.7 + - - +
263A HIS* 3.1 25.5 + - - +
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Residues in contact with PHE 260 (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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256A GLU* 3.2 30.9 + - + -
257A TYR* 2.8 25.2 + + - +
259A ALA* 1.3 74.9 - - + +
261A ILE* 1.3 63.9 + - - +
263A HIS* 3.2 2.1 + - + -
264A TYR* 2.9 45.2 + + + +
308A ILE* 3.9 18.2 - - + -
312A ARG* 3.5 57.4 - - - -
364A TYR* 4.0 7.4 - + - -
365A TRP* 3.8 26.5 - + - -
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Residues in contact with ILE 261 (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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257A TYR* 3.1 35.2 + - + +
258A PHE* 3.3 19.0 + - + +
260A PHE* 1.3 77.2 - - - +
262A GLU* 1.3 68.2 + - - +
264A TYR 3.4 16.6 - - - -
304A ARG* 4.1 31.9 - - - +
308A ILE* 3.8 21.8 - - + -
357A CYS* 6.3 3.4 - - + -
360A GLU* 3.9 12.1 - - - +
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Residues in contact with GLU 262 (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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258A PHE 3.1 14.0 + - - +
259A ALA* 3.9 7.9 - - - +
261A ILE* 1.3 86.9 - - - +
263A HIS* 1.3 60.9 + - - +
264A TYR 4.2 2.4 - - - -
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Residues in contact with HIS 263 (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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259A ALA 3.1 18.4 + - - +
260A PHE* 3.8 5.4 - - + +
262A GLU* 1.3 78.1 - - - +
264A TYR* 1.3 83.6 + + + +
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Residues in contact with TYR 264 (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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260A PHE* 2.9 41.6 + + + +
261A ILE* 3.4 17.0 - - - -
262A GLU 4.2 2.5 - - - -
263A HIS* 1.3 102.9 - + + +
307A PHE* 4.8 12.4 - - + -
308A ILE* 4.3 11.7 - - + -
311A ILE* 3.2 39.6 + - + -
312A ARG* 2.6 47.6 + - + +
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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
------------------------------------------------------------
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