Contacts of the helix formed by residues 408 - 422 (chain A) in PDB entry 1M6X
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 408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A PRO 5.1 0.4 + - - -
201A LYS 5.7 2.3 + - - -
203A PHE* 3.6 25.0 + - - +
204A LYS* 5.5 0.6 - - - -
406A ILE 3.6 4.6 + - - -
407A ILE* 1.3 77.0 - - - +
409A GLN* 1.3 65.2 + - - +
410A GLU* 3.3 23.9 + - - +
411A VAL* 3.1 11.9 + - - +
412A LEU* 3.0 17.7 + - - +
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Residues in contact with GLN 409 (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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394A ALA* 3.3 40.3 + - - +
397A SER* 4.0 13.1 + - - -
407A ILE 3.3 4.0 + - - -
408A SER* 1.3 68.6 + - - +
410A GLU* 1.3 66.9 + - - +
411A VAL 2.9 2.6 + - - -
412A LEU* 3.0 11.5 + - + -
413A ASP* 2.7 42.3 + - - +
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Residues in contact with GLU 410 (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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204A LYS* 5.3 1.7 - - - +
205A LEU* 3.4 44.5 + - + +
408A SER* 3.3 12.5 + - - +
409A GLN* 1.3 78.9 - - - +
411A VAL* 1.3 56.8 + - - +
413A ASP* 3.7 9.9 + - - +
414A TYR* 3.2 18.9 + - - +
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Residues in contact with VAL 411 (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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203A PHE* 3.8 24.0 - - + +
204A LYS* 3.9 11.2 - - - +
205A LEU* 4.0 19.3 - - + +
215A ILE* 4.2 31.0 - - + -
245A LEU* 6.1 0.9 - - + -
249A LEU* 6.4 1.3 - - + -
407A ILE* 4.0 15.5 - - + -
408A SER* 3.3 25.6 - - - +
409A GLN 2.9 0.4 - - - -
410A GLU* 1.3 75.3 - - + +
412A LEU* 1.3 67.9 + - + +
413A ASP 3.0 1.3 - - - -
414A TYR* 2.9 3.8 + - - +
415A LEU* 2.9 26.1 + - + +
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Residues in contact with LEU 412 (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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249A LEU* 4.6 6.5 - - + -
396A GLY* 3.6 12.5 - - - -
397A SER* 4.6 5.8 - - - +
400A TYR* 3.6 41.2 - - + +
403A TRP* 3.9 15.7 - - + +
404A ASN* 4.2 17.5 - - - +
405A GLY 4.9 0.7 - - - +
407A ILE* 3.1 46.4 - - + +
408A SER 3.0 9.2 + - - +
409A GLN* 3.0 13.6 + - + +
411A VAL* 1.3 79.6 - - + +
413A ASP* 1.3 58.1 + - - +
415A LEU* 4.8 1.8 - - + -
416A SER* 3.0 30.1 + - - -
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Residues in contact with ASP 413 (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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393A SER 3.4 23.4 - - - +
394A ALA* 3.7 6.8 - - - +
396A GLY* 3.4 14.2 + - - +
409A GLN* 2.7 42.4 + - - +
410A GLU* 3.7 8.0 - - - +
412A LEU* 1.3 75.6 - - - +
414A TYR* 1.3 57.1 - - - +
416A SER* 3.1 4.7 + - - -
417A SER* 2.7 42.3 + - - +
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Residues in contact with TYR 414 (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* 3.5 42.8 - - + -
211A LEU 5.4 1.4 + - - -
213A VAL* 3.8 25.8 + - + +
214A ILE* 5.6 0.2 - - - -
215A ILE* 4.2 21.3 - - + -
234A SER* 5.0 3.8 - - - -
242A LEU* 4.0 25.1 - - + +
384A TRP* 3.7 31.5 - + + +
387A ILE* 4.0 26.2 - - + +
410A GLU 3.2 2.6 + - - +
411A VAL 2.9 7.7 + - - +
413A ASP* 1.3 78.9 - - - +
415A LEU* 1.3 59.2 + - - +
417A SER* 3.6 4.3 - - - -
418A TYR* 2.9 42.9 + + + +
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Residues in contact with LEU 415 (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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215A ILE* 4.5 7.2 - - + -
242A LEU* 3.6 46.9 - - + +
245A LEU* 3.8 18.8 - - + -
246A ASP* 4.0 7.4 - - - -
249A LEU* 3.7 24.5 - - + -
400A TYR* 3.2 27.4 - - + +
411A VAL* 2.9 16.6 + - + +
412A LEU* 4.1 3.8 - - + +
414A TYR* 1.3 77.1 - - - +
416A SER* 1.3 68.7 + - - +
417A SER 3.2 0.2 + - - -
418A TYR* 3.5 4.8 - - + +
419A ILE* 2.9 33.2 + - + +
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Residues in contact with SER 416 (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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395A GLU* 3.6 11.3 + - - +
396A GLY* 3.6 22.1 - - - -
399A ARG* 3.8 12.6 - - - +
400A TYR* 3.8 13.6 + - - -
412A LEU 3.0 21.9 + - - -
413A ASP* 3.4 4.5 - - - -
415A LEU* 1.3 78.2 - - - +
417A SER* 1.3 63.7 + - - +
419A ILE* 3.3 2.5 + - - +
420A ASN* 2.9 36.6 + - - -
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Residues in contact with SER 417 (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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387A ILE* 3.4 31.0 + - - +
390A LEU 5.7 1.0 + - - -
393A SER* 5.2 8.1 + - - -
413A ASP* 2.7 26.8 + - - +
414A TYR* 3.6 0.4 - - - -
416A SER* 1.3 71.7 - - - +
418A TYR* 1.3 67.4 + - - +
419A ILE 2.8 1.2 + - - -
420A ASN* 2.9 7.8 + - - +
421A ARG* 2.6 30.0 + - - +
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Residues in contact with TYR 418 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A SER* 2.7 30.9 + - - -
235A ALA 4.7 0.2 + - - -
240A ASP* 2.4 30.4 + - - -
242A LEU* 3.5 37.9 - - + -
243A VAL* 4.8 3.1 - - + -
361A TYR* 4.6 1.4 + - - -
383A GLU* 4.0 17.0 + - - -
387A ILE* 3.6 27.6 - - + +
414A TYR* 2.9 29.0 + - + +
415A LEU* 3.5 6.5 - - + +
417A SER* 1.3 75.5 - - - +
419A ILE* 1.3 79.2 + - + +
421A ARG* 3.4 3.8 - - - +
422A ARG* 3.2 34.3 + - + +
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Residues in contact with ILE 419 (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 4.0 10.1 - - - +
243A VAL* 4.4 12.1 - - + -
246A ASP* 3.5 25.1 - - + +
399A ARG* 3.3 32.3 - - - +
400A TYR* 3.7 16.6 - - - +
415A LEU* 2.9 23.9 + - + +
416A SER 3.4 7.2 - - - +
417A SER 2.8 3.2 + - - -
418A TYR* 1.3 83.7 - - + +
420A ASN* 1.3 61.7 + - - +
422A ARG* 2.8 31.0 + - - +
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Residues in contact with ASN 420 (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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395A GLU* 4.4 14.0 + - - -
399A ARG* 3.9 20.2 + - - +
416A SER* 2.9 32.7 + - - -
417A SER* 2.9 8.3 + - - +
419A ILE* 1.3 77.8 - - - +
421A ARG* 1.3 54.2 + - - +
422A ARG 2.7 20.8 + - - +
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Residues in contact with ARG 421 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383A GLU* 3.2 42.2 + - - +
386A HIS* 2.7 45.7 + - - +
387A ILE* 3.9 16.6 - - + -
417A SER* 2.6 27.0 + - - +
418A TYR* 3.4 8.1 - - - +
420A ASN* 1.3 72.4 - - - +
422A ARG* 1.3 57.8 + - - +
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Residues in contact with ARG 422 (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 ALA 5.0 3.2 + - - -
237A GLY 4.0 20.4 + - - +
240A ASP* 3.1 35.5 + - - +
243A VAL* 4.1 10.2 - - - +
383A GLU* 5.6 5.2 - - - +
418A TYR* 3.2 23.8 + - + +
419A ILE* 2.8 21.9 + - - +
420A ASN* 2.7 8.7 + - - +
421A ARG* 1.3 82.5 - - - +
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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