Contacts of the helix formed by residues 379 - 389 (chain D) 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 ASN 379 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D TYR* 5.3 4.0 + - - -
376D ASP 5.7 0.2 - - - -
377D GLU 3.6 4.8 + - - +
378D THR* 1.3 73.7 - - - +
380D PRO* 1.3 72.6 - - - +
381D ILE* 2.6 39.8 + - - +
382D GLU* 3.0 41.5 + - + +
383D GLU* 3.0 24.3 + - - +
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Residues in contact with PRO 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D TYR 3.3 21.3 - - - +
211D LEU* 3.5 35.4 - - + +
234D SER* 5.7 4.5 - - - +
361D TYR* 3.7 37.4 - - + -
362D TYR* 3.9 15.0 - - + +
378D THR* 3.6 2.1 - - + +
379D ASN* 1.3 91.1 - - - +
381D ILE* 1.3 65.6 + - - +
383D GLU* 3.8 5.7 + - + +
384D TRP* 3.4 16.1 + - - +
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Residues in contact with ILE 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D LYS* 3.5 24.5 - - - +
210D TYR 3.7 17.0 - - - +
211D LEU 4.3 3.8 - - - -
212D GLY* 3.7 20.4 - - - +
362D TYR* 4.2 6.7 - - - +
379D ASN* 2.6 18.5 + - - +
380D PRO* 1.3 70.4 - - + +
382D GLU* 1.3 68.6 + - + +
384D TRP* 2.9 20.5 + - + +
385D GLN* 3.2 26.6 + - - +
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Residues in contact with GLU 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D ASN* 3.0 35.2 + - + +
381D ILE* 1.3 80.7 - - + +
383D GLU* 1.3 63.6 + - - +
385D GLN* 3.1 34.3 + - - +
386D HIS* 3.4 18.6 + - + +
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Residues in contact with GLU 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D SER* 5.0 0.5 + - - -
361D TYR* 5.1 0.2 + - - -
378D THR* 3.9 20.2 - - + +
379D ASN 3.0 17.4 + - - +
380D PRO* 4.2 5.7 - - + +
382D GLU* 1.3 77.3 - - - +
384D TRP* 1.3 61.2 + - - +
386D HIS* 3.7 10.2 + - - +
387D ILE* 3.2 26.3 + - + +
418D TYR* 4.0 10.8 - - - -
421D ARG* 3.2 38.2 + - - +
422D ARG* 3.4 34.8 + - - +
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Residues in contact with TRP 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D LEU* 5.9 2.2 - - - +
207D GLN* 3.6 26.7 - - - -
211D LEU 4.5 2.5 - - - +
212D GLY* 4.0 21.5 - - - -
213D VAL* 3.4 43.5 - - + +
380D PRO 3.4 11.3 + - - +
381D ILE* 2.9 12.6 + - + +
383D GLU* 1.3 77.1 - - - +
385D GLN* 1.3 90.3 + - - +
387D ILE* 3.0 8.5 + - - +
388D GLU* 2.8 58.6 + - + +
414D TYR* 3.7 21.9 - + + +
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Residues in contact with GLN 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D ILE* 3.2 30.7 + - - +
382D GLU* 3.1 26.3 + - - +
384D TRP* 1.3 95.1 - - - +
386D HIS* 1.3 70.1 + - + +
388D GLU* 2.9 19.8 + - - +
389D GLN* 2.8 35.9 + - + +
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Residues in contact with HIS 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D GLU* 3.4 21.3 + - + +
383D GLU* 3.8 6.1 - - - +
385D GLN* 1.3 83.2 - - + +
387D ILE* 1.3 62.5 + - - +
389D GLN* 3.2 25.1 + - + +
421D ARG* 2.7 37.7 + - - +
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Residues in contact with ILE 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D GLU* 3.2 23.8 + - + +
384D TRP* 3.0 10.1 + - + +
386D HIS* 1.3 75.9 - - - +
388D GLU* 1.3 62.3 + - - +
389D GLN 3.4 2.9 + - - -
414D TYR* 4.0 29.4 - - + +
417D SER* 3.4 30.4 + - - +
418D TYR* 3.6 40.8 - - + +
421D ARG* 3.9 25.4 - - + -
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Residues in contact with GLU 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D TRP* 2.8 57.0 + - + +
385D GLN* 3.4 8.4 - - - +
387D ILE* 1.3 76.7 - - - +
389D GLN* 1.3 90.9 + - - +
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Residues in contact with GLN 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D GLN* 2.8 50.5 + - + +
386D HIS* 3.4 19.7 - - + +
387D ILE 3.2 5.1 - - - -
388D GLU* 1.3 107.6 + - - +
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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