Contacts of the helix formed by residues 379 - 390 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362B TYR* 4.6 9.7 + - - -
373B ALA* 5.3 9.1 - - - +
376B ASP 5.0 1.1 - - - +
377B GLU 3.0 10.0 + - - +
378B THR* 1.3 74.1 - - - +
380B PRO* 1.3 71.6 - - - +
381B ILE* 3.1 30.6 + - - +
382B GLU* 3.1 38.1 + - - +
383B GLU* 3.4 9.7 + - - +
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Residues in contact with PRO 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B TYR 3.6 18.6 - - - +
211B LEU* 4.1 21.3 - - + +
234B SER* 5.6 3.8 - - - +
361B TYR* 3.5 53.1 - - + +
362B TYR* 4.3 5.4 - - + +
378B THR* 3.6 3.2 - - + +
379B ASN* 1.3 88.7 - - - +
381B ILE* 1.3 67.9 + - - +
383B GLU* 3.0 20.4 + - + +
384B TRP* 3.0 12.1 + - - +
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B LYS 3.2 26.2 - - - +
210B TYR 3.5 18.2 - - - +
211B LEU 4.3 1.3 + - - -
212B GLY* 3.8 24.0 - - - +
362B TYR* 4.2 7.4 - - - +
379B ASN* 3.1 14.4 + - - +
380B PRO* 1.3 73.7 - - - +
382B GLU* 1.3 68.5 + - + +
384B TRP* 2.9 16.4 + - + +
385B GLN* 3.2 30.1 + - - +
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Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B GLU 6.1 0.2 - - - -
379B ASN* 3.1 32.3 + - - +
381B ILE* 1.3 80.7 - - + +
383B GLU* 1.3 63.1 + - - +
385B GLN* 3.0 34.3 + - - +
386B HIS* 3.4 18.0 + - + +
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Residues in contact with GLU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B SER* 5.0 2.3 + - - -
361B TYR* 5.1 3.1 + - - -
378B THR* 5.1 16.5 - - + +
379B ASN 3.4 7.1 + - - +
380B PRO* 3.0 13.4 + - + +
382B GLU* 1.3 79.0 - - - +
384B TRP* 1.3 61.1 + - - +
386B HIS* 3.7 10.5 + - - +
387B ILE* 3.2 25.4 + - + +
418B TYR* 4.1 20.6 - - - -
421B ARG* 3.2 38.9 + - - +
422B ARG* 5.3 5.9 - - - +
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Residues in contact with TRP 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B LEU* 6.0 2.4 - - - +
207B GLN* 3.3 28.0 - - - -
211B LEU 4.5 3.1 - - - +
212B GLY* 3.9 24.0 - - - -
213B VAL* 3.4 44.1 - - + +
380B PRO 3.0 9.5 + - - +
381B ILE* 2.9 13.2 + - + +
383B GLU* 1.3 73.6 - - - +
385B GLN* 1.3 89.9 + - - +
387B ILE* 3.0 9.4 + - - +
388B GLU* 2.8 58.6 + - + +
414B TYR* 3.8 21.7 - + + +
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Residues in contact with GLN 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B ILE* 3.2 30.9 + - - +
382B GLU* 3.0 26.6 + - - +
384B TRP* 1.3 93.6 - - - +
386B HIS* 1.3 70.0 + - + +
388B GLU* 2.9 12.5 + - - +
389B GLN* 2.8 43.3 + - + +
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Residues in contact with HIS 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B GLU* 3.4 20.2 + - + +
383B GLU* 3.8 7.1 - - - +
384B TRP 3.3 0.6 - - - -
385B GLN* 1.3 83.0 - - + +
387B ILE* 1.3 63.1 + - - +
389B GLN* 3.2 23.6 + - + +
390B LEU* 3.7 4.9 + - - +
421B ARG* 2.7 37.7 + - - +
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Residues in contact with ILE 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B GLU* 3.2 22.9 + - + +
384B TRP* 3.0 10.1 + - + +
386B HIS* 1.3 76.9 - - - +
388B GLU* 1.3 63.0 + - - +
389B GLN 3.4 0.7 + - - -
390B LEU 3.7 14.9 - - - +
391B LYS* 5.1 1.4 - - - +
414B TYR* 4.0 30.5 - - + +
417B SER* 3.4 30.4 + - - +
418B TYR* 3.6 40.2 - - + -
421B ARG* 3.9 25.8 - - + -
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Residues in contact with GLU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B TRP* 2.8 57.1 + - + +
385B GLN* 3.4 9.5 - - - +
387B ILE* 1.3 77.1 - - - +
389B GLN* 1.3 89.4 + - - +
391B LYS* 3.2 38.2 + - - +
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Residues in contact with GLN 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B GLN* 2.8 49.8 + - + +
386B HIS* 3.4 14.6 - - + +
387B ILE 3.2 0.4 - - - -
388B GLU* 1.3 107.7 + - - +
390B LEU* 1.3 61.3 + - - +
391B LYS* 3.1 10.4 + - - +
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B HIS 3.7 7.2 + - - +
387B ILE 3.7 10.8 - - - +
389B GLN* 1.3 77.4 - - - +
391B LYS* 1.3 75.4 + - - +
393B SER* 3.9 18.6 + - - +
417B SER* 5.2 4.2 + - - -
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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