Contacts of the helix formed by residues 408 - 418 (chain A) in PDB entry 6MOL
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 HIS 408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A ALA 3.4 11.9 + - - -
372A THR 3.3 24.9 - - - -
373A MET 3.3 19.5 + - - -
374A GLY* 3.5 15.2 - - - -
403A ALA* 3.0 16.0 + - + +
406A MET* 3.6 26.1 + - + +
407A GLY* 1.3 74.8 + - - -
409A VAL* 1.3 64.9 + - - +
410A GLU* 3.5 3.4 - - + +
411A ILE* 4.3 18.8 - - + -
412A VAL* 3.2 27.2 + - - +
444A LEU* 4.3 2.6 - - - +
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Residues in contact with VAL 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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407A GLY 4.1 1.7 + - - +
408A HIS* 1.3 71.9 - - - +
410A GLU* 1.3 90.3 + - - +
412A VAL* 3.4 4.1 + - - +
413A GLU* 3.1 28.9 + - - +
443A ASP* 4.5 20.4 - - + +
444A LEU* 3.6 32.8 - - + +
447A ILE* 6.0 5.6 - - + +
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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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376A LEU* 4.0 24.9 - - + -
408A HIS* 3.5 1.6 - - - -
409A VAL* 1.3 98.7 + - - +
411A ILE* 1.3 63.4 + - + +
413A GLU* 3.2 22.4 + - - +
414A VAL* 3.2 23.7 + - - +
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Residues in contact with ILE 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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370A ALA 4.1 2.9 - - - +
371A ALA* 4.2 14.1 - - + +
374A GLY* 3.5 39.5 - - - +
375A HIS 3.8 3.4 - - - +
376A LEU* 4.0 21.5 - - + -
379A VAL* 3.8 40.2 - - + -
403A ALA* 4.7 2.7 - - + -
408A HIS* 3.9 16.2 + - + +
409A VAL 3.3 0.6 - - - -
410A GLU* 1.3 75.1 - - + +
412A VAL* 1.3 61.7 + - - +
414A VAL* 3.0 3.9 + - - +
415A LEU* 2.8 41.5 + - + +
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Residues in contact with VAL 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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400A LEU* 3.7 28.5 - - + +
403A ALA* 3.7 23.8 - - + -
404A ALA* 4.5 3.8 - - + +
408A HIS 3.2 19.0 + - - +
409A VAL* 3.4 7.7 + - - +
411A ILE* 1.3 76.8 - - - +
413A GLU* 1.3 60.4 - - - +
415A LEU* 3.9 1.2 - - - +
416A LEU* 3.0 38.5 + - + +
444A LEU* 4.2 17.5 - - + -
447A ILE* 4.9 9.9 - - + -
448A LEU* 4.5 13.7 - - + -
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Residues in contact with GLU 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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409A VAL* 3.1 16.8 + - - +
410A GLU* 3.3 26.5 - - - +
411A ILE 3.1 0.4 - - - -
412A VAL* 1.3 78.5 - - - +
414A VAL* 1.3 60.6 + - + +
416A LEU* 3.7 7.1 + - - +
417A LYS* 3.2 35.0 + - - +
447A ILE* 4.8 27.4 - - + +
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Residues in contact with VAL 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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376A LEU* 3.9 20.2 - - + -
379A VAL* 4.6 6.7 - - + -
380A GLU* 4.4 24.0 - - + +
383A LEU* 3.8 20.9 - - + -
410A GLU 3.3 14.4 - - - +
411A ILE* 3.0 7.5 + - - +
413A GLU* 1.3 76.0 - - + +
415A LEU* 1.3 67.1 + - - +
417A LYS* 3.1 18.7 + - + +
418A TYR* 3.1 28.7 + - + -
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Residues in contact with LEU 415 (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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367A LEU* 4.0 16.2 - - + -
371A ALA* 4.7 1.6 - - + -
379A VAL* 4.6 4.3 - - + -
383A LEU* 4.2 11.0 - - + -
389A VAL* 3.5 23.9 - - + +
399A PRO* 3.5 46.0 - - + +
400A LEU* 3.8 15.7 - - + +
403A ALA* 4.3 4.7 - - + -
411A ILE* 2.8 34.1 + - + +
412A VAL 3.9 3.6 - - - +
414A VAL* 1.3 77.2 - - - +
416A LEU* 1.3 61.0 + - - +
418A TYR 3.1 8.7 + - - -
419A GLY 3.2 1.2 + - - -
420A ALA* 3.0 30.5 + - + +
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Residues in contact with LEU 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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400A LEU* 4.2 4.5 - - + -
412A VAL* 3.0 32.5 + - + +
413A GLU* 4.1 4.9 - - - +
415A LEU* 1.3 75.9 - - - +
417A LYS* 1.3 60.7 + - - +
419A GLY* 3.2 12.0 + - - -
420A ALA* 3.7 32.4 + - + +
422A VAL* 3.8 20.9 - - + -
447A ILE* 3.7 30.5 - - + +
448A LEU* 4.9 5.2 - - + -
451A ALA* 4.1 22.0 - - + -
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Residues in contact with LYS 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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413A GLU* 3.2 23.7 + - - +
414A VAL* 3.1 16.5 + - + +
416A LEU* 1.3 75.4 - - - +
418A TYR* 1.3 66.6 + - + +
419A GLY 3.4 0.6 + - - -
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Residues in contact with TYR 418 (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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380A GLU* 4.3 3.1 + - - -
383A LEU* 3.5 61.9 - - + -
384A LYS* 3.5 29.0 - - - +
389A VAL* 3.5 13.5 - - + +
414A VAL* 3.1 35.4 + - + +
415A LEU 3.1 8.9 + - - +
417A LYS* 1.3 83.1 - - + +
419A GLY* 1.3 61.0 + - - +
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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