Contacts of the helix formed by residues 393 - 401 (chain A) in PDB entry 2I6W
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 LEU 393 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A TYR* 4.2 20.6 - - + -
36A PRO* 3.8 21.1 - - + -
391A ASN* 2.7 9.4 - - + -
392A THR* 1.3 81.9 - - - +
394A THR* 1.3 59.6 + - - +
395A MET 3.3 1.3 - - - -
396A PHE* 4.0 20.4 + - - +
397A GLY 4.5 2.1 + - - -
466A ILE* 3.2 49.4 - - + +
469A GLN* 3.6 22.5 - - + +
470A PHE* 5.3 3.0 - - + -
564A LEU* 5.1 3.1 - - + -
671A ILE* 4.8 5.2 - - + -
926A TYR* 4.8 14.1 - - + +
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Residues in contact with THR 394 (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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383A LEU* 4.3 21.5 - - + -
388A PHE* 4.8 0.7 - - + -
389A SER 2.8 9.6 + - - +
390A ILE* 4.7 2.2 - - - -
391A ASN* 2.5 40.4 + - - +
393A LEU* 1.3 76.3 - - - +
395A MET* 1.3 65.6 + - - +
396A PHE 3.2 1.8 + - - -
397A GLY 3.7 2.3 + - - +
398A MET* 3.5 15.6 + - - +
469A GLN* 3.5 38.1 - - - +
473A THR* 3.5 24.4 - - + +
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Residues in contact with MET 395 (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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337A ILE* 5.9 9.0 - - + -
340A VAL* 3.8 40.1 - - + +
341A VAL* 4.4 18.4 - - + -
344A LEU* 5.2 8.7 - - + +
380A PHE* 4.1 29.2 - - + -
390A ILE* 4.1 23.3 - - + -
391A ASN 3.1 16.4 + - - +
392A THR* 5.2 4.3 - - - -
393A LEU 3.3 1.3 - - - +
394A THR* 1.3 77.7 - - - +
396A PHE* 1.3 61.7 + - + +
398A MET* 2.8 40.7 - - + +
399A VAL* 3.7 5.7 + - - +
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Residues in contact with PHE 396 (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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340A VAL* 5.1 13.0 - - + -
392A THR 3.7 24.5 - - - -
393A LEU* 4.2 11.2 - - - +
394A THR 3.2 0.8 - - - -
395A MET* 1.3 73.0 - - + +
397A GLY* 1.3 57.5 + - - +
398A MET 2.4 17.6 + - - -
399A VAL* 2.6 32.5 + - + +
400A LEU* 3.0 6.5 + - + -
567A GLU* 5.6 0.2 - - - -
926A TYR* 3.8 18.4 - + + -
929A VAL* 6.5 0.7 - - + -
989A LEU* 4.8 6.1 - - + -
996A GLY* 4.3 3.1 - - - -
999A ALA* 3.7 17.3 - - + -
1000A GLN* 3.4 53.6 - - + -
1003A VAL* 3.4 27.1 - - + -
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Residues in contact with GLY 397 (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 LEU 4.5 2.6 + - - -
394A THR 3.7 7.1 + - - -
395A MET 3.6 0.2 - - - -
396A PHE* 1.3 77.4 - - - +
398A MET* 1.3 60.2 + - - +
400A LEU* 3.9 14.5 - - - +
401A ALA* 3.0 26.3 + - - +
470A PHE* 5.0 4.9 - - - -
473A THR* 4.5 5.4 - - - +
474A ILE* 3.6 27.2 - - - +
929A VAL* 5.6 1.3 - - - +
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Residues in contact with MET 398 (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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344A LEU* 4.5 15.3 - - + -
376A LEU* 4.1 35.2 - - + +
379A THR* 4.3 15.5 - - - -
380A PHE* 3.2 46.0 - - + -
383A LEU* 5.3 4.3 - - - -
394A THR 3.5 13.7 + - - +
395A MET* 2.8 33.2 - - - +
396A PHE 2.4 12.9 + - - -
397A GLY* 1.3 72.6 - - - +
399A VAL* 1.3 56.4 + - - +
401A ALA* 3.7 3.3 - - - +
402A ILE* 3.0 23.4 + - - +
405A LEU* 4.6 0.5 - - - +
473A THR* 4.2 17.0 - - - +
477A ALA* 5.7 2.9 - - - +
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Residues in contact with VAL 399 (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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340A VAL* 5.0 5.6 - - + +
343A THR* 3.9 26.2 - - + +
344A LEU* 3.9 21.5 - - + -
347A ALA* 5.3 3.8 - - + -
395A MET 4.0 6.3 - - - +
396A PHE* 2.6 32.3 + - + +
398A MET* 1.3 71.8 - - - +
400A LEU* 1.3 60.2 + - + +
401A ALA 2.8 5.3 + - - -
402A ILE* 2.6 48.7 + - + +
403A GLY 3.8 2.1 + - - -
982A PHE* 4.5 4.7 - - - -
985A GLY 6.1 0.4 - - - +
986A VAL* 5.3 3.2 - - + +
989A LEU* 4.0 24.5 - - + -
1003A VAL* 5.6 0.2 - - + -
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Residues in contact with LEU 400 (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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396A PHE* 3.0 10.7 + - + +
397A GLY* 4.0 9.2 - - - +
399A VAL* 1.3 81.7 - - - +
401A ALA* 1.3 57.9 + - - +
403A GLY* 4.3 1.6 + - - -
404A LEU* 4.9 0.9 + - - +
470A PHE* 5.1 1.8 - - + -
474A ILE* 5.7 2.0 - - + -
926A TYR 5.2 0.2 - - - +
929A VAL* 3.2 35.4 - - + -
930A GLY* 4.1 6.3 - - - -
933A THR* 3.3 44.2 + - + +
982A PHE* 4.1 11.3 - - + -
986A VAL* 5.5 2.9 - - + -
989A LEU* 5.9 0.7 - - - -
1003A VAL* 4.0 25.4 - - + -
1007A VAL* 3.5 29.6 - - + -
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Residues in contact with ALA 401 (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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397A GLY 3.0 19.9 + - - +
398A MET 3.7 4.7 - - - +
399A VAL 2.9 0.6 - - - -
400A LEU* 1.3 75.4 - - - +
402A ILE* 1.3 54.7 + - - +
403A GLY 2.8 6.3 - - - -
404A LEU* 2.6 35.3 + - + +
405A LEU* 3.1 14.0 + - + +
453A PHE* 6.1 0.2 - - - -
474A ILE* 3.9 31.0 - - + +
477A ALA* 4.5 12.8 - - + -
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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