Contacts of the strand formed by residues 408 - 414 (chain A) in PDB entry 3M6L
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 408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A PRO* 4.4 12.3 - - + -
325A PHE* 3.9 36.6 - - + -
355A LEU* 4.0 23.6 - - + -
357A GLY* 2.9 13.0 + - - +
358A PHE* 3.4 23.3 - - + +
359A LEU* 3.3 20.1 + - - +
406A ILE 5.6 0.9 - - - +
407A PHE* 1.3 78.2 - - - +
409A PRO* 1.3 64.1 - - - +
434A LYS* 4.5 17.9 - - + -
436A PHE* 4.4 18.8 - - + -
487A LEU* 5.1 1.6 - - + -
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Residues in contact with PRO 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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359A LEU* 3.2 12.8 - - + +
398A ASN* 3.5 45.8 - - - +
401A PHE* 4.0 9.0 - - + -
402A ALA* 3.9 15.0 - - + +
407A PHE* 3.7 7.4 - - + +
408A LEU* 1.3 88.7 - - - +
410A PHE* 1.3 60.6 + - - +
434A LYS 3.5 16.2 - - - +
435A HIS* 3.7 7.1 - - + -
436A PHE* 3.1 29.7 + - - -
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Residues in contact with PHE 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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348A LEU* 4.1 14.1 - - + -
358A PHE* 3.6 36.6 - + + -
359A LEU 3.0 22.7 + - - -
360A GLY* 3.3 18.1 - - - -
361A GLY* 3.3 47.8 + - - -
371A THR* 3.9 35.2 - - - -
373A LEU* 4.0 15.9 - - + -
384A ASN* 5.7 0.2 - - - -
398A ASN* 2.9 14.9 - - - +
409A PRO* 1.3 73.8 - - - +
411A SER* 1.4 59.0 + - - +
412A ALA* 4.6 0.9 - - + -
435A HIS* 4.6 0.2 - - - -
436A PHE* 3.1 19.1 - - + +
438A ILE* 4.1 21.5 - - + -
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Residues in contact with SER 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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361A GLY 3.7 3.1 - - - -
394A MSE 3.8 23.5 - - - +
395A ALA* 3.9 4.5 - - - -
398A ASN* 2.8 18.3 + - - +
410A PHE* 1.4 73.0 - - - +
412A ALA* 1.3 61.5 + - - +
421A LEU* 5.0 1.6 - - - -
435A HIS* 2.7 29.4 + - - -
436A PHE 3.0 5.3 + - - -
437A PHE* 3.5 16.6 - - - +
438A ILE* 2.7 26.9 + - - +
439A PHE* 5.3 1.4 - - - -
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Residues in contact with ALA 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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361A GLY 3.0 16.1 + - - +
362A SER* 3.3 4.0 + - - -
363A ALA 3.1 26.3 + - - -
369A ASN* 3.4 14.8 - - - +
371A THR* 3.6 26.2 - - + -
394A MSE 3.5 5.7 - - - +
410A PHE* 4.6 1.1 - - + -
411A SER* 1.3 77.7 - - - +
413A THR* 1.3 64.4 + - - +
438A ILE* 3.2 15.3 - - + +
439A PHE* 5.6 0.4 - - - -
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Residues in contact with THR 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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363A ALA* 4.7 2.3 - - - +
365A LEU* 3.8 14.0 - - - +
369A ASN* 3.4 16.4 - - - +
391A GLU* 3.9 17.5 + - + +
394A MSE 4.5 0.7 - - - -
412A ALA* 1.3 77.1 - - - +
414A PHE* 1.3 80.9 + - - +
417A PHE* 3.7 31.4 - - - +
421A LEU* 4.1 19.7 - - + -
438A ILE 3.1 14.7 + - - +
439A PHE* 3.2 14.4 - - + -
440A THR 3.2 12.1 + - - -
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Residues in contact with PHE 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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365A LEU* 3.6 33.6 - - + +
368A SER* 3.9 13.2 - - - -
369A ASN* 3.5 14.1 + - - -
413A THR* 1.3 84.3 + - - +
415A PHE* 1.3 66.5 + - - +
416A ILE* 4.2 8.3 - - + -
417A PHE* 2.9 40.8 + + + -
418A SER 3.4 7.1 + - - -
440A THR* 3.5 4.7 - - - +
441A HIS* 3.4 54.3 - + + +
449A ASP* 5.4 4.7 - - - -
453A HIS* 4.7 15.5 - + + +
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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