Contacts of the strand formed by residues 394 - 403 (chain A) in PDB entry 5IXM
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 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A ARG* 3.9 2.1 - - - +
390A ILE* 3.1 58.1 + - + -
391A ASN* 2.8 31.3 + - - +
393A GLN* 1.3 79.5 - - - +
395A GLY* 1.3 58.9 + - - +
416A MET* 4.0 24.5 - - + -
417A GLU 3.6 20.4 - - - +
418A TYR* 3.9 18.8 - - + +
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Residues in contact with GLY 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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387A PHE* 5.7 0.7 - - - -
388A TRP 3.7 6.3 - - - -
389A ARG* 4.8 2.5 - - - -
390A ILE* 4.7 2.0 - - - -
393A GLN 4.1 0.2 + - - -
394A LEU* 1.3 76.6 - - - +
396A LEU* 1.3 61.1 + - - -
416A MET* 3.3 7.4 - - - +
417A GLU 2.8 36.9 + - - +
556A PHE* 3.2 22.2 - - - -
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Residues in contact with LEU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A THR* 6.4 0.4 - - + -
387A PHE* 3.5 0.3 - - - -
388A TRP* 2.9 66.3 + - + +
390A ILE* 4.1 13.5 - - + -
395A GLY* 1.3 74.8 - - - +
397A LYS* 1.3 72.3 + - - +
414A ALA* 5.5 2.0 - - + -
415A ILE 3.6 13.0 - - - +
416A MET* 3.9 17.5 - - + -
556A PHE* 3.3 8.6 - - - -
604A C8E 4.1 39.3 - - + -
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Residues in contact with LYS 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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386A THR* 3.2 16.2 - - - +
387A PHE* 4.1 8.7 - - + -
396A LEU* 1.3 81.2 - - - +
398A GLY* 1.3 61.6 + - - +
413A ASN* 6.0 3.4 - - - +
414A ALA* 3.4 2.3 - - - +
415A ILE* 2.8 57.1 + - + +
555A ALA* 5.1 7.4 - - - +
556A PHE* 3.8 21.2 - - + +
604A C8E 4.3 5.6 - - - +
79B GLN* 5.6 1.5 + - - -
103B PHE* 3.4 42.6 - - - +
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Residues in contact with GLY 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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385A ASP* 3.3 4.9 - - - +
386A THR* 2.9 34.9 + - - +
397A LYS* 1.3 77.5 - - - +
399A GLY* 1.3 57.7 + - - -
413A ASN* 3.2 17.5 - - - -
414A ALA* 3.9 2.5 - - - -
604A C8E 3.7 15.9 - - - -
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Residues in contact with GLY 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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384A GLY 3.2 13.0 - - - -
385A ASP* 4.0 4.7 - - - -
398A GLY* 1.3 74.3 - - - -
400A ALA* 1.3 59.5 + - - -
401A GLN* 5.7 0.7 - - - -
412A GLY* 3.3 2.2 - - - -
413A ASN* 2.8 40.1 + - - +
604A C8E 3.3 11.8 + - - +
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Residues in contact with ALA 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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383A ALA* 3.4 1.0 - - - -
384A GLY* 2.9 34.2 + - - +
399A GLY* 1.3 76.3 - - - +
401A GLN* 1.3 69.0 + - - +
402A TYR* 4.2 20.9 - - + +
409A LEU* 4.2 6.7 - - + -
411A LEU 3.4 10.1 - - - +
412A GLY* 4.1 0.2 - - - -
604A C8E 4.3 17.7 - - - -
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Residues in contact with GLN 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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309A GLN* 4.3 7.0 - - - +
310A SER* 2.8 30.3 + - - +
311A ASP* 3.5 19.0 - - - +
382A TRP 3.6 6.7 - - - +
383A ALA* 4.5 9.6 - - + -
399A GLY 5.7 0.2 - - - -
400A ALA* 1.3 82.6 - - - +
402A TYR* 1.3 64.8 + - - +
409A LEU* 3.4 7.8 - - - +
410A THR* 2.9 36.9 + - - +
411A LEU* 2.8 47.0 + - + +
437A TYR* 4.8 4.5 + - - -
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Residues in contact with TYR 402 (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 LEU 4.4 0.9 - - - -
381A VAL* 3.5 6.8 - - - +
382A TRP* 2.9 57.5 + - + +
383A ALA* 5.3 0.9 - - - -
400A ALA* 4.2 16.8 - - + +
401A GLN* 1.3 78.1 - - - +
403A ASP* 1.3 62.5 + - - +
408A SER* 3.4 13.2 - - - +
409A LEU* 3.4 53.3 - - + +
410A THR* 4.3 1.6 - - - -
604A C8E 6.1 0.5 - - - -
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Residues in contact with ASP 403 (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 LEU 3.5 5.6 - - - +
381A VAL* 3.9 10.8 - - + +
402A TYR* 1.3 76.2 - - - +
404A THR* 1.3 64.5 + - - +
405A ARG* 3.1 52.3 + - - +
406A LEU* 3.0 27.7 + - + +
407A GLY 3.2 8.7 + - - -
408A SER* 2.9 16.5 + - - +
410A THR* 4.0 15.2 - - + +
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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