Contacts of the helix formed by residues 389 - 403 (chain A) in PDB entry 3KSS
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 389 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ASP* 2.8 17.7 + - + +
39A LEU 3.9 1.3 - - - -
40A PRO* 2.9 56.8 - - + +
387A ASN* 3.5 23.7 - - + +
388A ALA* 1.3 88.9 - - - +
390A ILE* 1.3 67.4 + - - +
391A MET 4.1 0.7 - - - +
392A SER* 2.9 37.0 + - - -
393A LEU* 3.3 12.6 + - - +
477A PRO* 3.5 13.7 - - - +
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Residues in contact with ILE 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP 3.8 0.8 + - - +
38A ALA* 3.7 30.5 - - + -
39A LEU* 3.8 13.2 - - + +
40A PRO* 5.4 0.2 - - + -
330A LEU* 6.4 0.9 - - + -
334A ALA* 5.3 12.1 - - + -
389A ASN* 1.3 74.9 - - - +
391A MET* 1.3 82.1 + - + +
393A LEU* 3.5 9.3 + - - +
394A GLY* 2.7 32.2 + - - -
474A LEU* 6.3 0.2 - - + -
478A LEU* 6.3 0.4 - - + -
565A ILE* 4.1 18.2 - - + -
1005A GLY* 5.3 8.1 - - - +
1008A VAL* 3.9 22.9 - - + -
1009A MET* 6.0 1.8 - - + -
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Residues in contact with MET 391 (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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40A PRO* 3.9 15.5 - - + -
389A ASN* 3.1 1.5 - - - +
390A ILE* 1.3 95.8 - - + +
392A SER* 1.3 54.6 + - - +
394A GLY* 2.8 4.7 + - - -
395A GLY 2.8 31.0 + - - -
474A LEU* 3.4 40.4 - - + +
475A PHE* 3.8 37.9 - - + -
477A PRO* 3.6 18.6 - - + -
478A LEU* 3.4 25.5 - - + +
565A ILE* 5.2 4.3 - - - -
1008A VAL* 4.5 13.0 - - + -
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Residues in contact with SER 392 (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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378A PHE* 5.7 0.3 - - - -
381A MET* 4.0 17.3 - - - -
386A LEU* 6.1 2.3 - - - +
387A ASN* 4.5 3.3 + - - -
388A ALA* 4.3 11.6 - - - -
389A ASN* 2.9 25.9 + - - -
391A MET* 1.3 72.5 - - - +
393A LEU* 1.3 61.2 + - - +
395A GLY* 3.0 13.9 + - - -
396A ILE* 3.3 9.9 + - - +
477A PRO* 3.8 9.7 - - - +
481A THR* 2.7 41.8 + - - +
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Residues in contact with LEU 393 (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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36A VAL* 4.7 7.0 - - + -
334A ALA* 5.8 3.4 - - + +
335A ILE* 3.7 31.2 - - + -
338A LEU* 3.8 19.9 - - + +
378A PHE* 5.0 17.9 - - + -
381A MET* 5.9 2.0 - - + -
388A ALA* 3.4 28.3 - - + +
389A ASN 3.3 13.2 + - - +
390A ILE* 3.7 9.4 - - - +
391A MET 3.2 0.4 - - - -
392A SER* 1.3 78.2 - - - +
394A GLY* 1.3 65.8 + - - +
396A ILE* 3.0 31.3 - - + +
397A ALA* 3.4 5.7 + - - +
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Residues in contact with GLY 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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338A LEU* 5.7 0.9 - - - +
390A ILE* 2.7 21.0 + - - -
391A MET* 2.8 6.0 + - - -
393A LEU* 1.3 73.5 - - - +
395A GLY* 1.3 59.7 + - - +
397A ALA* 3.5 15.7 + - - +
398A ILE* 2.9 23.3 - - - +
478A LEU* 4.1 8.7 - - - -
1009A MET* 4.6 19.7 - - - +
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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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391A MET 2.8 9.1 + - - -
392A SER 3.0 7.0 + - - -
394A GLY* 1.3 74.9 - - - +
396A ILE* 1.3 64.7 + - - +
398A ILE* 3.0 16.5 - - - +
399A ALA* 3.2 6.1 + - - +
478A LEU* 3.5 26.7 - - - +
481A THR* 4.7 2.2 - - - -
482A LYS* 3.1 21.5 - - - +
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Residues in contact with ILE 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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338A LEU* 3.7 19.5 - - + -
342A LEU* 4.3 17.5 - - + -
374A LEU* 4.1 21.3 - - + -
377A ALA* 4.1 17.5 - - + -
378A PHE* 4.2 18.6 - - + -
392A SER 3.3 1.6 + - - +
393A LEU* 3.0 25.8 - - + +
395A GLY* 1.3 74.3 - - - +
397A ALA* 1.3 79.4 + - - +
399A ALA* 3.4 8.6 - - - +
400A VAL* 3.1 27.9 + - + +
481A THR* 3.3 26.9 - - + +
482A LYS* 5.2 0.2 - - - -
485A ALA* 5.1 3.6 - - + -
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Residues in contact with ALA 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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338A LEU* 3.9 17.9 - - + -
341A LYS* 3.4 24.7 + - + +
342A LEU* 4.8 2.5 - - - -
393A LEU 3.4 8.5 + - - +
394A GLY* 3.5 13.5 - - - +
395A GLY 3.1 0.6 - - - -
396A ILE* 1.3 86.4 - - - +
398A ILE* 1.3 61.7 + - + +
400A VAL* 3.2 26.0 - - - +
401A GLY 3.7 1.4 + - - -
1009A MET* 4.8 11.0 - - - -
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Residues in contact with ILE 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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341A LYS* 5.3 1.1 - - - +
394A GLY 2.9 25.6 - - - +
395A GLY* 3.0 19.5 - - - +
397A ALA* 1.3 77.5 - - + +
399A ALA* 1.3 66.0 + - - +
401A GLY* 3.0 13.5 + - - +
402A ALA* 3.2 10.9 + - - +
478A LEU* 3.7 5.4 - - + -
482A LYS* 3.4 26.3 + - + +
928A THR* 5.9 0.2 - - + -
932A ALA* 5.8 4.5 - - + -
995A LEU* 6.0 9.6 - - + -
1009A MET* 5.2 10.5 - - + +
1012A ILE* 3.4 42.6 - - + -
1013A ALA* 5.8 4.3 - - + -
1016A MET* 5.6 10.9 - - - +
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Residues in contact with ALA 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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395A GLY 3.2 14.0 + - - +
396A ILE* 3.4 15.7 - - - +
398A ILE* 1.3 76.1 - - - +
400A VAL* 1.3 65.5 + - - +
402A ALA 3.0 9.9 + - - +
403A MET* 3.0 33.9 + - + +
482A LYS* 3.2 24.7 - - + +
485A ALA* 5.0 12.3 - - + -
486A MET* 4.7 4.5 - - + -
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Residues in contact with VAL 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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341A LYS* 4.9 1.1 - - - +
342A LEU* 3.7 26.9 - - + +
345A GLU* 3.9 25.6 - - + -
370A LEU* 3.6 35.8 - - + +
374A LEU* 6.1 5.6 - - + -
396A ILE* 3.1 17.7 - - + +
397A ALA 3.2 9.6 - - - +
399A ALA* 1.3 77.9 - - - +
401A GLY* 1.3 60.0 + - - +
403A MET* 3.5 23.0 + - + +
404A VAL* 3.4 15.4 - - - +
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Residues in contact with GLY 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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341A LYS* 5.4 2.6 - - - +
345A GLU* 5.3 7.4 - - - -
397A ALA 3.7 2.3 + - - -
398A ILE* 3.0 12.8 + - - -
400A VAL* 1.3 82.0 - - - +
402A ALA* 1.3 56.0 + - - +
403A MET 3.4 0.7 - - - -
404A VAL* 3.1 19.5 - - - +
991A ILE* 3.3 26.2 - - - +
994A GLY* 6.2 2.0 - - - -
995A LEU* 5.8 8.5 - - - -
1016A MET* 6.3 2.2 - - - -
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Residues in contact with ALA 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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398A ILE 3.2 9.4 + - - +
399A ALA 3.0 4.2 + - - +
401A GLY* 1.3 75.4 - - - +
403A MET* 1.3 59.7 + - - +
404A VAL 3.3 4.7 + - - -
405A ASP* 4.6 9.4 - - - +
454A LEU* 4.4 12.8 - - - +
457A ILE* 5.2 7.0 - - + +
482A LYS* 4.5 3.6 - - - +
486A MET* 3.6 27.2 - - + +
932A ALA* 5.4 13.5 - - + +
936A VAL* 5.6 14.8 - - + +
991A ILE* 5.7 0.2 - - - -
1016A MET* 5.6 5.8 - - - -
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Residues in contact with MET 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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369A SER* 5.4 3.2 + - - -
370A LEU* 3.5 47.0 - - + +
373A GLY* 4.7 7.9 - - - -
374A LEU* 5.3 0.7 - - - +
399A ALA* 3.0 23.6 + - + +
400A VAL* 3.5 22.8 + - + +
401A GLY 3.4 0.8 - - - -
402A ALA* 1.3 79.8 - - - +
404A VAL* 1.3 63.0 + - - +
405A ASP* 3.4 3.4 - - - -
406A ALA* 4.1 10.9 + - - +
407A ALA* 4.2 8.8 + - - +
454A LEU* 5.4 6.5 - - + -
485A ALA* 4.8 3.6 - - - +
486A MET* 4.7 9.9 - - + +
489A ALA* 3.5 33.2 - - + -
492A LEU* 4.0 13.2 - - + -
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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