Contacts of the helix formed by residues 382 - 398 (chain A) in PDB entry 1KB9
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 382 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A SER* 3.1 9.9 + - - +
381A GLY* 1.3 78.7 - - - +
383A PRO* 1.3 69.7 - - - +
384A VAL* 3.1 38.5 + - - +
385A ASN* 3.3 31.2 + - - +
386A ASP* 2.9 16.3 + - - +
327B VAL* 6.0 2.1 - - - +
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Residues in contact with PRO 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA* 5.2 7.2 - - + +
48A THR* 3.8 33.7 - - - +
50A SER* 3.4 19.3 - - - +
211A THR* 2.8 29.0 + - - +
212A GLY* 4.2 15.7 - - - +
381A GLY 3.9 6.3 - - - +
382A ASN* 1.3 89.8 - - - +
384A VAL* 1.3 58.3 + - + +
385A ASN 3.2 0.2 - - - -
386A ASP* 3.2 11.6 + - + +
387A ALA* 2.9 16.8 + - - +
327B VAL* 6.5 0.7 - - + -
329B ASN* 5.1 2.2 - - - +
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A SER* 3.7 6.3 - - - +
94A SER* 4.6 17.3 - - - +
105A ILE* 3.9 14.6 - - + +
107A SER* 3.3 26.2 - - - +
382A ASN* 3.1 33.1 + - - +
383A PRO* 1.3 76.7 - - + +
385A ASN* 1.3 74.0 + - - +
387A ALA* 3.5 7.2 + - - +
388A ASN* 2.9 30.5 + - - +
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Residues in contact with ASN 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 5.2 4.3 - - + +
380A SER* 4.3 15.0 + - - -
382A ASN* 3.3 29.5 + - - +
383A PRO 3.2 0.8 - - - -
384A VAL* 1.3 86.7 - - - +
386A ASP* 1.3 66.0 + - - +
388A ASN* 3.3 8.9 + - - +
389A LEU* 3.0 35.8 + - + +
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Residues in contact with ASP 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU* 4.2 16.4 - - - +
211A THR* 3.9 16.4 - - + -
377A LEU 5.8 0.7 - - - -
378A TYR 3.0 26.0 - - - +
379A GLU* 4.8 1.6 - - - -
380A SER* 3.9 12.8 + - - +
382A ASN 2.9 25.5 - - - +
383A PRO* 3.4 10.6 - - + +
385A ASN* 1.3 78.7 - - - +
387A ALA* 1.3 56.6 - - - +
389A LEU* 3.4 9.6 + - - +
390A LEU* 2.9 31.9 + - - +
400A LYS* 5.3 1.9 + - - +
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A SER* 5.1 3.1 - - - +
52A GLY 6.2 1.1 - - - +
54A VAL* 4.8 4.1 - - + +
105A ILE* 3.7 24.5 - - + -
209A VAL* 3.9 17.1 - - + +
211A THR* 3.6 20.1 - - + +
383A PRO 2.9 15.8 + - - +
384A VAL* 3.6 7.6 - - - +
386A ASP* 1.3 76.1 - - - +
388A ASN* 1.3 53.5 + - - +
390A LEU* 3.8 0.7 - - - +
391A GLY* 2.7 34.5 + - - -
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Residues in contact with ASN 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 5.8 1.8 - - - -
96A ASN* 3.8 20.4 + - - +
101A PHE* 3.9 16.5 - - + -
103A SER* 2.8 34.1 + - - -
105A ILE* 3.7 9.7 - - - +
384A VAL* 2.9 19.7 + - - +
385A ASN* 3.3 12.6 + - - +
387A ALA* 1.3 77.7 - - - +
389A LEU* 1.3 62.2 + - + +
391A GLY* 5.1 0.2 - - - -
392A ALA* 3.0 33.3 + - - +
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Residues in contact with LEU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 3.5 41.7 - - + +
378A TYR* 3.9 33.9 - - + +
385A ASN* 3.0 28.8 + - + +
386A ASP* 3.7 7.6 - - - +
388A ASN* 1.3 75.1 - - + +
390A LEU* 1.3 66.9 + - - +
392A ALA* 4.2 2.6 - - - +
393A GLU* 3.4 26.2 + - - +
400A LYS* 5.1 11.5 - - - +
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 5.0 7.4 - - + -
39A ALA* 4.2 11.2 - - + -
40A THR* 3.8 17.9 - - - +
41A GLU* 3.7 32.1 - - + +
209A VAL* 3.9 19.7 - - + -
211A THR* 4.1 5.4 - - + -
386A ASP 2.9 17.5 + - - +
387A ALA 3.8 2.5 - - - +
389A LEU* 1.3 75.3 - - - +
391A GLY* 1.3 66.2 + - - +
393A GLU* 3.2 3.6 + - - +
394A VAL* 3.1 46.2 + - + +
400A LYS* 4.3 28.6 - - + +
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Residues in contact with GLY 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 4.2 11.7 - - - -
207A VAL* 5.4 0.2 - - - -
209A VAL* 3.8 22.1 - - - +
387A ALA 2.7 21.4 + - - -
388A ASN 4.1 0.2 - - - -
390A LEU* 1.3 72.8 - - - +
392A ALA* 1.3 60.5 + - - +
394A VAL* 3.2 6.7 - - - +
395A LEU* 3.2 33.6 + - - +
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Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 4.6 2.2 - - - +
101A PHE* 3.5 36.7 - - + -
388A ASN 3.0 19.7 + - - +
389A LEU* 4.2 3.8 - - - +
391A GLY* 1.3 73.7 - - - +
393A GLU* 1.3 61.5 + - + +
395A LEU* 3.8 6.8 + - - +
396A ILE* 3.3 31.4 + - + +
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Residues in contact with GLU 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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378A TYR* 3.4 23.7 + - - +
389A LEU 3.4 16.5 + - - +
390A LEU 3.2 4.8 + - - +
392A ALA* 1.3 78.1 - - + +
394A VAL* 1.3 64.4 + - - +
396A ILE* 3.2 5.7 + - - +
397A LYS* 3.1 58.8 + - + +
399A SER 3.7 6.4 - - - +
400A LYS* 3.4 27.4 - - + +
401A LEU* 3.6 20.8 + - - +
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 5.6 1.8 - - + -
31A GLN* 4.8 13.2 + - + +
39A ALA* 4.2 12.8 - - + -
207A VAL* 3.9 27.4 - - + +
390A LEU* 3.1 31.8 + - + +
391A GLY* 3.2 21.8 - - - +
393A GLU* 1.3 76.3 - - - +
395A LEU* 1.3 58.5 + - - +
398A GLY* 2.9 27.2 + - - +
399A SER* 3.8 30.1 - - - +
400A LYS* 4.2 2.5 - - + +
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Residues in contact with LEU 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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54A VAL* 3.6 32.5 - - + +
55A PHE 3.7 14.8 - - - +
56A GLY* 3.7 26.5 - - - +
101A PHE* 4.0 10.3 - - + -
205A ASN* 4.9 0.9 - - - -
206A ALA* 4.5 6.7 - - - +
207A VAL* 3.6 28.0 - - + -
391A GLY 3.2 21.2 + - - +
392A ALA* 3.9 7.0 - - - +
393A GLU 3.2 0.4 - - - -
394A VAL* 1.3 77.6 - - - +
396A ILE* 1.3 63.6 + - + +
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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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100A ASP* 4.6 20.6 - - + +
101A PHE* 6.1 2.0 - - + -
270A VAL* 3.5 43.3 - - + +
271A ASN* 5.2 5.7 + - + -
323A LYS* 4.8 28.4 + - + +
392A ALA* 3.3 21.5 - - + +
393A GLU* 3.2 6.3 + - - +
395A LEU* 1.3 84.5 - - + +
397A LYS* 1.3 63.5 + - + +
398A GLY 3.6 0.4 - - - -
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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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270A VAL* 5.9 3.6 - - + -
271A ASN* 3.5 41.6 + - + +
393A GLU* 3.1 42.3 + - + +
396A ILE* 1.3 78.8 - - + +
398A GLY* 1.3 61.1 + - - +
399A SER* 3.1 30.1 + - - +
401A LEU* 4.5 24.7 - - - +
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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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31A GLN* 3.4 27.6 + - - +
394A VAL* 2.9 24.6 + - - -
396A ILE 3.6 1.4 - - - -
397A LYS* 1.3 76.9 - - - +
399A SER* 1.3 61.6 + - - +
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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
------------------------------------------------------------
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