Contacts of the helix formed by residues 381 - 396 (chain A) in PDB entry 1KYO
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 381 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A SER* 3.1 9.7 + - - +
380A GLY* 1.3 79.2 - - - +
382A PRO* 1.3 71.6 - - - +
383A VAL* 3.2 29.5 + - - +
384A ASN* 3.1 43.3 - - + +
385A ASP* 2.8 18.3 - - - +
327B VAL* 5.5 5.1 - - - +
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Residues in contact with PRO 382 (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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45A ALA* 5.8 4.5 - - + -
46A HIS* 5.6 4.0 - - + +
47A THR* 3.3 37.5 - - - +
49A SER* 3.8 11.2 - - - -
106A SER* 4.9 2.0 - - - +
210A THR* 2.8 36.5 + - - +
211A GLY* 4.3 4.9 - - - +
380A GLY 4.1 5.4 - - - +
381A ASN* 1.3 88.0 - - - +
383A VAL* 1.3 59.1 + - + +
384A ASN 3.0 2.0 - - - -
385A ASP* 3.1 9.4 + - + +
386A ALA 2.8 25.3 + - - -
327B VAL* 5.0 6.5 - - + -
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Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER* 3.8 6.7 - - - +
93A SER* 4.6 21.8 - - - +
104A ILE* 4.4 11.0 - - + -
106A SER* 3.4 26.5 - - - +
381A ASN* 3.2 28.0 - - - +
382A PRO* 1.3 77.5 - - + +
384A ASN* 1.3 66.1 + - - +
386A ALA* 3.4 7.8 - - - +
387A ASN* 2.8 41.4 + - - +
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Residues in contact with ASN 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LEU* 5.3 12.2 - - + +
379A SER* 4.5 16.8 + - - -
381A ASN* 3.1 41.3 + - + +
382A PRO 3.0 0.6 - - - -
383A VAL* 1.3 83.7 - - - +
385A ASP* 1.3 66.9 + - - +
386A ALA 3.1 0.9 + - - -
387A ASN* 3.1 14.6 + - - +
388A LEU* 3.2 21.9 + - + +
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Residues in contact with ASP 385 (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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41A GLU* 3.7 18.7 - - - +
210A THR* 4.0 17.0 - - + -
376A LEU 5.6 0.7 - - - -
377A TYR 2.8 27.4 - - - +
378A GLU* 4.5 2.1 - - - -
379A SER 4.1 12.8 + - - +
381A ASN 2.8 24.7 + - - +
382A PRO* 3.1 9.2 + - - +
384A ASN* 1.3 79.7 - - - +
386A ALA* 1.3 56.4 + - - +
388A LEU* 3.4 9.9 + - - +
389A LEU* 2.8 31.4 + - - +
399A LYS* 4.7 4.7 + - - +
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Residues in contact with ALA 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER 5.5 1.1 - - - +
51A GLY 6.2 0.2 - - - +
53A VAL* 4.8 2.2 - - - +
104A ILE* 3.7 24.7 - - + -
208A VAL* 4.0 17.0 - - + +
210A THR* 3.4 19.9 - - - +
382A PRO 2.8 17.5 + - - +
383A VAL* 3.4 8.7 - - - +
385A ASP* 1.3 73.3 - - - +
387A ASN* 1.3 58.8 + - - +
388A LEU 3.0 4.3 - - - -
389A LEU* 3.0 1.6 + - - +
390A GLY* 2.8 30.3 + - - -
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Residues in contact with ASN 387 (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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53A VAL* 5.8 2.6 - - - +
95A ASN* 3.6 27.8 + - - +
100A PHE* 4.0 17.3 - - + -
102A SER* 2.9 29.2 + - - -
104A ILE* 3.4 12.2 - - - +
383A VAL* 2.8 27.6 + - - +
384A ASN* 3.1 5.6 + - - +
386A ALA* 1.3 78.5 - - - +
388A LEU* 1.3 62.4 + - + +
390A GLY* 4.4 1.3 - - - -
391A ALA* 3.4 19.9 + - - +
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Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LEU* 3.8 44.0 - - + +
377A TYR* 3.6 38.6 - - + -
384A ASN* 3.2 18.1 + - + +
385A ASP* 3.7 10.5 - - - +
386A ALA 3.0 0.4 - - - -
387A ASN* 1.3 79.5 - - + +
389A LEU* 1.3 66.5 + - - +
391A ALA* 3.5 5.9 - - + +
392A GLU* 3.5 24.6 + - - +
399A LYS* 5.0 9.1 - - - +
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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
----------------------------------------------------------
29A VAL* 5.1 5.8 - - + -
39A ALA* 4.3 9.9 - - + +
40A THR* 4.0 26.7 - - - -
41A GLU* 4.0 8.7 - - + -
208A VAL* 3.8 20.9 - - + -
210A THR* 3.9 15.3 - - + -
385A ASP 2.8 17.3 + - - +
386A ALA 3.0 4.0 + - - +
388A LEU* 1.3 72.7 - - - +
390A GLY* 1.3 66.4 + - - +
391A ALA 3.0 2.6 + - - -
392A GLU* 3.1 12.0 + - - +
393A VAL* 3.2 35.7 + - + +
399A LYS* 4.1 32.7 - - + +
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Residues in contact with GLY 390 (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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53A VAL* 3.9 21.3 - - - -
206A VAL* 5.4 0.2 - - - -
208A VAL* 3.7 22.3 - - - +
386A ALA 2.8 17.0 + - - -
387A ASN 4.9 0.2 - - - -
389A LEU* 1.3 73.3 - - - +
391A ALA* 1.3 60.9 + - - +
393A VAL* 3.3 5.1 - - - +
394A LEU* 3.2 30.9 + - - +
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Residues in contact with ALA 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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53A VAL* 4.6 1.4 - - - +
100A PHE* 3.7 30.4 - - + -
387A ASN 3.4 21.5 + - - +
388A LEU* 3.5 9.8 + - + +
389A LEU 3.0 0.2 - - - -
390A GLY* 1.3 80.1 - - - +
392A GLU* 1.3 64.1 + - + +
394A LEU* 3.5 4.1 + - - +
395A ILE* 3.5 27.5 + - + +
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Residues in contact with GLU 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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269A VAL* 5.7 9.6 - - + -
377A TYR* 3.6 26.1 + - - +
388A LEU* 3.5 10.1 + - - +
389A LEU 3.1 7.0 + - - +
391A ALA* 1.3 75.6 - - + +
393A VAL* 1.3 56.0 + - - +
394A LEU 3.0 4.7 - - - -
395A ILE* 2.9 5.1 + - - -
396A LYS* 2.7 60.7 + - + +
397A GLY 3.5 0.2 + - - -
398A SER 3.5 11.0 - - - +
399A LYS* 3.6 21.6 - - + +
400A LEU* 3.4 24.7 + - - +
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Residues in contact with VAL 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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29A VAL* 6.0 1.6 - - + -
31A GLN* 4.0 23.7 + - + +
39A ALA* 4.0 15.3 - - + -
206A VAL* 3.7 29.1 - - + +
208A VAL* 4.9 0.4 - - + -
389A LEU* 3.2 36.3 + - + +
390A GLY* 3.3 17.7 - - - +
392A GLU* 1.3 74.4 - - - +
394A LEU* 1.3 57.2 + - - +
397A GLY* 3.3 18.2 + - - -
398A SER 3.7 23.8 - - - +
399A LYS* 4.4 1.1 - - + +
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Residues in contact with LEU 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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53A VAL* 3.4 36.8 - - + +
54A PHE 3.8 1.1 - - - -
55A GLY* 3.6 40.4 - - - +
100A PHE* 3.9 11.2 - - + -
203A SER 6.0 0.7 - - - +
204A ASN* 4.7 8.3 - - - +
205A ALA 4.8 0.2 - - - -
206A VAL* 3.8 24.5 - - + -
322A LYS* 5.5 2.9 + - - -
390A GLY 3.2 16.2 + - - +
391A ALA* 3.6 6.3 - - - +
392A GLU 3.0 0.6 - - - -
393A VAL* 1.3 79.7 - - - +
395A ILE* 1.3 63.6 + - + +
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Residues in contact with ILE 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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99A ASP* 4.1 25.1 - - + +
100A PHE* 5.6 4.3 - - + -
269A VAL* 3.6 45.8 - - + +
270A ASN* 5.2 3.6 - - + -
322A LYS* 4.7 30.0 + - + +
391A ALA* 3.5 19.0 + - + +
392A GLU* 2.9 4.2 + - - +
394A LEU* 1.3 86.9 - - + +
396A LYS* 1.3 63.9 + - + +
397A GLY 3.6 0.7 - - - -
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Residues in contact with LYS 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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269A VAL* 6.3 2.2 - - + -
270A ASN* 2.9 46.9 + - + +
392A GLU* 2.7 49.3 + - + +
395A ILE* 1.3 74.9 - - + +
397A GLY* 1.3 61.5 - - - +
398A SER* 3.2 35.9 + - - +
400A LEU* 4.1 31.4 - - - +
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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