Contacts of the helix formed by residues 381 - 394 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379L SER* 3.1 13.2 + - - +
380L GLY* 1.3 79.6 - - - +
382L PRO* 1.3 63.3 - - - +
383L VAL* 3.0 39.8 + - - +
384L ASN* 3.0 33.2 + - - +
385L ASP* 3.2 11.1 - - - +
327M VAL* 5.4 8.0 - - - +
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Residues in contact with PRO 382 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L ALA* 6.2 2.9 - - + -
46L HIS* 5.1 5.2 - - - +
47L THR* 4.1 24.9 - - - +
49L SER* 4.2 14.8 - - - +
210L THR* 3.0 23.4 + - - +
211L GLY* 3.8 27.1 - - - +
380L GLY 3.9 6.7 - - - +
381L ASN* 1.3 90.7 - - - +
383L VAL* 1.3 51.4 + - + +
384L ASN 3.0 0.9 - - - -
385L ASP* 3.1 12.3 + - + +
386L ALA* 2.7 33.4 + - - +
327M VAL* 5.3 2.2 - - + -
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Residues in contact with VAL 383 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L SER* 3.9 7.9 - - - +
93L SER* 3.9 26.2 - - - +
104L ILE* 4.2 9.3 - - + +
106L SER* 3.2 26.5 - - - +
381L ASN* 3.0 35.7 - - - +
382L PRO* 1.3 75.8 - - + +
384L ASN* 1.3 67.8 + - - +
386L ALA* 4.0 7.3 - - - +
387L ASN* 3.3 28.1 + - - +
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Residues in contact with ASN 384 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376L LEU* 5.1 7.0 - - + +
379L SER* 3.7 22.4 + - - +
381L ASN* 3.0 22.5 + - - +
383L VAL* 1.3 94.0 + - - +
385L ASP* 1.3 65.2 + - - +
386L ALA 3.1 0.2 - - - -
387L ASN* 3.2 8.1 + - - +
388L LEU* 3.1 28.0 + - + +
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Residues in contact with ASP 385 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L GLU* 4.4 11.3 - - - +
210L THR* 4.0 15.6 - - + +
211L GLY 5.7 0.2 + - - -
376L LEU 4.8 1.0 - - - +
377L TYR* 2.6 29.6 - - - +
379L SER* 3.7 15.4 + - - +
381L ASN 3.2 17.0 - - - +
382L PRO* 3.4 17.5 - - + +
384L ASN* 1.3 77.7 - - - +
386L ALA* 1.3 54.9 + - - +
388L LEU* 3.3 9.3 + - - +
389L LEU* 2.9 29.6 + - - +
399L LYS* 4.4 6.2 + - - +
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Residues in contact with ALA 386 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L SER* 5.4 3.6 - - - +
51L GLY 6.2 1.3 - - - +
53L VAL* 5.1 2.8 - - - +
104L ILE* 3.4 30.5 - - + -
208L VAL* 4.6 14.0 - - + +
210L THR* 3.8 17.4 - - + +
382L PRO 2.7 20.0 + - - +
383L VAL* 4.0 2.9 - - - +
385L ASP* 1.3 68.4 - - - +
387L ASN* 1.3 61.3 + - - +
388L LEU 3.0 1.3 - - - -
389L LEU* 2.9 4.6 + - - +
390L GLY* 2.8 29.8 + - - -
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Residues in contact with ASN 387 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L VAL* 5.3 2.6 - - - +
95L ASN* 3.2 30.6 + - - +
100L PHE* 3.3 19.8 - - + -
102L SER* 2.9 28.9 + - - -
104L ILE* 4.1 8.2 - - - +
383L VAL* 3.3 16.2 + - - +
384L ASN* 3.2 10.4 + - - +
386L ALA* 1.3 78.5 - - - +
388L LEU* 1.3 62.5 + - + +
390L GLY* 4.8 0.7 - - - +
391L ALA* 3.4 25.9 + - - +
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Residues in contact with LEU 388 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376L LEU* 3.5 44.4 - - + +
377L TYR* 3.5 34.8 - - + +
384L ASN* 3.1 17.9 + - + +
385L ASP* 3.6 11.2 - - - +
386L ALA 3.0 1.2 - - - -
387L ASN* 1.3 80.6 - - + +
389L LEU* 1.3 64.6 + - - +
391L ALA* 4.5 2.7 - - + +
392L GLU* 3.6 27.5 + - - +
399L LYS* 4.3 12.2 - - - +
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Residues in contact with LEU 389 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L VAL* 4.8 7.2 - - + -
30L THR 5.8 0.4 - - - +
39L ALA* 4.0 15.5 - - + -
40L THR* 3.8 15.3 - - - +
41L GLU* 3.4 35.2 - - + +
208L VAL* 3.9 18.6 - - + -
210L THR* 4.1 3.8 - - + -
385L ASP 2.9 14.1 + - - +
386L ALA 2.9 4.1 + - - +
388L LEU* 1.3 75.6 - - - +
390L GLY* 1.3 65.3 + - - +
392L GLU* 3.4 1.9 + - - +
393L VAL* 3.0 50.7 + - + +
399L LYS* 3.8 27.1 - - + +
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Residues in contact with GLY 390 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53L VAL* 4.3 17.0 - - - -
206L VAL* 5.1 1.1 - - - -
208L VAL* 4.0 16.5 - - - +
386L ALA 2.8 13.9 + - - -
389L LEU* 1.3 77.7 - - - +
391L ALA* 1.3 64.2 + - - +
392L GLU 3.1 0.5 + - - -
393L VAL* 3.3 8.7 - - - +
394L LEU* 2.8 29.5 + - - +
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Residues in contact with ALA 391 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53L VAL* 4.5 4.0 - - - +
100L PHE* 3.4 35.2 - - + -
387L ASN 3.4 22.0 + - - +
388L LEU* 4.5 3.6 - - + +
390L GLY* 1.3 73.3 - - - +
392L GLU* 1.3 62.8 + - + +
394L LEU* 3.5 7.4 + - - +
395L ILE* 3.3 31.1 - - + +
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Residues in contact with GLU 392 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377L TYR* 3.8 19.5 + - - +
388L LEU* 3.6 15.2 + - + +
389L LEU 3.4 3.7 + - - +
390L GLY 3.2 0.6 - - - -
391L ALA* 1.3 76.4 - - + +
393L VAL* 1.3 58.4 + - - +
394L LEU 3.0 4.3 - - - -
395L ILE* 2.9 7.5 + - - +
396L LYS* 2.9 64.0 + - + +
398L SER 3.8 5.3 - - - +
399L LYS* 3.3 26.6 - - + +
400L LEU* 3.3 27.2 + - - +
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Residues in contact with VAL 393 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L VAL* 5.7 0.9 - - + -
31L GLN* 3.2 31.5 + - + +
39L ALA* 4.3 4.9 - - + -
206L VAL* 3.8 25.9 - - + +
389L LEU* 3.0 40.1 + - + +
390L GLY* 3.3 7.6 - - - +
392L GLU* 1.3 73.3 - - - +
394L LEU* 1.3 59.2 + - - +
395L ILE 3.2 2.0 - - - -
397L GLY* 3.1 19.0 + - - -
398L SER* 3.4 32.3 - - - +
399L LYS* 3.8 2.2 - - + +
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Residues in contact with LEU 394 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53L VAL* 3.6 28.3 - - + +
54L PHE 3.5 7.9 - - - +
55L GLY* 3.3 44.2 - - - +
100L PHE* 4.1 8.7 - - + -
204L ASN* 4.8 9.2 - - - +
205L ALA 5.1 0.2 - - - +
206L VAL* 4.0 23.3 - - + -
390L GLY 2.8 15.1 + - - +
391L ALA* 3.6 7.0 - - - +
392L GLU 3.0 0.4 - - - -
393L VAL* 1.3 76.4 - - - +
395L ILE* 1.3 63.7 + - + +
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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