Contacts of the helix formed by residues 389 - 405 (chain A) in PDB entry 1KL1
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 SER 389 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A ASN* 3.1 21.1 + - - +
387A VAL 3.3 0.6 - - - -
388A GLY* 1.3 77.4 - - - +
390A GLU* 1.3 61.3 + - - +
391A GLN* 3.2 20.2 + - - +
392A ALA* 3.0 25.5 + - - +
393A LEU* 3.1 24.7 + - - +
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Residues in contact with GLU 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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333A GLU* 4.7 6.1 - - - +
387A VAL 5.3 2.1 - - - +
388A GLY 3.8 6.5 + - - +
389A SER* 1.3 71.4 - - - +
391A GLN* 1.3 57.7 + - - +
393A LEU* 3.3 26.5 + - - +
394A GLU* 2.9 28.9 + - - +
397A ARG* 4.7 11.3 + - - -
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Residues in contact with GLN 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A SER* 3.2 19.4 + - - +
390A GLU* 1.3 74.7 - - - +
392A ALA* 1.3 63.5 + - - +
394A GLU* 3.3 6.2 + - - +
395A GLU* 3.0 24.1 + - - +
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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
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382A LEU* 3.5 30.6 - - + +
386A ASN* 3.7 27.6 - - + +
389A SER* 3.0 22.5 + - - +
391A GLN* 1.3 77.1 - - - +
393A LEU* 1.3 59.7 + - + +
395A GLU* 3.4 4.8 + - - -
396A ALA* 2.9 28.9 + - - +
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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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330A VAL* 3.7 17.3 - - + -
333A GLU* 3.8 22.9 - - + +
334A VAL* 3.5 17.1 - - + +
383A VAL* 3.7 40.8 - - + +
386A ASN 4.4 8.1 - - - +
387A VAL 4.1 10.5 - - - +
389A SER 3.1 13.5 + - - +
390A GLU* 3.3 27.8 + - - +
391A GLN 3.3 0.2 - - - -
392A ALA* 1.3 76.3 - - - +
394A GLU* 1.3 59.0 + - - +
396A ALA* 3.3 3.2 + - - +
397A ARG* 3.0 38.1 + - - +
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Residues in contact with GLU 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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390A GLU 2.9 16.7 + - - +
391A GLN* 3.9 6.1 - - - +
392A ALA 3.3 0.4 - - - -
393A LEU* 1.3 72.7 - - - +
395A GLU* 1.3 66.1 + - - +
397A ARG* 2.9 39.3 + - - +
398A GLN* 2.9 53.6 + - - +
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Residues in contact with GLU 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A LEU* 3.6 18.3 - - + +
391A GLN 3.0 17.5 + - - +
392A ALA* 3.7 5.6 - - - +
394A GLU* 1.3 73.8 - - - +
396A ALA* 1.3 66.3 + - - +
398A GLN* 3.2 10.8 + - + +
399A ARG* 2.8 59.8 + - + +
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Residues in contact with ALA 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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334A VAL* 3.9 6.7 - - + -
379A ILE* 3.7 16.7 - - + +
382A LEU* 3.8 8.3 - - + +
383A VAL* 3.4 33.2 - - + -
392A ALA 2.9 15.1 + - - +
393A LEU 3.5 5.4 - - - +
395A GLU* 1.3 77.2 - - - +
397A ARG* 1.3 57.3 + - - +
399A ARG* 3.0 5.8 + - - +
400A VAL* 2.8 33.6 + - - +
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Residues in contact with ARG 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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333A GLU* 3.2 35.4 + - - +
334A VAL* 3.7 29.5 - - - +
390A GLU* 4.7 11.3 + - - -
393A LEU* 3.0 24.9 + - - +
394A GLU* 2.9 59.1 + - - +
396A ALA* 1.3 74.6 - - - +
398A GLN* 1.3 59.5 + - + +
400A VAL* 3.4 2.3 + - - +
401A ALA* 3.0 28.1 + - - +
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Residues in contact with GLN 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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394A GLU* 2.9 43.9 + - - +
395A GLU* 3.2 10.8 + - + +
397A ARG* 1.3 77.1 - - + +
399A ARG* 1.3 60.2 + - + +
401A ALA* 3.4 7.9 + - - +
402A ALA* 3.0 27.0 + - - +
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Residues in contact with ARG 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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375A GLU* 2.9 43.8 + - - +
378A ALA* 3.4 25.9 + - - +
379A ILE* 3.7 20.0 - - + +
382A LEU* 3.8 17.6 - - - +
395A GLU* 2.8 50.6 + - + +
396A ALA 3.0 6.9 + - - +
398A GLN* 1.3 75.5 - - + +
400A VAL* 1.3 63.3 + - - +
402A ALA* 3.3 8.3 + - - +
403A LEU* 3.2 25.6 + - - +
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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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24A ALA 4.3 14.1 - - - +
26A ILE* 4.0 20.2 - - + -
334A VAL* 3.5 25.6 - - + +
335A GLY* 4.0 16.6 - - - +
336A ILE* 3.8 27.6 - - + -
379A ILE* 4.2 11.2 - - + -
396A ALA 2.8 19.8 + - - +
397A ARG 3.7 3.1 - - - +
399A ARG* 1.3 76.2 - - - +
401A ALA* 1.3 63.0 + - - +
403A LEU* 3.0 14.2 + - - +
404A THR* 3.0 13.5 + - - +
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Residues in contact with ALA 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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24A ALA 5.7 0.4 - - - -
397A ARG 3.0 17.5 + - - +
398A GLN* 3.6 8.3 - - - +
400A VAL* 1.3 78.0 - - - +
402A ALA* 1.3 55.9 + - - +
404A THR* 3.6 8.0 + - - -
405A ASP* 2.9 34.8 + - - +
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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 GLN 3.0 14.2 + - - +
399A ARG* 3.6 11.7 - - - +
400A VAL 3.3 0.4 - - - -
401A ALA* 1.3 75.5 - - - +
403A LEU* 1.3 61.6 + - + +
405A ASP* 3.9 6.5 + - - +
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Residues in contact with LEU 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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26A ILE* 3.4 26.5 - - + -
366A ARG* 5.0 0.2 + - - -
368A PHE* 3.6 26.7 - - + -
372A GLU* 3.9 31.1 - - + +
375A GLU* 3.9 22.9 - - + -
376A ILE* 3.9 13.0 - - + -
379A ILE* 3.8 23.8 - - + -
399A ARG 3.2 7.7 + - - +
400A VAL 3.0 7.4 + - - +
402A ALA* 1.3 80.5 - - + +
404A THR* 1.3 60.9 + - - +
405A ASP* 3.4 1.1 + - - +
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Residues in contact with THR 404 (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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23A HIS* 3.1 34.9 + - - +
24A ALA* 3.4 25.0 + - - +
25A LYS 3.9 4.9 - - - +
26A ILE* 3.7 28.3 - - + -
366A ARG* 3.5 19.7 + - - +
368A PHE* 4.6 1.1 - - + -
400A VAL 3.0 10.5 + - - +
401A ALA* 3.6 8.8 + - - -
403A LEU* 1.3 77.6 - - + +
405A ASP* 1.3 77.1 + - - +
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Residues in contact with ASP 405 (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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23A HIS* 3.4 25.2 + - + -
24A ALA* 5.7 0.7 - - - -
401A ALA* 2.9 17.8 + - - -
402A ALA 3.9 5.5 + - - +
403A LEU 3.4 3.9 - - - +
404A THR* 1.3 90.9 + - - +
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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