Contacts of the strand formed by residues 409 - 418 (chain A) in PDB entry 1KIX
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 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A VAL* 3.9 7.9 - - + -
388A LYS 3.5 3.9 - - - +
389A GLY* 4.1 0.5 - - - -
392A ARG* 5.5 1.2 + - - -
400A LEU* 3.3 38.5 - - - +
407A GLY* 2.8 22.8 + - - +
408A ASP* 1.3 77.6 - - - +
410A ILE* 1.3 70.5 + - - +
448A ALA* 3.1 35.6 + - - +
449A ASP* 4.2 1.2 - - - +
450A ASN* 4.1 9.5 - - - +
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Residues in contact with ILE 410 (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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387A VAL* 3.1 9.2 - - - +
388A LYS* 3.0 36.2 + - - +
390A TYR* 3.7 37.5 - - + -
392A ARG* 4.4 11.0 - - - +
397A SER* 4.2 3.6 - - - +
408A ASP 5.1 0.2 - - - +
409A ASN* 1.3 80.8 - - - +
411A PHE* 1.3 66.2 + - - +
412A GLN* 3.6 36.3 - - + +
435A THR* 3.5 13.5 - - - +
436A GLN* 3.7 30.3 - - + +
448A ALA* 4.1 3.4 - - - -
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Residues in contact with PHE 411 (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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386A TRP* 3.4 11.2 - + + -
387A VAL* 3.5 23.3 - - + -
410A ILE* 1.3 75.0 - - - +
412A GLN* 1.3 66.9 + - - +
413A VAL* 4.4 7.6 - - + -
433A LEU* 3.2 16.0 - - + +
435A THR* 2.9 47.6 + - + +
440A GLY 5.6 0.7 - - - -
441A ALA* 4.7 11.9 - - - -
444A PHE* 3.7 37.7 - + + -
446A VAL 3.6 25.4 - - - -
447A LYS 4.3 2.5 - - - -
448A ALA* 3.7 25.8 - - + -
461A LEU* 4.0 21.1 - - + -
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Residues in contact with GLN 412 (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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380A PRO* 3.7 18.4 - - - +
385A GLU 5.0 1.1 - - - +
386A TRP 3.1 11.6 + - - +
388A LYS* 4.6 15.9 - - + +
390A TYR* 5.1 1.4 - - - -
397A SER* 2.9 34.7 + - - -
410A ILE* 3.6 15.7 - - + +
411A PHE* 1.3 79.7 - - - +
413A VAL* 1.3 59.5 + - - +
414A GLN* 5.4 0.5 - - - +
434A TYR* 3.4 47.4 + - + +
436A GLN* 3.2 26.1 + - - +
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Residues in contact with VAL 413 (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 ILE* 3.4 31.4 - - + -
379A GLU 3.6 4.7 - - - +
386A TRP* 3.6 46.4 - - + +
411A PHE* 4.4 5.8 - - + -
412A GLN* 1.3 79.0 - - - +
414A GLN* 1.3 64.3 - - - +
415A PHE* 3.7 18.3 + - + -
432A LEU* 3.5 2.4 - - - -
433A LEU* 2.8 46.6 + - + +
434A TYR* 3.6 3.3 - - - -
444A PHE* 4.3 9.6 - - + -
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Residues in contact with GLN 414 (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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377A LYS 3.9 0.3 - - - +
378A ILE* 3.3 6.9 - - - +
379A GLU* 2.7 53.5 + - + +
412A GLN 5.4 0.4 - - - +
413A VAL* 1.3 74.3 - - - +
415A PHE* 1.3 65.6 + - - +
416A LEU* 4.0 1.8 + - + +
430A ARG* 3.1 46.9 + - + +
431A VAL 3.7 2.9 - - - +
432A LEU* 3.2 27.9 - - + +
434A TYR* 4.1 15.9 + - - +
485A PHE* 6.0 2.8 - - - -
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Residues in contact with PHE 415 (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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373A PHE* 4.9 4.9 - + - -
375A VAL* 4.2 14.6 - - + -
377A LYS 3.7 1.8 - - - -
378A ILE* 3.7 30.3 - - + -
413A VAL* 3.7 18.6 - - + -
414A GLN* 1.3 79.7 - - - +
416A LEU* 1.3 63.9 + - - +
417A VAL* 3.4 17.9 + - + +
429A TYR 3.4 0.7 - - - +
430A ARG* 3.3 4.7 - - - -
431A VAL* 2.9 39.2 + - + +
433A LEU* 4.6 9.6 - - + -
443A PHE* 4.1 15.7 - + - -
444A PHE* 4.0 18.4 - + - -
468A LEU* 3.9 19.7 - - + -
475A VAL* 5.7 1.1 - - + -
488A ILE* 3.7 31.6 - - + -
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Residues in contact with LEU 416 (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 VAL* 3.6 0.9 - - - -
376A THR* 2.8 41.4 + - - +
377A LYS* 2.9 38.1 + - + +
379A GLU* 3.6 20.0 - - + +
414A GLN 4.4 5.4 - - - +
415A PHE* 1.3 74.3 - - - +
417A VAL* 1.3 61.8 + - - +
428A THR* 3.3 33.9 - - + +
429A TYR 3.3 4.3 - - - -
430A ARG* 3.4 36.3 - - + +
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Residues in contact with VAL 417 (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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350A LEU* 3.8 22.2 - - + -
373A PHE* 3.3 40.4 - - + -
374A TYR 3.5 6.3 - - - +
375A VAL* 4.3 2.7 - - + -
376A THR* 4.7 0.7 - - - -
415A PHE* 3.6 20.6 - - + +
416A LEU* 1.3 80.9 - - - +
418A LYS* 1.3 77.2 + - - +
428A THR* 5.4 0.2 - - - -
429A TYR* 2.7 39.5 + - + +
431A VAL* 4.0 20.2 - - + -
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Residues in contact with LYS 418 (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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350A LEU* 3.4 8.7 - - - -
373A PHE* 3.1 5.5 - - - +
374A TYR* 3.0 56.6 + - + +
376A THR* 4.1 14.1 - - + -
417A VAL* 1.3 84.1 - - - +
419A ASP* 1.3 60.1 + - - +
422A THR* 2.8 25.9 + - - +
423A GLN* 3.7 8.7 - - - +
425A ASN* 2.7 47.6 + - - -
426A ASN* 5.4 0.4 - - - +
427A ASN 2.9 21.8 + - - -
428A THR* 5.2 0.9 - - - +
429A TYR* 3.8 5.5 - - + -
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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