Contacts of the strand formed by residues 432 - 448 (chain A) in PDB entry 1XKW
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 THR 432 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A GLY 3.7 1.0 - - - +
392A GLU* 3.2 4.7 - - - -
393A THR* 2.9 45.0 + - - +
430A GLY 4.0 1.6 + - - -
431A THR* 1.3 70.6 - - - +
433A THR* 1.3 61.5 + - - +
434A THR* 4.2 3.4 + - - +
464A GLN* 3.6 38.6 - - + +
465A ASP 3.1 6.7 - - - +
466A THR* 3.8 7.7 - - + +
467A PRO* 3.6 19.8 - - - +
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Residues in contact with THR 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLN* 3.9 30.3 - - + +
391A GLY 3.3 10.1 - - - +
392A GLU* 3.9 18.7 - - + +
431A THR* 4.0 9.2 + - - +
432A THR* 1.3 74.8 + - - +
434A THR* 1.3 63.0 + - - +
435A THR* 4.2 2.7 - - - +
463A ASP* 4.0 1.7 - - - +
464A GLN* 3.2 3.3 - - - -
465A ASP* 2.8 47.4 + - - +
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Residues in contact with THR 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ALA 3.8 0.7 - - - +
390A GLN* 3.1 5.9 - - - +
391A GLY* 2.9 35.8 + - - -
432A THR* 4.2 4.2 + - - +
433A THR* 1.3 71.9 - - - +
435A THR* 1.3 66.0 + - - +
436A GLN* 5.7 2.0 - - + +
462A TRP* 3.4 40.6 - - + +
463A ASP 3.5 4.9 - - - +
464A GLN* 2.8 25.2 + - - +
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Residues in contact with THR 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A TYR* 4.0 22.7 - - + -
389A ALA 3.3 9.6 - - - +
390A GLN* 2.8 32.4 + - - +
433A THR* 4.2 4.0 - - - +
434A THR* 1.3 75.1 - - - +
436A GLN* 1.3 64.3 + - - +
437A LYS* 4.2 14.4 - - - +
461A TRP 3.8 0.5 - - - +
462A TRP* 3.4 4.9 - - - -
463A ASP* 2.9 55.8 + - - +
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Residues in contact with GLN 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A HIS 5.3 1.8 - - - -
168A GLY* 3.6 10.3 - - - -
169A THR* 3.1 51.7 + - + +
387A THR* 3.9 1.5 - - - +
388A TYR* 3.4 3.8 - - - -
389A ALA* 2.7 48.4 + - + +
434A THR* 4.3 2.1 - - + +
435A THR* 1.3 75.9 - - - +
437A LYS* 1.3 74.3 + - - +
458A ARG* 4.5 6.8 + - - +
460A SER* 4.7 6.1 + - - -
461A TRP 3.3 10.3 - - - +
462A TRP* 3.9 13.7 - - + +
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Residues in contact with LYS 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A THR* 3.3 8.1 - - - +
388A TYR* 3.8 32.7 - - + -
435A THR* 4.2 12.0 - - + +
436A GLN* 1.3 84.4 - - - +
438A GLY* 1.3 59.6 + - - +
460A SER* 3.5 3.8 - - - -
461A TRP* 2.8 55.1 + - + +
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Residues in contact with GLY 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A VAL* 3.2 7.4 - - - +
387A THR* 2.8 43.9 + - - +
437A LYS* 1.3 78.8 - - - +
439A LEU* 1.3 61.1 + - - +
440A TYR* 4.3 1.1 - - - -
458A ARG* 4.1 12.8 - - - -
459A GLU 3.3 7.6 - - - -
461A TRP* 4.4 2.9 - - - -
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Residues in contact with LEU 439 (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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385A GLY 3.5 7.4 - - - +
386A VAL* 3.4 28.5 - - + -
438A GLY* 1.3 74.1 - - - -
440A TYR* 1.3 63.6 + - - +
458A ARG* 3.2 2.7 - - - +
459A GLU* 2.7 39.9 + - + +
461A TRP* 4.1 23.8 - - + -
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Residues in contact with TYR 440 (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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71A LYS* 3.5 28.3 + - + +
165A LEU* 4.0 15.9 - - + +
166A LEU* 5.3 3.6 - - + -
366A ASP* 5.5 2.8 + - - +
367A ALA 4.2 3.1 + - - -
368A ASN* 3.6 18.7 + - - +
383A LEU* 3.8 31.0 - - + -
384A GLY* 3.4 2.7 - - - -
385A GLY* 2.8 59.8 + - - +
386A VAL 5.2 0.2 + - - -
387A THR* 3.6 26.6 - - + +
439A LEU* 1.3 80.2 - - - +
441A ALA* 1.3 65.9 + - - +
442A LEU* 5.8 0.7 - - + -
457A GLY 3.3 12.1 - - - +
458A ARG* 3.5 31.9 - - + -
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Residues in contact with ALA 441 (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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165A LEU* 4.1 1.6 - - - +
383A LEU 3.1 11.7 - - - +
384A GLY* 4.5 3.1 - - - -
440A TYR* 1.3 80.0 - - - +
442A LEU* 1.3 63.1 + - - +
456A GLY* 3.2 2.1 - - - -
457A GLY 3.0 31.0 + - - +
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Residues in contact with LEU 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLY 5.6 1.6 - - - +
74A LEU* 6.6 0.4 - - + -
165A LEU* 3.6 32.1 - - + -
166A LEU* 5.0 7.0 - - + -
381A GLU 4.0 0.5 - - - +
382A LEU* 3.6 3.0 - - - +
383A LEU* 2.8 57.9 + - + +
440A TYR* 5.8 0.7 - - + -
441A ALA* 1.3 76.7 - - - +
443A GLY* 1.3 61.3 + - - +
444A ARG* 4.8 14.1 - - + -
454A VAL* 3.5 28.9 - - + -
455A VAL 3.3 24.0 - - - +
456A GLY* 3.8 0.9 - - - +
480A TYR* 3.9 4.3 - - + -
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Residues in contact with GLY 443 (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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381A GLU 3.4 7.2 - - - -
382A LEU* 4.1 12.3 - - - -
442A LEU* 1.3 76.5 - - - +
444A ARG* 1.3 63.8 + - - -
445A ILE* 3.6 9.9 - - - -
453A LEU 3.5 1.7 - - - +
454A VAL* 3.4 5.9 - - - +
455A VAL* 2.8 37.6 + - - +
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Residues in contact with ARG 444 (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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72A VAL* 4.3 11.8 - - - +
74A LEU* 3.7 26.7 - - - +
78A GLU* 3.5 44.5 + - - +
379A THR 4.8 1.0 - - - +
380A HIS* 3.6 4.2 - - - -
381A GLU* 2.8 65.4 + - + +
442A LEU* 4.8 13.2 - - + -
443A GLY* 1.3 73.4 - - - +
445A ILE* 1.3 60.7 + - - +
446A LYS* 3.9 2.4 + - - +
452A THR* 4.0 14.2 - - + +
453A LEU 3.7 4.3 - - - -
454A VAL* 4.2 21.5 - - + -
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Residues in contact with ILE 445 (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 HIS* 3.3 34.1 - - + +
382A LEU* 4.3 10.5 - - + -
443A GLY* 4.1 18.4 - - - +
444A ARG* 1.3 78.3 - - - +
446A LYS* 1.3 64.4 + - - +
447A LEU* 3.2 15.3 + - + -
452A THR* 3.2 3.8 - - - -
453A LEU* 2.7 54.0 + - + +
455A VAL* 4.7 11.7 - - + -
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Residues in contact with LYS 446 (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 LEU* 3.4 32.6 - - + +
379A THR 3.0 27.1 - - - +
380A HIS* 3.1 18.3 + - + -
444A ARG 3.9 2.7 + - - +
445A ILE* 1.3 72.4 - - - +
447A LEU* 1.3 62.6 + - - +
448A ALA 3.3 13.4 + - - +
449A GLU* 2.5 35.0 + - - +
450A PRO 5.0 0.2 - - - -
451A LEU 3.3 5.4 - - - +
452A THR* 3.4 28.0 - - + +
486A ASP* 5.5 2.5 + - - -
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Residues in contact with LEU 447 (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 LEU* 4.3 3.7 - - - +
445A ILE* 3.2 11.5 + - + +
446A LYS* 1.3 75.3 - - - +
448A ALA* 1.3 61.6 + - - +
451A LEU* 2.7 35.6 + - + +
453A LEU* 4.0 41.1 - - + +
483A LEU* 4.4 9.4 - - + -
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Residues in contact with ALA 448 (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 LEU* 3.9 13.5 - - - -
446A LYS* 3.0 8.5 - - - +
447A LEU* 1.3 79.2 - - - +
449A GLU* 1.3 67.3 + - - +
450A PRO* 3.2 12.3 - - + -
451A LEU* 2.9 30.1 + - + +
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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