Contacts of the helix formed by residues 422 - 446 (chain B) in PDB entry 2KWI
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 ASP 422 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B LYS* 1.3 79.2 - - - +
423B LEU* 1.3 68.4 + - - +
424B SER* 2.7 38.4 + - - -
425B LYS* 2.8 41.6 + - + +
426B GLU* 3.0 18.9 + - - +
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 5.3 17.7 - - + +
421B LYS* 4.4 9.0 - - - +
422B ASP* 1.3 83.8 + - - +
424B SER* 1.3 61.4 + - - +
426B GLU* 3.1 19.4 - - - +
427B GLU* 3.2 32.5 + - + +
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Residues in contact with SER 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ASP* 2.7 19.3 + - - -
423B LEU* 1.3 77.0 - - - +
425B LYS* 1.3 60.6 + - - +
427B GLU* 4.2 2.8 - - - +
428B ARG* 3.1 29.7 + - - +
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Residues in contact with LYS 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LEU* 4.0 17.3 - - + +
415B ASP* 6.3 1.0 - - - +
416B LEU* 3.5 36.1 - - + -
420B ILE* 4.3 17.3 - - - +
421B LYS* 3.6 7.2 - - - +
422B ASP* 2.8 41.7 + - + +
424B SER* 1.3 79.5 - - - +
426B GLU* 1.3 54.8 + - - +
428B ARG* 3.2 2.5 + - - +
429B LEU* 2.7 41.4 + - - +
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Residues in contact with GLU 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP 5.3 0.9 - - - +
81A ASN* 3.6 24.7 - - - +
84A ARG* 3.6 34.3 - - + +
85A SER* 4.1 2.5 - - - +
114A VAL* 5.6 5.0 - - - +
416B LEU* 5.0 4.3 - - + -
421B LYS* 2.7 44.4 + - + +
422B ASP 3.0 7.1 + - - +
423B LEU* 3.1 33.6 + - - +
425B LYS* 1.3 77.7 - - + +
427B GLU* 1.3 62.4 + - - +
429B LEU* 3.2 21.3 - - - +
430B TRP* 3.3 16.9 + - + -
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Residues in contact with GLU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 2.7 35.2 + - - +
85A SER* 2.6 29.7 + - - -
423B LEU* 3.2 19.3 + - + +
424B SER* 4.2 3.1 - - - +
426B GLU* 1.3 73.2 - - - +
428B ARG* 1.3 60.7 + - - +
430B TRP* 3.4 4.9 + - - +
431B GLU* 3.0 28.1 + - - +
434B ARG* 4.6 3.3 + - - -
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Residues in contact with ARG 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLN* 5.6 0.2 + - - -
408B LEU* 3.9 28.0 - - - +
412B LEU* 3.8 19.1 - - + -
424B SER 3.1 18.8 + - - +
425B LYS* 3.6 5.6 - - - +
427B GLU* 1.3 77.0 - - - +
429B LEU* 1.3 58.1 + - - +
431B GLU* 2.6 46.7 + - - +
432B VAL* 2.8 45.5 + - + +
435B ILE* 4.4 10.6 - - - +
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA 3.9 7.4 - - - +
81A ASN 4.2 11.2 - - - +
82A TYR* 3.3 47.0 + - + +
409B LEU* 4.3 3.1 - - + -
412B LEU* 3.3 33.4 - - + +
413B HIS* 3.6 14.4 - - + -
416B LEU* 3.5 28.9 - - + -
425B LYS 2.7 22.1 + - - +
426B GLU* 3.2 10.1 - - - +
427B GLU 3.2 0.2 - - - -
428B ARG* 1.3 73.2 - - - +
430B TRP* 1.3 61.6 + - - +
432B VAL* 3.4 5.5 - - - +
433B GLN* 3.1 23.7 + - - +
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Residues in contact with TRP 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 3.9 13.9 - - + -
17A VAL 4.8 0.7 - - - -
18A ILE* 3.6 37.0 - - + -
65A ASP* 3.3 37.9 - - - -
67A LEU* 3.6 32.3 - - + -
81A ASN 5.5 0.2 - - - -
82A TYR* 2.7 37.4 + + - -
85A SER* 3.4 36.5 - - - -
426B GLU* 3.3 9.6 + - + +
427B GLU 3.7 6.1 - - - +
429B LEU* 1.3 78.8 - - - +
431B GLU* 1.3 64.0 + - - +
433B GLN* 3.1 9.4 - - + +
434B ARG* 2.9 66.7 + - + +
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B GLU 3.0 18.7 + - - +
428B ARG* 2.6 44.3 + - - +
430B TRP* 1.3 75.4 - - - +
432B VAL* 1.3 63.0 + - - +
434B ARG* 3.1 30.3 + - - +
435B ILE* 3.1 23.6 + - + +
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Residues in contact with VAL 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLN* 3.4 33.0 - - - +
408B LEU* 3.5 28.9 - - + -
409B LEU* 3.5 17.7 - - + -
412B LEU* 4.2 12.6 - - + -
428B ARG* 2.8 33.2 + - - +
429B LEU* 3.4 9.2 - - - +
431B GLU* 1.3 70.7 - - - +
433B GLN* 1.3 57.8 + - - +
435B ILE* 3.0 12.2 + - + +
436B LEU* 2.7 33.1 + - - +
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Residues in contact with GLN 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ALA* 3.1 26.2 + - - +
49A ASP* 4.9 0.6 - - - +
50A SER* 3.4 26.7 + - - +
65A ASP* 5.7 2.7 - - - +
66A ILE 5.3 0.8 + - - -
67A LEU* 3.9 25.7 - - + +
82A TYR* 4.4 3.7 + - + +
409B LEU* 3.6 25.7 - - + +
429B LEU 3.1 17.3 + - - +
430B TRP* 3.1 13.7 - - + +
432B VAL* 1.3 77.0 - - - +
434B ARG* 1.3 62.6 + - + +
436B LEU* 3.1 12.7 + - - +
437B THR* 2.9 30.7 + - - +
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Residues in contact with ARG 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 3.1 31.0 - - - +
52A ARG* 3.2 26.4 + - - +
65A ASP* 2.8 26.9 + - - +
85A SER* 4.4 8.5 + - - -
427B GLU* 4.6 2.4 + - - -
430B TRP* 2.9 60.3 + - + +
431B GLU* 3.1 19.0 + - - +
433B GLN* 1.3 78.2 - - + +
435B ILE* 1.3 58.7 + - + +
437B THR* 3.1 12.9 - - - +
438B ALA* 3.1 26.5 + - - +
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Residues in contact with ILE 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B GLN* 3.4 29.8 - - - +
428B ARG* 4.4 11.4 - - - +
431B GLU* 3.2 31.2 - - + +
432B VAL* 3.0 17.2 + - + +
434B ARG* 1.3 77.8 - - + +
436B LEU* 1.3 52.9 + - - +
438B ALA* 3.2 6.0 + - + +
439B LEU* 2.7 46.6 + - + +
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Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASP* 4.8 7.4 - - + +
402B ILE* 3.8 14.8 - - + +
405B GLN* 3.7 25.3 - - + +
406B GLU* 3.6 32.1 - - + +
409B LEU* 4.9 12.3 - - + -
432B VAL 2.7 16.8 + - - +
433B GLN* 3.1 21.1 + - - +
435B ILE* 1.3 74.2 - - - +
437B THR* 1.3 60.2 + - - +
439B LEU* 3.2 5.3 + - + +
440B LYS* 2.9 50.9 + - + +
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Residues in contact with THR 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A SER 2.9 27.1 + - - +
51A TYR* 3.2 27.2 - - - -
52A ARG* 4.2 26.4 + - + +
65A ASP* 5.8 0.2 - - - +
433B GLN* 2.9 14.0 + - - +
434B ARG* 3.1 30.5 - - - +
436B LEU* 1.3 78.5 - - - +
438B ALA* 1.3 61.2 + - - +
440B LYS* 3.2 24.2 - - - +
441B ARG* 3.3 7.6 + - - +
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Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ARG* 4.3 13.2 - - - +
434B ARG 3.1 19.1 + - - +
435B ILE* 3.2 9.2 + - + +
437B THR* 1.3 76.7 - - - +
439B LEU* 1.3 61.9 + - + +
441B ARG* 3.1 21.3 + - - +
442B LYS* 2.9 32.9 + - + +
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Residues in contact with LEU 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B ILE* 3.6 25.0 - - + +
401B GLU* 3.6 40.2 - - + -
402B ILE* 3.7 18.9 - - + +
405B GLN* 4.0 9.0 - - + +
435B ILE* 2.7 44.8 + - + +
436B LEU* 3.3 9.4 - - - +
438B ALA* 1.3 73.6 - - + +
440B LYS* 1.3 60.7 + - - +
442B LYS* 3.1 16.1 + - + +
443B LEU* 2.8 28.6 + - - +
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Residues in contact with LYS 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A TYR* 5.6 0.2 + - - -
49A ASP* 2.7 32.3 + - - +
51A TYR* 3.5 30.0 + - + +
402B ILE* 4.8 18.4 - - + -
406B GLU* 5.6 4.0 - - - -
436B LEU* 2.9 35.6 + - + +
437B THR* 3.2 14.1 - - - +
439B LEU* 1.3 75.8 - - - +
441B ARG* 1.3 62.3 + - - +
443B LEU* 3.3 21.6 + - + +
444B ARG* 3.3 25.1 + - - +
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Residues in contact with ARG 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TYR* 5.3 0.4 - - + -
437B THR 3.3 7.9 + - - +
438B ALA* 3.1 19.6 + - - +
440B LYS* 1.3 79.8 - - - +
442B LYS* 1.3 75.4 + - - +
444B ARG* 3.2 13.8 + - - +
445B GLU* 2.8 56.9 + - - +
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Residues in contact with LYS 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ILE* 3.7 37.1 - - + +
438B ALA* 2.9 20.8 + - + +
439B LEU* 3.1 22.2 + - + +
441B ARG* 1.3 95.5 - - - +
443B LEU* 1.3 60.7 + - - +
445B GLU* 2.6 53.5 + - - +
446B ALA* 3.3 7.1 + - - +
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Residues in contact with LEU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B GLN* 3.0 44.1 + - + +
398B ILE* 3.4 12.5 - - + +
399B LYS* 3.7 34.8 - - + -
402B ILE* 3.7 20.0 - - + -
439B LEU 2.8 12.5 + - - +
440B LYS* 3.4 16.6 - - + +
441B ARG 3.2 0.4 - - - -
442B LYS* 1.3 79.0 - - - +
444B ARG* 1.3 66.5 + - + +
445B GLU 3.3 0.7 + - - -
446B ALA* 3.7 5.2 + - - +
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Residues in contact with ARG 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 4.5 10.2 + - - -
51A TYR* 3.4 42.4 + - - -
395B GLN* 5.2 0.7 - - - +
440B LYS* 3.3 20.0 + - - +
441B ARG* 3.2 11.6 + - - +
443B LEU* 1.3 83.1 - - + +
445B GLU* 1.3 61.6 + - - +
446B ALA 3.5 2.2 - - - +
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Residues in contact with GLU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ARG* 2.8 45.2 + - - +
442B LYS* 2.6 47.1 + - - +
443B LEU 3.1 0.4 - - - -
444B ARG* 1.3 80.5 - - - +
446B ALA* 1.3 67.5 + - - +
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Residues in contact with ALA 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B THR* 4.0 30.7 - - + -
395B GLN* 3.4 44.8 + - + +
398B ILE* 4.9 2.7 - - + -
442B LYS 3.3 10.7 + - - +
443B LEU 3.7 1.4 + - - +
444B ARG 3.5 2.5 - - - +
445B GLU* 1.3 86.0 - - - +
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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
------------------------------------------------------------
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