Contacts of the helix formed by residues 426 - 445 (chain A) in PDB entry 1K89
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 LEU 426 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A TYR* 3.6 27.3 + - + +
220A VAL* 4.2 5.4 - - + -
365A VAL* 4.1 19.5 - - + -
366A VAL 3.7 17.1 + - - +
367A ALA* 4.4 2.2 - - + -
368A PRO* 3.5 14.1 - - + +
410A HIS* 3.9 17.9 - - + +
413A SER* 4.2 6.3 - - - -
414A ALA* 4.1 21.3 - - - +
424A TYR* 3.6 48.0 + - + +
425A ASN* 1.3 73.3 - - - +
427A VAL* 1.3 62.2 + - - +
429A GLY* 3.8 2.2 - - - +
430A ALA* 3.1 17.2 + - - +
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Residues in contact with VAL 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 6.2 4.3 - - + -
31A SER* 6.1 1.1 - - - -
355A LEU* 4.9 13.0 - - + -
359A MET* 3.8 30.7 - - + -
366A VAL* 3.9 26.9 - - + +
368A PRO* 3.8 25.7 - - + +
370A LYS* 5.5 1.5 + - - +
425A ASN* 3.1 7.5 + - - +
426A LEU* 1.3 75.5 - - - +
428A ALA* 1.3 66.4 + - - +
430A ALA* 3.4 5.0 + - - +
431A ASN* 3.4 28.8 + - - +
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Residues in contact with ALA 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 4.0 28.7 - - - +
422A LEU* 3.9 22.9 - - + -
425A ASN* 3.0 27.7 + - - +
427A VAL* 1.3 74.4 - - - +
429A GLY* 1.3 67.1 + - - +
431A ASN* 3.1 3.6 + - - +
432A ILE* 2.9 29.8 + - + +
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Residues in contact with GLY 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A SER* 3.4 28.5 - - - -
416A ALA* 4.7 0.4 - - - -
417A ALA* 4.1 10.7 - - - +
425A ASN 3.0 15.9 + - - -
426A LEU 4.0 1.3 - - - -
427A VAL 3.3 0.2 - - - -
428A ALA* 1.3 78.5 - - - +
430A ALA* 1.3 61.7 + - - +
432A ILE* 4.5 3.6 - - - -
433A VAL* 3.0 30.0 + - - +
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Residues in contact with ALA 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 5.7 0.2 - - - +
116A LEU* 3.7 12.9 - - + +
368A PRO* 3.8 16.2 - - + -
370A LYS* 4.1 16.2 - - + +
371A ALA* 4.0 18.2 - - + -
413A SER* 4.0 10.2 - - - +
426A LEU 3.1 19.2 + - - +
427A VAL 3.8 4.5 - - - +
428A ALA 3.2 0.2 - - - -
429A GLY* 1.3 73.8 - - - +
431A ASN* 1.3 67.2 + - - +
432A ILE 3.1 0.2 + - - -
434A GLY* 3.0 20.8 + - - -
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Residues in contact with ASN 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 4.3 6.1 + - - +
28A VAL* 4.0 26.6 - - + +
31A SER* 2.9 30.8 + - - +
32A LEU* 3.9 7.5 - - + +
112A PHE* 3.9 7.8 - - - -
370A LYS* 2.8 36.9 + - - +
427A VAL* 3.4 20.7 + - - +
428A ALA 3.1 5.0 + - - +
430A ALA* 1.3 79.5 - - - +
432A ILE* 1.3 56.7 + - - +
434A GLY* 3.8 0.7 - - - -
435A PHE* 2.8 30.8 + - - +
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Residues in contact with ILE 432 (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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31A SER 4.1 12.3 - - - +
32A LEU* 4.0 16.4 - - + -
34A PRO* 5.8 1.1 - - + -
35A VAL* 3.9 32.1 - - + -
416A ALA* 3.9 20.9 - - + +
417A ALA* 5.0 0.2 - - - -
420A TYR* 4.3 20.0 - - + -
422A LEU* 4.0 26.2 - - + -
428A ALA 2.9 21.3 + - - +
429A GLY* 3.8 6.7 - - - +
431A ASN* 1.3 74.1 - - - +
433A VAL* 1.3 67.9 + - - +
435A PHE* 3.2 2.1 + - - +
436A GLN* 2.9 32.0 + - + +
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Residues in contact with VAL 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER* 4.3 2.5 + - - +
116A LEU* 3.5 26.9 - - + +
409A ILE* 6.1 0.9 - - - +
412A GLY* 3.5 23.8 - - - +
413A SER* 4.0 1.8 - - - +
416A ALA* 3.5 23.3 - - + -
429A GLY 3.0 17.2 + - - +
430A ALA* 5.0 0.2 - - - -
432A ILE* 1.3 77.7 - - - +
434A GLY* 1.3 65.2 + - - +
436A GLN* 3.4 10.9 + - - +
437A LYS* 3.6 9.9 + - - +
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Residues in contact with GLY 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 4.0 16.8 - - - -
115A SER* 2.8 35.2 + - - -
116A LEU* 3.5 11.9 - - - +
430A ALA 3.0 14.5 + - - -
431A ASN 3.8 0.9 - - - -
433A VAL* 1.3 78.0 - - - +
435A PHE* 1.3 62.5 + - - +
438A ILE* 3.5 10.0 + - - +
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Residues in contact with PHE 435 (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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32A LEU* 3.7 30.3 - - + -
35A VAL* 3.8 24.0 - - + -
36A VAL* 4.4 9.2 - - + -
42A TYR* 3.6 37.5 - + - -
47A LEU* 4.0 6.1 - - + -
48A LEU* 3.9 19.3 - - + -
51A MET* 3.7 35.7 - - + -
112A PHE* 3.8 12.2 - + + -
431A ASN 2.8 21.0 + - - +
432A ILE 3.2 3.8 + - - +
434A GLY* 1.3 73.9 - - - +
436A GLN* 1.3 61.1 + - - +
438A ILE* 3.2 6.5 + - - +
439A ALA* 2.9 37.2 + - + +
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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
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35A VAL* 3.0 33.8 - - + +
39A HIS* 3.6 12.7 + - - -
42A TYR* 3.2 23.3 + - - -
419A ARG* 6.4 0.4 - - - +
420A TYR* 4.6 7.1 + - + +
432A ILE* 2.9 27.5 + - + +
433A VAL* 4.0 5.2 - - - +
434A GLY 3.4 0.4 - - - -
435A PHE* 1.3 76.9 - - - +
437A LYS* 1.3 61.9 + - - +
439A ALA* 3.4 1.1 + - - +
440A ASP* 3.1 39.5 + - - +
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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
----------------------------------------------------------
85A ILE* 4.2 24.2 - - + -
115A SER* 3.5 28.5 + - - +
118A THR* 3.4 36.1 + - - +
119A LEU 4.1 6.9 + - - -
120A PRO* 5.5 1.7 - - - +
433A VAL 3.6 7.9 + - - +
434A GLY 4.2 0.2 - - - +
435A PHE 3.3 0.8 - - - -
436A GLN* 1.3 74.3 - - - +
438A ILE* 1.3 66.9 + - - +
440A ASP* 3.4 9.9 + - + +
441A ALA* 3.0 24.0 + - + +
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Residues in contact with ILE 438 (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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51A MET* 4.4 12.6 - - + -
82A ASN* 3.7 30.7 - - - +
84A ALA* 4.9 1.1 - - + -
85A ILE* 4.3 16.8 - - + -
111A ALA* 3.7 38.4 - - + +
112A PHE* 4.5 13.9 - - + +
115A SER* 3.8 10.3 - - - +
434A GLY 3.5 15.5 - - - +
435A PHE* 3.2 9.3 + - - +
437A LYS* 1.3 78.3 - - - +
439A ALA* 1.3 56.7 + - - +
441A ALA* 3.3 2.4 + - - +
442A MET* 2.9 38.5 + - + +
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Residues in contact with ALA 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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42A TYR* 3.7 22.2 - - + +
47A LEU* 3.7 29.1 - - + +
51A MET* 5.5 0.9 - - - -
435A PHE* 2.9 28.4 + - + +
436A GLN 3.8 4.5 - - - +
438A ILE* 1.3 75.1 - - - +
440A ASP* 1.3 55.3 + - - +
442A MET* 3.3 3.1 + - - +
443A MET* 2.8 42.6 + - - +
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Residues in contact with ASP 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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42A TYR* 4.8 2.6 + - - -
436A GLN* 3.1 32.7 + - - +
437A LYS* 3.5 11.6 - - + +
439A ALA* 1.3 74.0 - - - +
441A ALA* 1.3 65.5 + - - +
443A MET* 3.7 5.6 - - - +
444A ALA* 3.0 26.5 + - - +
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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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84A ALA* 3.9 15.7 - - + +
85A ILE* 3.5 25.6 - - + -
437A LYS* 3.0 14.7 + - + +
438A ILE 3.7 2.5 - - - +
440A ASP* 1.3 81.8 - - - +
442A MET* 1.3 57.8 + - - +
444A ALA* 3.4 5.0 + - - +
445A GLN* 3.0 39.7 + - - +
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Residues in contact with MET 442 (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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47A LEU* 3.8 24.2 - - + -
50A ARG* 3.9 38.7 + - + +
51A MET* 3.9 23.3 - - + +
55A GLU* 5.9 2.7 - - - +
82A ASN* 3.8 25.6 - - - +
84A ALA* 3.8 17.0 - - + -
438A ILE* 2.9 27.2 + - - +
439A ALA 3.9 0.9 - - - +
441A ALA* 1.3 69.4 - - - +
443A MET* 1.3 67.7 + - - +
445A GLN* 3.3 5.6 + - - +
446A GLY* 3.2 24.9 + - - +
447A ILE* 5.5 0.3 - - - +
449A TRP* 4.2 12.6 - - + +
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Residues in contact with MET 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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41A GLU* 3.9 26.9 - - + +
42A TYR* 3.9 31.4 - - + -
45A VAL* 3.5 39.3 - - + -
47A LEU* 4.7 9.4 - - + -
50A ARG* 5.3 0.9 - - - +
439A ALA 2.8 27.5 + - - +
440A ASP* 3.7 5.8 - - - +
442A MET* 1.3 73.8 - - - +
444A ALA* 1.3 63.8 + - - +
446A GLY* 3.4 10.0 + - - -
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Residues in contact with ALA 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ASP 3.0 18.1 + - - +
441A ALA* 3.8 5.8 - - - +
443A MET* 1.3 78.1 - - - +
445A GLN* 1.3 61.4 + - + +
446A GLY 3.3 1.3 + - - -
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Residues in contact with GLN 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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83A GLY 5.2 0.2 - - - +
84A ALA* 2.7 40.7 + - - +
441A ALA* 3.0 28.1 + - - +
442A MET* 3.3 5.9 + - - +
444A ALA* 1.3 77.4 - - + +
446A GLY* 1.3 63.7 + - - +
448A ALA* 4.5 11.6 - - - +
449A TRP* 6.2 0.2 - - - -
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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