Contacts of the helix formed by residues 433 - 451 (chain A) in PDB entry 1K4S
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 433 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A TRP* 4.9 0.2 - - - -
348A GLU* 3.0 31.6 + - - +
349A ARG 3.7 3.3 + - - -
429A LEU* 3.3 17.9 - - - +
430A ASN* 2.6 41.3 + - - +
431A PRO 3.0 5.4 - - - +
432A SER* 1.3 80.2 + - - +
434A ARG* 1.3 52.5 + - - +
435A ILE* 3.8 4.5 - - - -
436A LYS* 3.3 0.9 + - - -
437A GLY* 2.8 30.8 + - - -
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Residues in contact with ARG 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TRP* 4.5 7.0 - - - +
205A TRP* 3.5 53.7 - - + +
211A TYR* 3.0 18.9 - - - -
216A LYS 2.6 27.3 + - - -
217A TRP* 4.2 0.2 - - - -
343A MET* 3.3 18.7 - - - -
344A ASP* 2.8 27.9 + - - +
348A GLU* 3.3 13.4 + - - +
432A SER 3.6 1.2 + - - -
433A SER* 1.3 69.1 - - - +
435A ILE* 1.3 96.0 + - - +
437A GLY 2.6 22.7 + - - -
438A GLU* 2.7 29.7 + - + +
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Residues in contact with ILE 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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216A LYS* 4.0 24.2 - - + +
343A MET* 4.2 7.2 - - + -
348A GLU* 4.3 1.6 - - - +
411A THR* 3.6 38.8 - - + +
429A LEU* 3.2 39.0 - - + -
433A SER* 3.8 6.7 - - - -
434A ARG* 1.3 110.1 - - - +
436A LYS* 1.3 67.5 + - + +
437A GLY 3.0 0.3 + - - -
438A GLU* 3.7 7.6 + - - +
439A LYS* 3.7 13.7 + - + +
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Residues in contact with LYS 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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411A THR* 5.0 7.9 - - + -
428A MET* 3.2 24.4 - - + +
429A LEU* 4.5 14.4 - - + +
430A ASN 3.0 31.9 - - - +
431A PRO* 3.9 19.4 - - + +
433A SER* 3.3 2.2 + - - +
434A ARG 3.2 0.8 - - - -
435A ILE* 1.3 81.9 - - + +
437A GLY* 1.3 61.3 + - - +
439A LYS* 4.4 1.8 - - - +
440A ASP* 3.9 15.1 + - - +
8B C 3.4 5.0 - - - +
9B 5IU 2.6 63.7 + - - +
10B 5IU 5.4 5.8 - - - -
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Residues in contact with GLY 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TRP* 3.7 16.2 - - - -
431A PRO 4.1 7.2 - - - -
433A SER 2.8 10.3 + - - -
434A ARG 2.6 14.3 + - - -
436A LYS* 1.3 69.8 - - - +
438A GLU* 1.3 51.7 + - - -
439A LYS 3.0 1.8 - - - -
440A ASP* 2.7 14.3 + - - +
441A TRP* 2.6 32.0 + - - -
751A LYS 5.9 0.9 - - - -
754A TRP* 5.3 5.1 - - - -
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Residues in contact with GLU 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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205A TRP* 3.2 37.1 - - + +
206A TRP* 5.3 2.4 - - - -
208A GLU 5.2 1.9 - - - +
209A GLU 4.9 3.3 - - - +
210A ARG* 4.9 11.0 - - - +
211A TYR* 4.7 20.7 + - - +
434A ARG* 2.7 28.0 + - + +
435A ILE* 4.4 3.1 - - - +
437A GLY* 1.3 68.5 - - - -
439A LYS* 1.3 53.0 + - - +
441A TRP* 3.1 31.7 - - + -
442A GLN* 2.6 41.1 + - + +
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Residues in contact with LYS 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A ILE* 3.7 13.9 + - + +
436A LYS 4.4 4.7 - - - +
437A GLY 3.0 0.8 - - - -
438A GLU* 1.3 77.8 - - - +
440A ASP* 1.3 51.8 + - - +
442A GLN* 3.1 19.3 - - - +
443A LYS* 2.5 36.8 + - + +
8B C 2.5 62.5 + - - +
9B 5IU 2.8 30.7 + - - +
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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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436A LYS 3.9 10.9 + - - +
437A GLY* 2.7 14.7 + - - +
439A LYS* 1.3 76.9 - - - +
441A TRP* 1.3 60.2 + - - +
443A LYS* 2.8 51.4 + - - +
444A TYR* 2.9 38.9 + - - -
722A ASN* 4.8 3.3 - - - +
726A PRO* 5.4 0.3 - - - +
751A LYS* 4.5 23.2 + - - -
752A PHE* 5.5 3.1 - - - -
754A TRP* 4.2 13.3 - - + -
9B 5IU 6.0 0.4 - - - +
10B 5IU 4.8 0.9 + - - -
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Residues in contact with TRP 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TRP* 3.9 13.2 - + + -
206A TRP* 5.8 4.0 - - + -
437A GLY 2.6 15.2 + - - +
438A GLU* 3.1 57.7 - - + +
440A ASP* 1.3 75.1 + - - +
442A GLN* 1.3 83.3 + - + +
444A TYR* 3.2 12.7 + - - +
445A GLU* 3.5 23.2 + - + +
727A ARG* 4.2 9.8 + - - +
754A TRP* 3.2 46.9 - + + -
758A MET* 3.9 23.9 - - + +
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Residues in contact with GLN 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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438A GLU* 2.6 29.6 + - + +
439A LYS* 3.1 20.1 - - - +
441A TRP* 1.3 95.4 - - + +
443A LYS* 1.3 69.0 + - - +
444A TYR 3.2 0.4 - - - -
445A GLU* 3.1 21.1 + - + +
446A THR* 2.8 23.1 + - - -
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Residues in contact with LYS 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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439A LYS* 2.5 20.2 + - + +
440A ASP* 2.8 45.1 + - - +
442A GLN* 1.3 81.1 - - - +
444A TYR* 1.3 89.5 + - + +
446A THR* 2.9 21.5 + - - -
447A ALA* 3.8 4.7 + - - +
587A LYS* 3.7 24.9 - - - +
588A VAL* 6.0 0.2 - - - +
591A THR* 4.2 14.0 - - + +
722A ASN* 3.4 19.2 + - - +
723A PTR 4.9 0.6 - - - -
9B 5IU 5.5 2.5 - - - -
10B 5IU 3.7 15.2 + - - -
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Residues in contact with TYR 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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440A ASP* 2.9 45.3 + - - -
441A TRP* 3.2 5.4 + - - +
442A GLN 3.2 0.2 - - - -
443A LYS* 1.3 100.1 + - + +
445A GLU* 1.3 60.9 + - - +
446A THR 3.0 2.8 + - - -
447A ALA* 3.2 4.8 + - - +
448A ARG* 2.7 30.1 + - - +
591A THR* 4.4 10.8 - - + -
595A SER* 4.8 3.6 - - - -
720A LYS 5.0 0.5 + - - -
722A ASN* 3.6 4.7 - - - -
723A PTR 3.5 19.4 + - - -
724A LEU* 3.1 19.0 + - - -
725A ASP* 3.0 44.4 - - + +
726A PRO* 4.1 11.9 - - + +
727A ARG* 3.5 19.7 - - - +
752A PHE* 6.0 1.8 - + - -
754A TRP* 5.1 2.9 - + + -
765A PHE* 3.6 4.9 - + + -
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Residues in contact with GLU 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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441A TRP* 3.5 26.3 + - + +
442A GLN* 3.1 21.4 + - + +
444A TYR* 1.3 79.3 - - - +
446A THR* 1.3 60.6 + - - +
448A ARG* 2.7 50.6 + - - +
449A ARG* 3.0 29.3 - - - +
727A ARG* 2.8 24.9 + - - +
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Residues in contact with THR 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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442A GLN* 2.8 20.7 + - - -
443A LYS* 2.9 13.9 + - - -
444A TYR 3.0 0.2 - - - -
445A GLU* 1.3 71.9 - - - +
447A ALA* 1.3 57.5 + - - +
449A ARG* 2.7 51.3 + - - +
450A LEU 3.1 9.7 + - - -
581A MET* 3.5 12.5 - - + +
582A GLU 4.7 1.3 - - - +
583A GLY* 4.4 18.6 - - - +
588A VAL* 4.5 12.6 - - + -
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Residues in contact with ALA 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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443A LYS 3.8 2.9 + - - +
444A TYR* 3.2 5.9 + - - +
446A THR* 1.3 77.5 - - - +
448A ARG* 1.3 64.0 + - - +
449A ARG 2.9 1.4 + - - -
450A LEU* 3.1 3.9 + - - +
451A LYS* 3.1 22.7 + - - +
588A VAL* 4.0 18.5 - - + +
591A THR* 4.3 13.9 - - + -
592A TYR* 3.9 30.2 - - + +
765A PHE* 3.8 17.9 - - + -
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Residues in contact with ARG 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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444A TYR 2.7 10.2 + - - +
445A GLU* 2.7 57.3 + - - +
447A ALA* 1.3 77.0 - - - +
449A ARG* 1.3 56.3 - - + +
451A LYS* 3.2 30.0 + - - +
452A LYS* 4.3 7.3 + - - +
727A ARG* 2.9 17.1 - - - +
763A TYR* 2.6 44.9 + - - -
764A GLU 3.2 14.5 + - - +
765A PHE* 3.1 41.7 + - - +
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Residues in contact with ARG 449 (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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445A GLU* 3.0 25.8 + - - +
446A THR* 2.7 33.1 + - - +
448A ARG* 1.3 80.0 - - + +
450A LEU* 1.3 62.8 + - - +
451A LYS 3.0 1.8 - - - -
452A LYS* 3.6 22.9 + - - +
453A CYS* 3.7 13.0 + - - +
581A MET* 3.3 27.1 - - - +
582A GLU* 3.7 18.0 + - - +
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Residues in contact with LEU 450 (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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446A THR 3.1 5.8 + - - +
447A ALA 3.1 4.3 + - - +
449A ARG* 1.3 76.3 - - - +
451A LYS* 1.3 66.4 + - - +
453A CYS 2.9 27.8 - - - +
454A VAL* 3.0 16.0 - - + +
457A ILE* 3.6 17.0 - - + -
581A MET* 3.3 23.4 - - + +
584A LEU* 3.5 20.9 - - + -
588A VAL* 4.7 8.3 - - + -
589A PHE* 3.3 42.0 - - + -
592A TYR* 3.8 34.1 - - + -
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Residues in contact with LYS 451 (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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447A ALA 3.1 11.5 + - - +
448A ARG* 3.2 19.6 + - - +
450A LEU* 1.3 77.1 - - - +
452A LYS* 1.3 82.4 + - + +
454A VAL* 2.9 17.4 - - - +
455A ASP* 4.9 0.7 - - - +
592A TYR* 3.6 34.6 + - + +
596A ILE* 5.2 6.7 - - + -
764A GLU 4.9 2.4 + - - -
765A PHE* 3.1 42.5 + - + +
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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
------------------------------------------------------------
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