Contacts of the helix formed by residues 522 - 536 (chain D) in PDB entry 3K0J
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 LYS 522 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520D LYS 4.3 0.6 + - - -
521D ILE* 1.3 82.1 - - + +
523D LYS* 1.3 61.1 + - - +
524D ASP 4.8 0.9 - - - +
525D GLU* 3.8 26.9 - - + +
526D LEU* 3.3 22.3 + - - +
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Residues in contact with LYS 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521D ILE 3.5 1.9 + - - -
522D LYS* 1.3 70.6 - - - +
524D ASP* 1.3 74.6 + - - +
525D GLU 3.0 4.0 - - - -
526D LEU* 2.8 22.8 + - - +
527D LYS* 2.9 26.8 + - - +
545D VAL* 3.1 53.3 + - + +
546D SER* 3.7 11.2 - - - +
547D ARG* 3.9 12.3 - - + +
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Residues in contact with ASP 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522D LYS* 4.8 1.4 - - + +
523D LYS* 1.3 90.2 + - - +
525D GLU* 1.3 63.3 + - + +
527D LYS* 3.7 14.2 + - - +
528D LYS* 3.1 44.9 + - - +
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Residues in contact with GLU 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ASN* 5.6 0.4 - - - +
283A ARG* 2.6 41.6 + - - +
521D ILE* 4.8 3.8 - - + -
522D LYS* 3.8 26.6 + - + +
523D LYS 3.0 0.4 - - - -
524D ASP* 1.3 79.0 - - + +
526D LEU* 1.3 61.5 + - - +
527D LYS 3.2 0.2 - - - -
528D LYS* 3.2 4.6 + - - +
529D SER* 2.9 29.2 + - - -
578D TYR* 4.6 8.1 - - - +
25E U 3.0 67.6 + - + +
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Residues in contact with LEU 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517D LEU* 4.1 29.2 - - + -
518D ASN 4.6 11.7 - - - +
519D GLU 6.0 0.2 - - - +
521D ILE* 4.7 11.7 - - + +
522D LYS 3.3 15.2 + - - +
523D LYS* 2.8 12.9 + - - +
525D GLU* 1.3 80.7 - - - +
527D LYS* 1.3 54.5 + - - +
529D SER* 3.7 3.4 + - - -
530D LEU* 3.1 29.8 + - + +
545D VAL* 4.5 20.0 - - + -
553D GLY* 6.1 3.4 - - - +
554D GLN 5.5 3.6 - - - +
577D PHE* 3.7 27.4 - - + -
578D TYR* 4.6 9.2 - - + -
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Residues in contact with LYS 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523D LYS* 2.9 22.2 + - - +
524D ASP* 4.0 14.8 - - - +
526D LEU* 1.3 76.5 - - - +
528D LYS* 1.3 60.5 + - + +
530D LEU* 3.2 7.4 + - - +
531D HIS* 2.8 30.0 + - + +
542D ASP* 5.3 1.0 + - - +
543D ILE* 3.1 49.1 + - + +
544D LEU* 4.3 3.8 - - - +
545D VAL* 4.0 31.9 + - + +
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Residues in contact with LYS 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ARG* 3.3 36.6 + - - +
524D ASP* 3.1 38.1 + - - +
525D GLU* 3.2 4.6 + - - +
527D LYS* 1.3 77.9 - - + +
529D SER* 1.3 58.7 + - - +
531D HIS* 3.3 7.3 + - - +
532D ALA* 2.9 28.1 + - - +
25E U 3.1 33.1 + - - +
26E G 3.7 9.1 + - - -
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Residues in contact with SER 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ASN* 3.9 4.2 + - - -
274A GLY* 5.4 0.3 - - - -
281A PRO* 4.2 4.9 - - - -
283A ARG* 3.2 16.8 + - - +
525D GLU 2.9 16.9 + - - -
526D LEU 3.9 2.5 - - - -
528D LYS* 1.3 79.1 - - - +
530D LEU* 1.3 57.5 + - - +
532D ALA* 3.1 9.9 - - - +
533D ILE* 3.0 30.1 + - - +
577D PHE* 3.5 24.2 - - - -
578D TYR* 3.0 24.6 + - - -
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Residues in contact with LEU 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514D ILE* 4.3 4.5 - - + -
517D LEU* 4.0 16.4 - - + -
526D LEU* 3.1 30.4 + - + +
527D LYS 3.2 4.4 + - - +
529D SER* 1.3 73.6 - - - +
531D HIS* 1.3 66.2 + - - +
532D ALA 3.0 1.1 - - - -
533D ILE* 3.3 2.3 + - + -
534D PHE* 3.0 55.4 + - + +
543D ILE* 3.7 24.7 - - + -
545D VAL* 4.5 4.0 - - + -
555D ALA* 3.8 28.9 - - + -
557D VAL* 4.8 5.4 - - + -
577D PHE* 3.7 22.7 - - + -
582D MET* 4.7 3.4 - - - -
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Residues in contact with HIS 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527D LYS* 2.8 17.5 + - + +
528D LYS* 3.6 8.1 - - - +
530D LEU* 1.3 77.4 - - - +
532D ALA* 1.3 58.3 + - - +
535D SER* 2.3 65.8 + - - -
540D ILE* 3.9 26.1 + - + +
543D ILE* 3.2 17.4 - - + +
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Residues in contact with ALA 532 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A GLN* 3.1 41.9 - - - +
274A GLY* 5.0 4.3 - - - -
283A ARG* 4.2 15.7 - - + -
528D LYS 2.9 14.4 + - - +
529D SER* 3.1 15.0 - - - +
531D HIS* 1.3 81.5 + - - +
533D ILE* 1.3 63.6 + - - +
535D SER* 3.8 10.0 + - - -
536D ARG* 4.3 1.0 - - - +
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Residues in contact with ILE 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A GLN 4.4 3.8 - - - +
274A GLY* 3.6 22.7 - - - +
529D SER 3.0 11.5 + - - +
530D LEU* 3.3 4.7 + - + +
532D ALA* 1.3 81.1 - - - +
534D PHE* 1.3 80.4 + - + +
536D ARG* 3.4 30.9 + - - +
537D PHE* 3.8 2.4 - - - -
572D MET* 3.6 27.4 - - + -
575D PHE* 3.9 24.0 - - + -
577D PHE* 3.2 37.7 - - + -
582D MET* 4.7 5.6 - - + -
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Residues in contact with PHE 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D ILE* 4.0 11.7 - - + -
514D ILE* 2.6 41.1 - - + -
530D LEU* 3.0 41.0 + - + +
533D ILE* 1.3 77.5 - - + +
535D SER* 1.3 67.1 + - - +
536D ARG 3.0 3.4 - - - -
537D PHE* 2.7 31.5 + + - +
540D ILE* 3.5 11.4 - - + -
557D VAL* 3.7 18.6 - - + -
559D PHE* 3.8 16.8 - + + -
568D ALA* 3.9 9.2 - - + -
572D MET* 3.3 34.8 - - + -
582D MET* 3.1 15.9 - - + -
584D ILE* 4.5 1.3 - - + -
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Residues in contact with SER 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531D HIS* 2.3 50.1 + - - -
532D ALA* 4.0 6.9 - - - -
533D ILE 3.5 0.8 - - - -
534D PHE* 1.3 74.0 - - - +
536D ARG* 1.3 58.5 + - - +
537D PHE 2.9 3.3 + - - -
538D GLY* 2.5 25.0 + - - +
540D ILE* 3.0 15.8 - - - +
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Residues in contact with ARG 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A LEU* 5.9 0.7 - - - -
270A ARG* 3.1 37.0 + - + +
271A SER 5.1 2.0 - - - -
273A GLN* 3.0 52.0 + - + +
275A PHE* 4.3 11.7 - - - -
532D ALA 4.3 1.1 - - - +
533D ILE* 3.4 22.6 + - - +
534D PHE 3.0 0.4 + - - -
535D SER* 1.3 76.7 - - - +
537D PHE* 1.3 74.5 + - + +
538D GLY 3.2 3.9 + - - -
572D MET* 4.5 17.6 - - - +
575D PHE* 6.0 1.4 - - - -
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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