Contacts of the helix formed by residues 535 - 551 (chain D) in PDB entry 5ON2
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 ILE 535 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219D MET* 4.0 48.9 - - + +
220D GLN* 4.6 4.7 - - + +
223D TRP* 3.3 55.0 - - + -
532D GLU 4.8 2.3 + - - +
533D HIS 3.4 0.6 - - - -
534D ALA* 1.3 80.5 - - + +
536D MET* 1.3 68.5 + - + +
539D LEU* 3.2 31.4 + - - +
3E C 5.2 4.5 - - - +
71E G 3.4 33.9 - - + +
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Residues in contact with MET 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D TRP* 4.7 8.7 - - + +
493D PHE* 4.3 20.9 - - + -
532D GLU 5.4 2.5 + - - +
533D HIS* 4.3 3.1 + - - +
535D ILE* 1.3 89.3 - - + +
537D HIS* 1.3 67.5 + - - +
539D LEU* 4.0 2.8 - - - +
540D TYR* 3.2 60.9 + - + +
71E G 4.9 1.6 - - - +
72E U 3.7 32.3 - - - +
73E A 3.9 43.1 - - - +
74E C 5.6 3.8 - - - +
76E A 4.5 7.9 - - - +
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Residues in contact with HIS 537 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D MET* 3.6 25.4 - - + -
493D PHE* 3.8 25.8 - - + -
496D SER* 3.3 31.3 + - - -
497D SER* 5.0 1.0 + - - -
499D TYR* 4.6 0.2 - + - -
527D TYR* 2.8 30.9 + - - -
533D HIS* 4.0 21.8 + - + +
536D MET* 1.3 78.0 - - - +
538D LEU* 1.3 58.3 + - + +
540D TYR* 3.1 6.3 + - - +
541D PHE* 2.7 52.0 + + + +
901D LSS 3.7 21.4 - - + +
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Residues in contact with LEU 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D MET* 4.3 5.4 - - + -
212D TRP* 4.0 6.5 - - + -
216D VAL* 4.2 3.4 - - + -
220D GLN* 3.7 8.7 - - - +
527D TYR* 3.6 36.3 - - + -
533D HIS* 3.3 23.6 + - + +
534D ALA* 3.7 21.3 - - - +
536D MET 3.5 0.4 - - - -
537D HIS* 1.3 84.2 - - + +
539D LEU* 1.3 56.5 + - - +
541D PHE* 3.6 16.3 - - + +
542D ARG* 3.2 32.6 + - - +
563D LEU* 3.6 33.9 - - + -
565D CYS* 4.3 6.5 - - - -
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Residues in contact with LEU 539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D ILE* 4.4 13.2 - - + -
202D LEU* 4.2 11.2 - - + -
220D GLN* 3.8 16.0 - - + +
223D TRP* 3.6 34.3 - - + +
224D ILE* 4.1 21.3 - - + -
417D LEU* 4.1 15.9 - - + -
535D ILE 3.2 20.2 + - - +
536D MET* 4.0 2.9 - - - +
537D HIS 3.2 0.8 - - - -
538D LEU* 1.3 76.1 - - - +
540D TYR* 1.3 63.0 + - + +
542D ARG* 3.5 23.9 + - - +
543D PHE* 2.9 29.7 + - - +
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Residues in contact with TYR 540 (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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195D ILE* 4.3 13.9 - - + -
420D TRP* 3.2 62.3 + + + +
491D ASP* 4.6 1.9 + - - -
493D PHE* 3.6 45.5 - + + -
497D SER* 3.5 16.8 - - - +
536D MET* 3.2 46.8 + - + +
537D HIS* 3.1 5.5 + - - +
539D LEU* 1.3 75.6 - - + +
541D PHE* 1.3 58.7 + - - +
543D PHE* 3.1 5.4 + - - +
544D PHE* 2.7 37.8 + - - +
73E A 5.1 2.4 + - - -
74E C 4.9 4.0 + - - -
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Residues in contact with PHE 541 (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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212D TRP* 4.6 4.5 - + - -
496D SER 5.2 0.4 - - - -
497D SER* 4.1 17.4 + - - +
499D TYR* 5.8 0.2 - + - -
500D TYR* 3.5 43.2 + + + -
524D VAL* 5.2 3.4 - - + -
527D TYR* 3.9 31.2 - + - -
537D HIS* 2.7 39.6 + + + +
538D LEU* 3.6 28.0 - - + +
540D TYR* 1.3 70.8 - - - +
542D ARG* 1.3 64.2 - - + +
545D HIS* 3.3 22.0 + - - +
559D PRO* 3.5 29.9 - - + +
560D ALA* 4.0 15.7 - - + -
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Residues in contact with ARG 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D LEU* 2.9 56.6 + - + +
205D ASP* 3.8 10.5 - - - +
206D LEU* 3.9 13.1 - - - +
209D LEU* 3.9 5.9 - - - +
212D TRP* 3.7 24.9 - - + -
220D GLN* 3.3 22.4 + - - -
538D LEU 3.2 19.1 + - - +
539D LEU* 3.8 8.9 - - - +
540D TYR 3.2 0.4 - - - -
541D PHE* 1.3 78.1 - - + +
543D PHE* 1.3 66.4 + - - +
545D HIS* 3.4 3.1 + - - +
546D LYS* 3.3 29.0 + - - +
558D GLU* 2.9 40.3 + - - +
559D PRO* 4.1 16.6 - - + +
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Residues in contact with PHE 543 (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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148D LEU* 6.2 0.9 - - + -
193D ILE* 3.7 27.6 - - + -
194D LYS 4.0 3.6 - - - -
195D ILE* 3.6 50.7 - - + -
198D TYR* 3.7 37.2 - + + -
202D LEU* 3.8 11.1 - - + +
420D TRP* 4.1 22.2 - + - -
539D LEU 2.9 19.7 + - - +
540D TYR* 3.5 4.0 - - - +
542D ARG* 1.3 76.8 - - - +
544D PHE* 1.3 64.0 + - + +
546D LYS* 3.3 5.7 + - - +
547D LEU* 3.2 45.3 + - + +
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Residues in contact with PHE 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D GLU* 5.3 4.0 - - + -
139D PHE* 3.4 39.5 - + + -
143D LEU* 5.3 3.4 - - + -
193D ILE* 5.5 1.3 - - + -
420D TRP* 4.3 14.4 - + - -
494D MET* 3.9 27.8 - - - -
497D SER* 3.7 30.5 - - - +
498D TRP* 3.8 35.7 - + + -
512D MET* 4.0 11.4 - - + -
540D TYR 2.7 20.7 + - - +
543D PHE* 1.3 71.3 - + - +
545D HIS* 1.3 65.0 + - - +
547D LEU* 3.4 16.0 + - + +
548D MET* 3.2 26.1 + - + +
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Residues in contact with HIS 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500D TYR* 2.7 34.1 + + - +
522D LEU* 4.9 6.1 - - + -
541D PHE 3.3 12.0 + - - +
542D ARG 3.5 9.0 - - - +
544D PHE* 1.3 79.6 - - - +
546D LYS* 1.3 56.3 - - - +
548D MET* 3.3 6.6 + - - +
549D ARG* 2.9 26.0 + - - +
554D VAL* 3.7 26.2 - - + +
556D SER* 2.9 39.4 + - - -
557D ASP 3.5 15.5 - - - -
558D GLU 3.4 7.8 - - - -
559D PRO* 3.4 34.1 - - + +
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Residues in contact with LYS 546 (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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198D TYR* 4.1 20.4 - - + -
201D GLU* 3.6 27.1 + - + +
202D LEU* 3.9 25.4 - - + -
205D ASP* 2.7 30.1 + - - -
542D ARG* 3.3 19.4 + - - +
543D PHE* 3.7 7.2 - - - +
544D PHE 3.3 0.4 - - - -
545D HIS* 1.3 74.5 - - + +
547D LEU* 1.3 64.5 + - - +
549D ARG* 3.5 10.4 + - - +
550D ASP* 3.0 31.9 + - - +
557D ASP 3.1 22.8 + - - +
558D GLU* 2.7 23.5 + - - -
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Residues in contact with LEU 547 (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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139D PHE* 3.8 19.7 - - + -
143D LEU* 4.0 25.8 - - + -
146D LYS* 5.2 1.9 + - - -
148D LEU* 3.6 31.2 - - + -
193D ILE* 4.9 1.3 - - + -
198D TYR* 3.6 26.5 - - + +
543D PHE* 3.2 45.4 + - + +
544D PHE* 3.7 17.0 - - + +
545D HIS 3.3 0.4 - - - -
546D LYS* 1.3 75.4 - - - +
548D MET* 1.3 61.5 + - - +
550D ASP* 3.3 4.2 + - - +
551D ALA* 3.2 21.8 + - - +
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Residues in contact with MET 548 (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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139D PHE* 4.1 11.7 - - + -
498D TRP* 4.2 10.1 - - + -
500D TYR* 3.3 32.5 - - + +
501D ALA* 4.5 7.0 - - + -
512D MET* 3.9 22.9 - - + -
513D LEU* 3.9 19.1 - - + -
544D PHE* 3.2 31.0 + - + +
545D HIS* 3.7 7.9 - - - +
547D LEU* 1.3 77.7 - - - +
549D ARG* 1.3 58.9 + - - +
551D ALA 3.6 0.3 + - - -
552D GLY 3.2 3.6 + - - -
553D MET* 3.0 53.4 + - + +
554D VAL* 3.5 11.9 + - + -
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Residues in contact with ARG 549 (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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198D TYR* 4.5 0.4 - - - -
201D GLU* 2.8 36.8 + - - -
205D ASP* 5.1 0.8 + - - -
545D HIS 2.9 16.2 + - - +
546D LYS* 3.6 13.5 + - - +
547D LEU 3.2 0.2 - - - -
548D MET* 1.3 76.7 - - - +
550D ASP* 1.3 92.3 + - - +
552D GLY* 3.1 14.9 + - - -
554D VAL* 3.4 27.9 - - + +
555D ASN 4.2 6.7 - - - +
556D SER 3.5 22.9 - - - +
557D ASP* 3.7 41.4 + - - +
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Residues in contact with ASP 550 (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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146D LYS* 4.3 14.5 + - - +
198D TYR* 2.6 32.7 + - - +
546D LYS 3.0 12.4 + - - +
547D LEU* 3.3 4.5 + - - +
549D ARG* 1.3 108.9 + - - +
551D ALA* 1.3 62.4 + - - +
552D GLY* 3.5 0.7 + - - -
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Residues in contact with ALA 551 (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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139D PHE* 4.9 4.7 - - + -
142D GLU* 5.6 3.4 - - - +
146D LYS* 4.2 15.4 - - - +
547D LEU 3.2 13.4 + - - +
549D ARG 3.3 0.2 - - - -
550D ASP* 1.3 75.8 - - - +
552D GLY* 1.3 58.5 + - - +
553D MET* 3.5 31.7 - - + +
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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