Contacts of the helix formed by residues 536 - 551 (chain A) in PDB entry 3ZJU
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 MET 536 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A TRP* 6.3 2.7 - - + -
493A PHE* 3.7 37.5 - - + -
532A GLU 5.3 7.9 - - - +
533A HIS* 3.1 8.9 + - + +
535A ILE* 1.3 86.9 - - + +
537A HIS* 1.3 70.9 + - - +
538A LEU 3.2 0.2 - - - -
539A LEU* 2.9 6.6 + - - +
540A TYR* 2.9 38.7 + - + +
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Residues in contact with HIS 537 (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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40A MET* 4.3 18.8 - - + -
493A PHE* 4.1 14.7 - - + -
496A SER* 2.8 41.8 + - - +
497A SER* 4.7 2.4 + - - -
499A TYR* 4.2 5.8 - + - -
527A TYR* 2.7 37.0 + + - -
533A HIS* 3.1 19.5 + + + +
536A MET* 1.3 78.9 - - - +
538A LEU* 1.3 68.3 + - + +
539A LEU 3.0 1.4 + - - -
540A TYR* 4.0 8.2 - - - -
541A PHE* 3.0 45.8 + + + +
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Residues in contact with LEU 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 4.1 15.3 - - + -
212A TRP* 3.9 5.5 - - + -
216A VAL* 4.0 8.1 - - + -
220A GLN* 3.2 13.4 + - - +
527A TYR* 4.2 5.8 - - + -
530A GLY 4.8 5.4 - - - +
531A ILE 5.4 0.7 - - - +
533A HIS* 3.0 17.2 + - + +
534A ALA* 3.4 36.8 - - + +
537A HIS* 1.3 77.8 - - + +
539A LEU* 1.3 56.4 + - - +
541A PHE* 3.6 24.1 - - + -
542A ARG* 3.4 23.4 - - - +
563A LEU* 3.7 45.3 - - + -
565A CYS* 5.2 0.7 - - - -
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Residues in contact with LEU 539 (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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195A ILE* 4.2 22.0 - - + -
202A LEU* 4.5 10.4 - - + +
220A GLN* 3.6 33.8 - - + +
223A TRP* 3.9 21.8 - - + +
224A ILE* 4.5 15.3 - - + -
417A LEU* 4.3 8.3 - - + -
534A ALA 4.0 0.4 + - - -
535A ILE* 3.9 22.4 - - + +
536A MET 2.9 7.9 + - - +
538A LEU* 1.3 79.7 - - - +
540A TYR* 1.3 70.1 + - + +
541A PHE 3.3 0.4 - - - -
542A ARG* 3.3 13.7 + - - +
543A PHE* 3.1 20.8 + - - +
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Residues in contact with TYR 540 (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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195A ILE* 4.4 14.8 - - + -
420A TRP* 3.5 55.7 + + + -
491A ASP* 4.9 0.5 + - - -
493A PHE* 3.7 44.3 - + + -
497A SER* 3.4 18.1 - - - +
535A ILE 5.2 2.0 + - - -
536A MET* 2.9 40.3 + - + +
537A HIS* 3.9 4.3 - - - +
539A LEU* 1.3 82.2 - - + +
541A PHE* 1.3 57.0 + - - +
543A PHE* 3.3 7.2 + - - +
544A PHE* 2.7 31.0 + - - +
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Residues in contact with PHE 541 (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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38A LEU* 5.9 0.2 - - + -
212A TRP* 4.0 11.9 - + - -
497A SER* 3.6 21.7 + - - +
499A TYR* 6.1 0.2 - + - -
500A TYR* 3.7 33.3 + + + -
524A VAL* 5.7 1.3 - - + -
527A TYR* 3.6 32.5 - + - -
537A HIS* 3.0 42.4 + + + -
538A LEU* 3.6 30.5 - - + -
540A TYR* 1.3 74.8 - - - +
542A ARG* 1.3 66.0 + - + +
544A PHE* 4.0 0.5 - - - +
545A HIS* 2.9 28.4 + - - +
559A PRO* 3.6 25.5 - - + +
560A ALA* 4.0 13.5 - - + -
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Residues in contact with ARG 542 (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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202A LEU* 3.1 53.2 + - + +
205A ASP* 3.7 10.7 - - - +
206A LEU* 3.7 14.5 - - - +
209A LEU* 3.8 3.8 - - - +
212A TRP* 3.5 31.4 - - + -
220A GLN* 2.8 30.0 + - - +
224A ILE* 5.4 0.2 - - - +
538A LEU 3.4 15.3 - - - +
539A LEU* 3.3 10.8 + - - +
540A TYR 3.3 0.4 - - - -
541A PHE* 1.3 76.6 - - + +
543A PHE* 1.3 66.0 + - - +
545A HIS* 3.3 3.8 + - - +
546A LYS* 3.2 30.0 + - - +
558A GLU* 2.9 41.8 + - - +
559A PRO* 3.9 16.1 - - + +
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Residues in contact with PHE 543 (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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148A LEU* 6.2 1.1 - - + -
193A ILE* 3.5 22.4 - - + -
194A LYS 4.3 2.0 - - - -
195A ILE* 3.7 50.5 - - + -
198A TYR* 3.9 27.1 - + + -
202A LEU* 3.8 13.6 - - + +
420A TRP* 3.6 33.9 - + - -
539A LEU 3.1 11.4 + - - +
540A TYR* 3.5 7.2 - - - +
542A ARG* 1.3 78.3 - - - +
544A PHE* 1.3 63.0 + - - +
546A LYS* 3.2 6.3 + - - +
547A LEU* 3.0 54.4 + - + +
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Residues in contact with PHE 544 (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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136A GLU* 5.3 2.2 - - + -
139A PHE* 3.6 36.6 - + - -
143A LEU* 5.2 1.8 - - + -
193A ILE* 5.3 2.9 - - + -
420A TRP* 4.0 22.0 - + - -
494A MET* 3.9 30.5 - - + -
497A SER* 3.5 30.7 - - - +
498A TRP* 3.7 39.3 - + + -
512A MET* 4.1 5.2 - - + -
540A TYR 2.7 18.2 + - - +
541A PHE 4.0 0.4 - - - +
543A PHE* 1.3 70.3 - - - +
545A HIS* 1.3 66.5 + - - +
547A LEU* 3.2 16.7 + - + +
548A MET* 2.9 32.8 + - + +
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Residues in contact with HIS 545 (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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500A TYR* 2.7 29.1 + + - +
522A LEU* 4.0 22.0 - - + +
541A PHE 2.9 16.2 + - - +
542A ARG 3.5 5.8 - - - +
543A PHE 3.3 0.2 - - - -
544A PHE* 1.3 76.0 - - - +
546A LYS* 1.3 57.0 + - - +
548A MET* 3.2 9.1 + - - +
549A ARG* 2.9 24.8 + - - +
554A VAL* 3.9 15.7 - - + +
556A SER* 3.1 43.8 + - - -
557A ASP 3.7 3.4 - - - -
558A GLU 3.5 22.8 + - - -
559A PRO* 3.6 23.4 - - + +
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Residues in contact with LYS 546 (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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198A TYR* 4.0 14.6 - - + -
201A GLU* 3.0 32.4 + - + +
202A LEU* 3.9 25.6 - - + -
205A ASP* 2.8 19.2 + - - -
542A ARG* 3.2 17.2 + - - +
543A PHE* 3.2 6.5 + - - +
545A HIS* 1.3 72.3 - - - +
547A LEU* 1.3 60.6 + - - +
549A ARG* 3.3 19.3 + - - +
550A ASP* 2.9 36.7 + - - -
557A ASP 2.6 32.2 + - - +
558A GLU* 2.7 26.6 + - - -
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Residues in contact with LEU 547 (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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139A PHE* 3.8 16.3 - - + -
143A LEU* 3.9 36.5 - - + +
146A LYS* 6.0 0.3 - - - -
148A LEU* 4.0 10.1 - - + -
193A ILE* 4.6 1.8 - - + -
198A TYR* 3.9 20.2 - - + +
543A PHE* 3.0 59.9 + - + +
544A PHE* 3.2 24.2 + - + +
546A LYS* 1.3 75.3 - - - +
548A MET* 1.3 56.8 + - - +
550A ASP* 3.3 6.1 + - + +
551A ALA* 3.1 26.3 + - - +
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Residues in contact with MET 548 (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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139A PHE* 4.0 18.4 - - + -
498A TRP* 3.8 23.3 - - + -
500A TYR* 3.4 25.8 - - + +
501A ALA* 4.0 14.1 - - + -
512A MET* 4.2 21.1 - - - -
513A LEU* 3.9 21.3 - - + -
544A PHE* 2.9 26.0 + - + +
545A HIS* 3.6 8.1 - - - +
547A LEU* 1.3 69.4 - - - +
549A ARG* 1.3 63.2 + - - +
551A ALA* 3.3 6.3 + - - +
553A MET* 2.9 45.6 + - + +
554A VAL* 4.0 9.2 - - + -
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Residues in contact with ARG 549 (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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201A GLU* 2.8 42.0 + - - -
545A HIS 2.9 14.4 + - - +
546A LYS* 3.6 17.5 - - - +
548A MET* 1.3 75.7 - - - +
550A ASP* 1.3 91.6 + - - +
552A GLY* 2.9 19.9 + - - -
554A VAL* 3.3 32.3 - - + +
555A ASN* 4.8 2.0 - - - -
556A SER 3.6 16.4 - - - +
557A ASP* 2.7 51.3 + - - +
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Residues in contact with ASP 550 (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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146A LYS* 4.0 18.0 - - + -
198A TYR* 2.4 42.9 + - - +
546A LYS 2.9 15.5 + - - +
547A LEU* 3.3 4.2 + - - +
548A MET 3.3 0.2 - - - -
549A ARG* 1.3 104.1 + - - +
551A ALA* 1.3 56.9 + - - +
552A GLY 3.3 1.2 + - - -
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Residues in contact with ALA 551 (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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139A PHE* 4.4 15.3 - - + -
142A GLU* 4.6 6.3 - - - +
146A LYS* 4.1 18.8 - - - +
547A LEU 3.1 15.0 + - - +
548A MET 3.8 4.7 - - - +
549A ARG 3.2 0.6 - - - -
550A ASP* 1.3 74.1 - - - +
552A GLY* 1.3 61.5 + - - +
553A MET* 3.2 19.8 + - + +
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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