Contacts of the helix formed by residues 524 - 542 (chain A) in PDB entry 2PZ5
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 THR 524 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A LEU* 5.3 0.3 - - - +
522A ASP 4.3 3.8 - - - +
523A ALA* 1.3 79.5 - - - +
525A GLU* 1.3 64.8 + - - +
526A LYS* 3.3 6.2 + - - +
527A ASP* 3.1 41.2 + - - +
528A LEU* 3.3 11.4 + - - +
663B GLY 3.5 11.6 + - - -
664B ARG* 3.5 27.1 - - + +
665B LEU 3.6 17.0 - - - -
666B PRO* 4.0 6.7 - - + -
667B VAL* 4.0 5.3 - - - +
709B VAL* 5.9 0.7 - - - +
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Residues in contact with GLU 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A THR* 1.3 72.8 - - - +
526A LYS* 1.3 66.4 + - - +
528A LEU* 3.1 20.3 + - + +
529A SER* 3.1 15.0 + - - +
659B LYS 4.5 1.8 - - - +
662B ASN 5.0 0.7 - - - +
663B GLY* 3.5 17.7 + - - +
665B LEU 4.2 2.8 + - - +
667B VAL* 3.9 11.8 - - + +
670B MET* 6.0 0.4 - - - -
675B LEU* 3.3 31.7 - - + +
678B ARG* 2.8 44.3 + - - -
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Residues in contact with LYS 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A SO4 3.7 16.1 + - - -
524A THR* 3.3 4.0 - - - +
525A GLU* 1.3 75.4 - - - +
527A ASP* 1.3 60.8 + - - +
529A SER* 3.1 17.5 + - - +
530A ASP* 2.9 39.3 + - - -
649A ARG* 4.9 3.2 - - - +
664A ARG* 3.4 43.9 - - - +
663B GLY* 2.9 23.5 + - - +
664B ARG* 4.6 11.2 - - + -
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Residues in contact with ASP 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A LEU* 3.5 21.9 - - + +
520A LYS* 6.0 1.9 - - - +
522A ASP 4.7 0.3 - - - +
523A ALA* 3.5 9.5 - - + +
524A THR* 3.1 45.3 + - - +
525A GLU 3.2 0.2 - - - -
526A LYS* 1.3 78.9 - - - +
528A LEU* 1.3 61.6 + - - +
530A ASP* 3.6 11.8 + - - +
531A LEU* 3.1 18.2 + - - +
664A ARG* 5.7 0.7 + - - -
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Residues in contact with LEU 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A LEU* 6.3 0.7 - - + -
519A LEU* 3.5 30.5 - - + +
524A THR 3.3 5.9 + - - +
525A GLU* 3.1 16.3 + - + +
527A ASP* 1.3 79.3 - - - +
529A SER* 1.3 61.5 + - - +
531A LEU* 3.2 3.0 + - + +
532A VAL* 3.0 45.0 + - + +
560A LEU* 4.8 9.9 - - + -
709B VAL* 5.6 1.6 - - + -
710B GLU* 4.3 30.7 - - + +
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Residues in contact with SER 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A GLU* 3.1 7.0 + - - +
526A LYS* 3.1 34.8 + - - +
528A LEU* 1.3 79.8 - - - +
530A ASP* 1.3 56.9 + - - +
532A VAL* 3.8 8.0 - - - +
533A SER* 2.8 30.9 + - - -
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Residues in contact with ASP 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A LYS* 2.9 30.7 + - - +
527A ASP* 3.7 11.9 - - - +
529A SER* 1.3 75.9 + - - +
531A LEU* 1.3 59.8 + - - +
533A SER* 3.3 6.5 + - - -
534A GLU* 2.8 32.9 + - - +
646A GLY* 4.0 22.1 - - - +
647A LEU* 5.1 1.0 - - - +
649A ARG* 4.6 5.0 + - - -
664A ARG* 2.8 43.4 + - - -
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Residues in contact with LEU 531 (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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517A LYS* 4.0 31.2 - - + +
518A MET* 4.0 24.9 - - - +
519A LEU* 4.0 23.8 - - + +
527A ASP 3.1 14.4 + - - +
528A LEU* 3.2 4.7 + - - +
530A ASP* 1.3 77.4 - - - +
532A VAL* 1.3 64.2 + - - +
534A GLU* 3.3 12.6 + - - +
535A MET* 3.0 22.0 + - - +
560A LEU* 4.0 23.8 - - + +
562A VAL* 3.8 20.4 - - + -
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Residues in contact with VAL 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A LEU* 4.4 28.3 - - + -
528A LEU* 3.0 31.1 + - + +
529A SER* 3.8 7.2 - - - +
531A LEU* 1.3 75.0 - - - +
533A SER* 1.3 65.6 + - - +
535A MET* 3.1 9.4 + - - +
536A GLU* 2.9 36.0 + - + +
560A LEU* 3.8 22.9 - - + -
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Residues in contact with SER 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A SER 2.8 18.9 + - - -
530A ASP* 3.5 8.3 - - - -
532A VAL* 1.3 78.7 - - - +
534A GLU* 1.3 56.8 + - - +
536A GLU* 3.3 6.5 + - - +
537A MET* 2.8 35.8 + - - +
645A PHE 5.3 0.9 + - - -
646A GLY 5.4 1.5 + - - -
648A ALA 4.0 6.2 + - - -
649A ARG* 3.8 24.3 + - - -
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Residues in contact with GLU 534 (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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300A ACP 4.8 0.5 + - - -
517A LYS* 2.7 46.7 + - - +
530A ASP 2.8 20.1 + - - +
531A LEU* 3.4 14.5 - - + +
532A VAL 3.2 0.2 - - - -
533A SER* 1.3 75.0 + - - +
535A MET* 1.3 64.3 + - - +
537A MET* 3.3 2.4 + - - +
538A MET* 3.1 39.2 + - - +
562A VAL* 5.7 3.9 - - + +
564A VAL* 6.2 0.2 - - - +
644A ASP* 4.3 1.6 - - - -
645A PHE* 3.6 36.5 + - + +
646A GLY* 3.5 18.6 + - - -
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Residues in contact with MET 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A LEU* 5.7 3.1 - - - -
531A LEU 3.0 13.3 + - - +
532A VAL* 3.1 12.1 + - - +
534A GLU* 1.3 76.9 - - - +
536A GLU* 1.3 75.7 + - - +
538A MET* 3.3 8.4 + - - +
539A LYS* 3.1 42.2 + - + +
550A LEU* 4.0 5.3 - - + +
553A ALA* 3.0 34.3 - - + -
555A THR* 3.7 11.7 - - + -
560A LEU* 3.4 31.0 - - + -
562A VAL* 3.6 28.9 - - + +
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Residues in contact with GLU 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ASP* 5.3 0.2 - - - +
532A VAL* 2.9 30.5 + - + +
533A SER* 3.8 6.5 - - - +
535A MET* 1.3 82.7 - - - +
537A MET* 1.3 66.6 + - + +
539A LYS* 2.8 42.9 + - - +
540A MET* 3.0 23.1 + - - +
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Residues in contact with MET 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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533A SER* 2.8 30.8 + - - +
534A GLU* 3.7 5.8 - - - +
536A GLU* 1.3 72.7 - - + +
538A MET* 1.3 58.4 + - - +
540A MET* 3.3 31.3 + - + +
541A ILE* 2.9 35.9 + - + +
622A CYS* 3.4 32.8 - - - -
645A PHE* 4.6 8.3 - - + +
648A ALA* 3.5 34.5 - - + +
649A ARG* 3.7 20.2 - - - +
650A ASP* 4.1 4.0 - - - -
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Residues in contact with MET 538 (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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474A TRP* 5.5 1.4 - - - -
534A GLU* 3.1 29.2 + - - +
535A MET 3.6 7.4 - - - +
536A GLU 3.2 0.2 - - - -
537A MET* 1.3 76.1 - - - +
539A LYS* 1.3 63.8 + - - +
541A ILE* 3.7 7.6 + - - +
542A GLY* 3.6 16.8 + - - +
547A ILE* 5.5 1.1 - - + -
548A ILE* 3.4 44.4 - - + +
550A LEU* 4.0 29.2 - - + +
562A VAL* 4.8 4.9 - - - -
564A VAL* 3.9 26.7 - - + -
645A PHE* 4.2 26.2 - - + -
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Residues in contact with LYS 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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471A ASP* 2.8 39.0 + - - +
474A TRP* 3.6 43.8 - - + +
535A MET* 3.1 33.3 + - - +
536A GLU* 2.8 44.6 + - - +
538A MET* 1.3 79.6 - - - +
540A MET* 1.3 64.3 + - - +
541A ILE 3.5 0.2 + - - -
542A GLY* 3.6 8.1 + - - -
550A LEU* 3.7 12.1 - - + -
553A ALA* 5.9 0.4 - - - -
555A THR* 5.9 1.8 - - - +
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Residues in contact with MET 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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536A GLU 3.0 12.0 + - - +
537A MET* 3.5 40.6 - - + +
539A LYS* 1.3 80.2 - - - +
541A ILE* 1.3 75.3 + - + +
542A GLY* 3.4 1.2 + - - -
620A GLN* 3.5 32.5 - - + +
621A LYS 4.1 6.7 - - - +
622A CYS* 3.7 6.3 - - + -
650A ASP* 3.8 23.3 - - - +
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Residues in contact with ILE 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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537A MET* 2.9 27.4 + - + +
538A MET* 4.0 7.4 - - - +
539A LYS 3.4 0.2 - - - -
540A MET* 1.3 88.8 - - + +
542A GLY* 1.3 62.7 + - - +
547A ILE* 3.9 22.9 - - + -
616A TYR* 2.7 42.6 + - + -
617A LEU* 3.3 16.2 - - + -
620A GLN* 3.4 17.1 - - + +
622A CYS* 3.2 40.6 - - + -
645A PHE* 4.5 7.6 - - + -
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Residues in contact with GLY 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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538A MET 3.6 10.9 + - - +
539A LYS 3.6 7.1 + - - -
540A MET 3.4 3.7 - - - -
541A ILE* 1.3 93.5 - - - +
543A LYS* 1.3 62.8 - - - -
544A HIS 3.9 0.9 + - - -
547A ILE* 4.9 5.7 - - - +
616A TYR* 3.8 6.2 - - - -
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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