Contacts of the helix formed by residues 548 - 565 (chain A) in PDB entry 4YOZ
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 548 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A SER* 4.6 3.5 + - - -
396A ARG* 3.7 17.3 - - - +
546A GLY 3.5 3.0 + - - -
547A LEU* 1.3 76.2 - - - +
549A ARG* 1.3 59.9 + - - +
550A ASP* 3.6 8.0 + - - +
551A MET* 3.1 39.5 + - - +
552A VAL* 2.9 28.3 + - - +
1002A SO4 3.4 17.9 - - - -
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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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548A SER* 1.3 73.2 - - - +
550A ASP* 1.3 61.1 + - - +
552A VAL* 3.4 7.6 + - - +
553A LYS* 2.9 41.7 + - - +
1002A SO4 2.4 46.1 + - - +
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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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393A SER* 5.0 6.5 - - - +
511A PHE* 3.7 15.6 - - + -
548A SER* 3.2 8.5 + - - +
549A ARG* 1.3 77.2 - - - +
551A MET* 1.3 60.3 + - - +
553A LYS* 3.5 21.9 + - - +
554A HIS* 3.0 28.1 + - - +
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Residues in contact with MET 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A SER* 3.2 44.4 - - - +
396A ARG* 3.8 21.8 - - + -
397A LEU* 4.2 9.4 - - + +
400A ILE* 4.9 1.8 - - - -
508A ILE* 4.6 19.4 - - + +
511A PHE* 4.0 18.2 - - + -
512A ALA* 4.7 5.4 - - + -
547A LEU* 3.9 28.3 - - + -
548A SER* 3.1 37.7 + - - +
550A ASP* 1.3 76.1 - - - +
552A VAL* 1.3 61.8 + - - +
554A HIS* 3.2 4.5 + - - +
555A LEU* 3.0 28.7 + - - +
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Residues in contact with VAL 552 (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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541A ILE* 4.1 29.8 - - + +
544A GLU 5.8 0.7 - - - +
547A LEU* 4.1 23.1 - - + +
548A SER 2.9 20.5 + - - +
549A ARG* 3.8 7.2 - - - +
551A MET* 1.3 72.9 - - - +
553A LYS* 1.3 61.0 + - - +
555A LEU* 3.2 9.2 + - - +
556A ASN* 2.9 45.7 + - - +
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Residues in contact with LYS 553 (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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549A ARG* 2.9 26.7 + - - +
550A ASP* 3.5 26.2 - - - +
552A VAL* 1.3 79.0 - - - +
554A HIS* 1.3 55.7 + - - +
556A ASN* 3.3 9.7 + - - +
557A SER* 2.8 36.5 + - - +
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Residues in contact with HIS 554 (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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507A GLU* 2.6 37.6 + - + -
508A ILE* 5.6 2.2 - - + -
511A PHE* 3.4 54.3 - + + +
518A THR* 6.3 2.7 - - + -
519A PHE* 5.2 2.7 - - + -
550A ASP 3.0 14.4 + - - +
551A MET 3.2 8.7 + - - +
553A LYS* 1.3 76.0 - - - +
555A LEU* 1.3 68.6 + - + +
557A SER* 3.0 11.5 + - - -
558A ILE* 3.0 40.1 + - + +
561A GLN* 5.9 0.9 - - - -
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Residues in contact with LEU 555 (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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504A CYS* 3.7 24.2 - - - -
507A GLU* 5.0 4.5 - - + -
508A ILE* 3.5 33.2 - - + -
537A ILE* 3.5 24.8 - - + +
540A VAL* 4.1 8.7 - - + -
541A ILE* 4.0 17.0 - - + -
547A LEU* 3.8 22.9 - - + -
551A MET 3.0 17.7 + - - +
552A VAL* 3.2 6.7 + - - +
554A HIS* 1.3 77.2 - - + +
556A ASN* 1.3 62.9 + - - +
558A ILE* 3.3 21.7 - - + +
559A GLU 3.2 17.0 + - - -
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Residues in contact with ASN 556 (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 ILE* 4.9 1.7 - - - +
541A ILE* 3.4 18.6 - - - +
552A VAL* 2.9 37.1 + - - +
553A LYS* 3.6 8.0 - - + +
555A LEU* 1.3 77.3 - - - +
557A SER* 1.3 60.6 + - - +
559A GLU* 3.4 15.9 + - - +
560A GLU* 3.0 36.1 + - - +
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Residues in contact with SER 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A LYS* 2.8 26.7 + - - +
554A HIS* 3.0 15.1 + - - -
556A ASN* 1.3 76.9 - - - +
558A ILE* 1.3 58.8 + - - +
560A GLU* 3.3 11.5 + - - +
561A GLN* 2.9 39.5 + - - +
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Residues in contact with ILE 558 (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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504A CYS* 5.5 0.2 - - - -
507A GLU* 3.9 26.5 - - + -
519A PHE* 3.7 42.1 - - + -
533A PHE* 4.6 5.8 - - + -
537A ILE* 3.9 12.8 - - + -
554A HIS* 3.0 34.2 + - + +
555A LEU* 3.3 31.2 - - + +
557A SER* 1.3 74.9 - - - +
559A GLU* 1.3 63.7 + - - +
561A GLN* 3.6 17.0 - - - +
562A ILE* 3.1 29.0 + - - +
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Residues in contact with GLU 559 (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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534A TYR* 4.1 22.7 - - + +
537A ILE* 3.6 24.4 - - + +
538A GLU* 4.6 7.8 + - - +
555A LEU 3.2 17.5 + - - +
556A ASN* 3.7 15.4 - - - +
557A SER 3.2 0.2 - - - -
558A ILE* 1.3 76.4 - - - +
560A GLU* 1.3 62.4 + - - +
562A ILE* 3.1 7.0 + - - +
563A LEU* 2.9 46.2 + - + +
794A LYS* 3.3 36.0 + - - -
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Residues in contact with GLU 560 (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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556A ASN* 3.0 25.3 + - + +
557A SER* 3.4 11.0 - - - +
559A GLU* 1.3 81.1 - - + +
561A GLN* 1.3 56.7 + - - +
563A LEU* 3.7 9.4 - - + +
564A GLU* 2.8 37.2 + - - +
798A LEU* 3.8 26.5 - - + +
802A ARG* 3.3 22.4 + - - +
872A PRO* 6.1 1.2 - - - +
873A GLN* 4.9 6.3 - - + +
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Residues in contact with GLN 561 (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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518A THR* 6.2 1.2 - - - +
519A PHE* 3.7 27.9 + - + +
520A PRO* 4.9 1.6 - - - +
554A HIS* 5.9 1.0 - - - -
557A SER* 2.9 27.6 + - - +
558A ILE* 3.6 24.4 - - - +
559A GLU 3.2 0.2 - - - -
560A GLU* 1.3 74.8 - - - +
562A ILE* 1.3 63.2 + - - +
564A GLU* 3.6 17.9 - - - +
565A SER* 3.1 29.8 + - - +
566A LEU* 3.2 15.1 + - + +
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Residues in contact with ILE 562 (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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519A PHE* 3.7 20.6 - - + -
530A PRO* 3.4 39.5 - - + +
533A PHE* 3.7 27.6 - - + -
534A TYR* 3.7 30.3 - - + -
537A ILE* 4.5 0.4 - - + -
558A ILE 3.1 17.5 + - - +
559A GLU* 3.1 7.7 + - - +
561A GLN* 1.3 78.0 - - - +
563A LEU* 1.3 65.4 + - + +
564A GLU 3.4 0.5 + - - -
565A SER 3.7 0.5 + - - -
566A LEU* 3.4 13.9 + - + -
567A ALA* 3.0 33.8 + - + +
791A PHE* 5.2 0.2 - - + -
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Residues in contact with LEU 563 (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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534A TYR* 4.3 15.0 - - + -
559A GLU* 2.9 40.6 + - + +
560A GLU* 3.8 5.8 - - + +
562A ILE* 1.3 77.5 - - - +
564A GLU* 1.3 52.5 + - - +
568A TRP* 2.7 27.5 + - - -
791A PHE* 3.7 32.1 - - + -
794A LYS* 3.7 41.5 - - + +
795A VAL* 4.2 15.8 - - + +
798A LEU* 4.0 18.2 - - + -
840A LEU* 4.2 5.7 - - - +
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Residues in contact with GLU 564 (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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560A GLU* 2.8 25.2 + - - +
561A GLN* 3.5 23.0 - - - +
563A LEU* 1.3 75.8 - - - +
565A SER* 1.3 66.2 + - - +
568A TRP* 3.8 6.1 - - - -
798A LEU* 4.6 1.6 - - + -
802A ARG* 2.8 43.2 + - - +
839A HIS* 3.4 28.3 + - + +
840A LEU* 2.7 40.0 + - + +
873A GLN* 3.7 15.3 - - - +
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Residues in contact with SER 565 (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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561A GLN* 3.1 10.3 + - - +
562A ILE 3.9 0.2 - - - -
563A LEU 3.6 0.6 - - - -
564A GLU* 1.3 88.9 + - - +
566A LEU* 1.3 79.9 + - - +
567A ALA 3.3 2.9 - - - -
568A TRP* 2.8 29.6 + - - +
569A SER* 3.7 3.8 + - - -
837A ASP* 5.8 0.5 - - - -
838A ARG 3.8 15.8 + - - +
839A HIS* 4.2 13.0 - - - -
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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