Contacts of the helix formed by residues 549 - 563 (chain A) in PDB entry 6WG4
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 549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547A VAL* 3.3 7.4 - - - +
548A ASP* 1.3 90.1 + - - +
550A GLU* 1.3 63.2 + - - +
551A LYS* 3.4 8.5 + - - +
552A THR* 3.0 40.2 + - - +
553A GLY 3.2 5.4 + - - -
572A PRO* 3.6 6.3 - - - -
574A ASP* 4.1 15.3 - - - -
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Residues in contact with GLU 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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549A SER* 1.3 72.1 - - - +
551A LYS* 1.3 63.7 + - - +
553A GLY* 3.2 1.8 + - - +
554A ARG* 3.0 31.2 + - - +
572A PRO* 3.5 27.7 - - + +
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Residues in contact with LYS 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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549A SER* 3.3 8.6 + - - +
550A GLU* 1.3 84.9 - - - +
552A THR* 1.3 55.2 + - + +
554A ARG* 3.1 11.7 + - + +
555A ASP* 2.7 73.4 + - - +
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Residues in contact with THR 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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511A TYR* 5.3 9.9 - - + -
514A SER* 4.1 14.3 + - - +
515A VAL* 5.0 1.0 - - - +
547A VAL* 3.6 12.2 - - - +
548A ASP* 3.0 28.5 + - - +
549A SER* 3.0 23.4 + - - +
551A LYS* 1.3 77.7 - - + +
553A GLY* 1.3 61.0 + - - +
555A ASP* 3.4 12.0 - - - +
556A CYS* 2.9 36.3 + - - -
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Residues in contact with GLY 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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547A VAL* 4.3 12.6 - - - -
549A SER 3.2 6.8 + - - -
550A GLU* 3.2 7.9 + - - -
551A LYS 3.2 0.8 - - - -
552A THR* 1.3 81.8 + - - +
554A ARG* 1.3 56.8 + - - +
556A CYS* 3.3 4.3 + - - +
557A ILE* 2.9 33.2 + - - +
570A PHE* 4.1 20.3 - - - -
572A PRO* 5.5 1.6 - - - -
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Residues in contact with ARG 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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550A GLU* 3.0 19.9 + - + +
551A LYS* 3.6 13.2 - - + +
553A GLY* 1.3 72.6 - - - +
555A ASP* 1.3 62.6 + - - +
557A ILE* 3.2 35.5 + - - +
558A GLN* 2.9 74.2 + - - +
561A LYS* 5.2 4.4 - - - +
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Residues in contact with ASP 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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511A TYR* 3.9 34.3 + - + +
551A LYS* 2.7 58.2 + - - +
552A THR* 3.4 12.6 - - - +
553A GLY 3.2 0.2 - - - -
554A ARG* 1.3 75.0 - - - +
556A CYS* 1.3 56.9 + - - +
558A GLN* 3.4 8.8 + - - +
559A TYR* 3.1 23.0 + - - +
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Residues in contact with CYS 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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507A ILE* 3.8 19.1 - - + -
511A TYR* 3.9 18.2 - - - -
515A VAL* 3.7 30.1 - - - -
547A VAL* 4.9 0.2 - - - -
552A THR 2.9 22.0 + - - +
553A GLY 3.9 0.2 - - - +
555A ASP* 1.3 74.2 - - - +
557A ILE* 1.3 65.8 + - - +
558A GLN 3.3 0.2 - - - -
559A TYR* 3.3 7.0 + - - +
560A ILE* 3.1 28.9 + - - +
570A PHE* 3.5 29.2 - - + -
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Residues in contact with ILE 557 (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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553A GLY 2.9 22.2 + - - +
554A ARG* 3.2 32.3 + - - +
556A CYS* 1.3 77.1 - - - +
558A GLN* 1.3 55.8 + - - +
560A ILE* 3.4 4.6 + - + +
561A LYS* 2.9 31.6 + - + +
567A PRO* 5.7 5.6 - - + -
568A GLU 3.8 14.8 - - - +
570A PHE* 3.6 27.4 - - + -
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Residues in contact with GLN 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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554A ARG* 2.9 46.4 + - - +
555A ASP* 3.7 9.0 - - - +
556A CYS 3.3 0.2 - - - -
557A ILE* 1.3 77.2 - - - +
559A TYR* 1.3 62.1 + - - +
561A LYS* 3.2 38.9 + - - +
562A GLU* 3.2 41.1 + - - +
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Residues in contact with TYR 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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503A ILE* 4.5 10.5 - - + -
506A SER* 2.6 32.8 + - - -
507A ILE* 3.6 24.0 - - + -
510A LEU* 3.6 28.0 - - + -
511A TYR* 5.1 5.2 - + + +
555A ASP 3.1 13.6 + - - +
556A CYS* 3.6 11.7 - - - +
557A ILE 3.2 0.4 - - - -
558A GLN* 1.3 74.9 - - - +
560A ILE* 1.3 65.0 + - + +
562A GLU* 2.9 28.5 + - - +
563A GLN* 3.2 55.4 + - + +
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Residues in contact with ILE 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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500A LYS* 4.8 1.1 - - + -
503A ILE* 4.2 27.1 - - + -
504A MET* 6.3 1.3 - - + -
507A ILE* 5.1 6.7 - - + -
556A CYS* 3.1 16.9 + - + +
557A ILE* 4.1 4.3 - - + +
559A TYR* 1.3 80.5 - - + +
561A LYS* 1.3 61.7 + - - +
563A GLN* 3.2 13.3 + - - +
564A ARG 3.6 0.5 + - - -
565A GLY* 3.4 33.7 + - - +
566A GLU 3.4 22.7 - - - +
567A PRO* 4.7 3.4 - - + -
568A GLU* 3.9 28.7 - - + +
570A PHE* 4.2 19.5 - - + -
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Residues in contact with LYS 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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554A ARG* 5.2 3.6 - - - +
557A ILE* 2.9 22.0 + - + +
558A GLN* 3.2 34.3 + - - +
560A ILE* 1.3 75.8 - - - +
562A GLU* 1.3 63.3 + - + +
564A ARG* 4.2 7.4 + - - -
565A GLY 5.4 0.9 - - - -
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Residues in contact with GLU 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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558A GLN* 3.2 37.9 + - + +
559A TYR* 2.9 22.4 + - - +
561A LYS* 1.3 83.1 - - + +
563A GLN* 1.3 67.0 + - + +
564A ARG 3.5 1.6 + - - -
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Residues in contact with GLN 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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499A ARG* 2.4 42.4 + - - +
503A ILE* 4.2 13.0 - - + +
559A TYR* 3.2 63.4 + - + +
560A ILE* 3.2 4.4 + - - +
562A GLU* 1.3 87.2 + - - +
564A ARG* 1.3 58.3 + - - +
565A GLY 3.0 4.0 - - - -
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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