Contacts of the helix formed by residues 553 - 562 (chain A) in PDB entry 6DWW
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 LYS 553 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A MET* 3.6 21.7 - - + +
461A LEU* 4.3 5.0 - - + +
462A GLU* 4.3 22.9 - - + +
518A VAL* 3.0 31.8 + - - -
519A SER 3.7 16.4 - - - -
520A PRO* 3.8 16.2 - - + +
523A GLU* 3.1 27.8 + - - +
552A PRO* 1.3 88.9 - - + +
554A LEU* 1.3 62.9 + - - +
556A LYS* 3.7 11.3 + - - +
557A LEU* 3.6 13.3 + - - +
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Residues in contact with LEU 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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434A PHE* 5.8 0.4 - - + -
435A PHE* 4.1 23.1 - - + -
458A MET* 3.6 32.3 - - + -
523A GLU* 2.8 27.0 + - + +
524A PHE* 4.2 25.4 - - + -
527A TYR* 4.1 23.6 - - + -
544A TRP* 3.8 27.4 - - + -
551A TYR* 4.4 6.5 - - + -
553A LYS* 1.3 75.0 - - - +
555A SER* 1.3 55.1 + - - +
556A LYS 3.0 5.2 - - - -
557A LEU* 3.0 6.4 + - + +
558A ALA* 2.8 25.6 + - - +
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Residues in contact with SER 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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544A TRP* 3.4 43.1 - - - -
547A ASN 4.4 0.7 - - - -
548A SER* 3.3 16.2 - - - -
551A TYR* 2.3 32.9 + - - +
552A PRO 3.6 3.6 + - - -
554A LEU* 1.3 78.8 - - - +
556A LYS* 1.3 58.8 + - - +
558A ALA* 3.8 1.3 - - - +
559A LEU* 3.3 33.1 + - - +
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Residues in contact with LYS 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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172A LYS* 5.8 2.2 - - - +
461A LEU* 4.4 16.7 - - + +
465A ASN* 3.3 28.8 - - - +
548A SER* 6.4 0.9 - - - -
552A PRO 3.1 21.3 - - - +
553A LYS* 3.7 11.6 + - - +
554A LEU 3.0 0.6 - - - -
555A SER* 1.3 77.7 + - - +
557A LEU* 1.3 64.7 + - - +
559A LEU* 3.6 3.4 + - - +
560A SER* 3.0 22.7 + - - -
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Residues in contact with LEU 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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173A ASP* 5.4 1.1 - - - +
435A PHE* 3.8 16.6 - - + -
453A PHE* 5.1 2.0 - - + -
454A CYS* 3.4 45.8 - - + +
457A LYS* 3.5 27.1 - - + -
458A MET* 3.9 24.2 - - + -
461A LEU* 3.9 11.3 - - + +
553A LYS 3.6 2.8 + - - +
554A LEU* 3.0 7.5 + - + +
556A LYS* 1.3 77.0 - - - +
558A ALA* 1.3 62.6 + - - +
560A SER* 3.2 8.1 + - - +
561A LEU* 3.0 39.0 + - + +
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Residues in contact with ALA 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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435A PHE* 3.5 33.4 - - + -
544A TRP* 3.8 35.2 - - + +
554A LEU 2.8 15.2 + - - +
555A SER 4.0 0.7 - - - +
556A LYS 3.3 0.2 - - - -
557A LEU* 1.3 77.6 - - - +
559A LEU* 1.3 56.8 + - - +
561A LEU* 2.9 5.5 + - - +
562A LEU* 2.8 32.9 + - - +
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Residues in contact with LEU 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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199A HIS* 3.5 41.3 - - + +
541A MET* 4.0 33.0 - - + +
544A TRP* 3.8 29.6 - - + +
545A ASN* 3.6 15.7 - - - +
548A SER* 6.4 1.1 - - - -
555A SER* 3.3 18.4 + - - +
556A LYS* 4.3 3.1 - - - +
558A ALA* 1.3 78.6 - - - +
560A SER* 1.3 59.2 + - - +
562A LEU* 3.9 16.5 - - + +
563A SER* 3.6 21.0 + - - -
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Residues in contact with SER 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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172A LYS 5.5 1.3 - - - -
173A ASP* 3.5 15.9 + - - -
174A GLY* 3.7 13.9 - - - -
244A LYS* 2.9 34.1 + - - -
461A LEU* 5.8 3.4 - - - -
556A LYS 3.0 16.3 + - - -
557A LEU* 3.3 15.0 - - - +
559A LEU* 1.3 77.7 - - - +
561A LEU* 1.3 63.5 + - - +
563A SER* 3.3 15.2 + - - -
564A ILE* 3.9 6.2 - - - +
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Residues in contact with LEU 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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173A ASP* 6.2 0.2 - - - +
382A LEU* 4.1 9.7 - - + +
428A TRP* 3.5 62.6 - - + +
431A THR* 4.1 17.3 - - + -
432A ALA* 4.3 12.3 - - + +
435A PHE* 4.2 10.8 - - + -
453A PHE* 4.4 7.6 - - + -
457A LYS* 5.6 1.1 - - + -
557A LEU* 3.0 33.8 + - + +
558A ALA 2.9 9.4 + - - +
560A SER* 1.3 81.6 - - - +
562A LEU* 1.3 60.8 + - + +
563A SER 3.2 3.5 + - - -
564A ILE* 3.4 23.4 + - + +
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Residues in contact with LEU 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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204A LEU* 4.8 2.3 - - - +
380A PRO* 3.5 33.2 - - + +
381A SER 4.5 2.0 + - - -
382A LEU* 5.9 2.5 - - - +
383A CYS* 4.0 24.0 - - + +
432A ALA* 4.0 24.7 - - + +
435A PHE* 4.2 11.0 - - + +
540A VAL* 3.8 17.9 - - + +
541A MET* 4.8 5.7 - - + +
544A TRP* 3.6 35.7 - - + +
558A ALA 2.8 19.6 + - - +
559A LEU* 3.8 17.9 + - + -
560A SER 3.4 0.4 - - - -
561A LEU* 1.3 77.2 - - + +
563A SER* 1.3 57.8 + - - +
564A ILE 3.4 2.1 - - - +
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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