Contacts of the helix formed by residues 510 - 521 (chain A) in PDB entry 4CQ8
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 510 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509A PHE* 1.3 78.1 - - - +
511A GLY* 1.3 64.0 + - - +
512A LEU* 3.4 12.3 + - - +
513A ASP* 3.1 29.2 + - - +
514A ALA* 3.0 18.2 + - - +
542A ILE* 3.5 14.2 - - - +
545A GLU* 3.3 14.6 - - - -
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Residues in contact with GLY 511 (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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510A SER* 1.3 73.2 - - - +
512A LEU* 1.4 56.0 + - - +
514A ALA* 3.3 4.0 + - - +
515A LEU* 2.9 30.0 + - - +
542A ILE* 3.8 7.7 - - - +
545A GLU* 3.0 30.9 + - - +
546A LEU* 3.9 19.3 - - - +
549A LEU* 3.6 8.3 - - - +
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Residues in contact with LEU 512 (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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510A SER* 3.2 10.7 - - - +
511A GLY* 1.4 72.0 - - - +
513A ASP* 1.4 66.0 + - - +
515A LEU* 3.4 3.7 + - + +
516A GLU* 3.1 41.2 + - + +
545A GLU* 5.3 0.2 - - - +
549A LEU* 3.5 22.4 - - + +
553A ARG* 3.5 28.9 - - - +
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Residues in contact with ASP 513 (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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270A ARG* 5.2 2.8 + - - -
482A LYS* 3.0 36.2 + - + +
507A GLY 3.5 4.9 - - - +
508A ILE* 3.9 10.5 - - + -
509A PHE* 2.9 36.0 + - - +
510A SER* 3.1 27.1 + - - +
512A LEU* 1.4 77.6 - - - +
514A ALA* 1.4 62.4 + - - +
516A GLU* 3.4 12.2 + - - +
517A LYS* 3.2 26.7 + - - +
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Residues in contact with ALA 514 (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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221A PHE* 3.6 36.8 - - + -
508A ILE* 3.9 9.8 - - + +
510A SER 3.0 12.2 + - - +
511A GLY* 3.5 10.1 - - - +
513A ASP* 1.4 73.2 - - - +
515A LEU* 1.3 64.4 + - - +
517A LYS* 3.2 5.6 + - - +
518A ILE* 3.0 28.6 + - - +
525A CYS* 4.1 9.3 - - - -
546A LEU* 4.6 6.7 - - + -
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Residues in contact with LEU 515 (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 GLY 2.9 16.7 + - - +
512A LEU* 3.4 5.4 + - + +
514A ALA* 1.3 75.6 - - - +
516A GLU* 1.4 57.3 + - - +
518A ILE* 3.3 7.2 + - + +
519A GLU* 2.8 55.8 + - + +
546A LEU* 4.1 10.9 - - + +
549A LEU* 3.7 31.9 - - + +
550A LEU* 4.2 12.6 - - + -
553A ARG* 3.8 31.0 - - + +
555A TYR* 4.2 5.4 - - + -
561A ALA* 4.0 19.7 - - + -
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Residues in contact with GLU 516 (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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482A LYS* 2.8 37.7 + - - +
486A THR* 4.2 16.2 + - + +
512A LEU* 3.1 31.9 + - + +
513A ASP* 3.4 11.3 - - - +
514A ALA 3.3 0.2 - - - -
515A LEU* 1.4 76.0 - - - +
517A LYS* 1.4 60.6 + - - +
519A GLU* 4.0 9.2 - - - +
520A ALA* 3.1 24.1 + - - +
565A LYS* 5.8 0.7 - - - +
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Residues in contact with LYS 517 (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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482A LYS* 3.3 10.7 + - - -
485A SER* 2.8 31.5 + - - -
486A THR* 3.1 29.0 + - - +
489A ILE* 3.7 18.4 - - + +
504A ALA* 3.6 19.7 - - + -
505A SER 4.6 1.2 + - - -
506A GLY* 2.9 21.9 + - - +
508A ILE* 3.7 26.9 - - + -
513A ASP 3.2 13.2 + - - +
514A ALA* 3.2 7.7 + - - +
516A GLU* 1.4 75.5 - - - +
518A ILE* 1.3 60.1 + - - +
520A ALA* 3.3 8.9 + - - +
521A GLY 3.2 6.8 + - - -
522A ALA* 3.0 23.6 + - + +
525A CYS* 4.3 3.8 - - - -
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Residues in contact with ILE 518 (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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220A PRO* 4.9 3.4 - - + -
514A ALA 3.0 25.6 + - - +
515A LEU* 3.7 9.4 - - + +
517A LYS* 1.3 75.0 - - - +
519A GLU* 1.3 57.3 + - - +
521A GLY 3.0 9.0 + - - -
522A ALA 3.3 23.9 + - - +
523A SER 5.0 3.1 - - - -
525A CYS* 4.4 17.3 - - - -
546A LEU* 4.2 14.4 - - + -
558A LEU* 3.7 35.7 - - + +
561A ALA* 3.8 15.3 - - + -
562A ILE* 3.4 28.7 - - + +
563A GLY 2.9 20.3 + - - -
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Residues in contact with GLU 519 (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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515A LEU* 2.8 46.8 + - + +
516A GLU* 4.2 7.1 - - - +
518A ILE* 1.3 71.7 - - - +
520A ALA* 1.3 56.8 + - - +
553A ARG* 4.6 11.2 + - - +
555A TYR* 2.7 33.8 + - - +
561A ALA 3.4 18.2 - - - +
563A GLY* 3.1 12.1 - - - +
564A ARG* 3.9 3.1 - - + +
565A LYS* 2.9 40.5 + - + +
566A HIS* 3.7 0.2 - - - -
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Residues in contact with ALA 520 (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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486A THR* 4.1 13.9 - - + +
489A ILE* 3.6 19.9 - - + +
490A CYS* 3.6 25.6 - - - -
493A TYR* 3.7 4.0 - - - +
516A GLU 3.1 19.4 + - - +
517A LYS* 3.3 8.7 - - - +
518A ILE 3.2 0.2 - - - -
519A GLU* 1.3 76.0 - - - +
521A GLY* 1.3 55.5 + - - +
565A LYS* 4.4 5.1 - - + +
566A HIS* 2.7 27.5 + - - -
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Residues in contact with GLY 521 (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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489A ILE* 4.0 6.1 - - - -
493A TYR* 3.8 30.8 - - - -
501A PRO* 5.7 0.5 - - - +
502A ILE* 3.8 12.6 + - - +
517A LYS 3.2 0.2 + - - -
518A ILE 3.0 8.0 + - - -
519A GLU 3.2 0.8 - - - -
520A ALA* 1.3 80.1 - - - +
522A ALA* 1.3 64.9 + - - +
523A SER* 3.8 1.2 + - - -
562A ILE* 3.8 7.0 - - - +
563A GLY* 3.8 11.2 - - - -
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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
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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