Contacts of the helix formed by residues 515 - 531 (chain A) in PDB entry 4PED
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 ASP 515 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483A HIS* 6.2 0.2 - - - -
513A GLU 4.4 0.2 + - - -
514A TYR* 1.3 77.5 - - - +
516A ARG* 1.3 66.8 + - + +
517A SER* 2.4 30.5 + - - +
518A PHE* 3.0 24.7 + - - +
519A THR* 3.2 19.2 + - - +
605A GLU* 5.1 2.4 + - - +
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Residues in contact with ARG 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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483A HIS* 6.1 2.7 - - + -
515A ASP* 1.3 74.3 - - + +
517A SER* 1.3 72.6 + - - +
519A THR* 3.7 8.5 - - - -
520A ASP* 2.7 54.2 + - - +
640A TYR* 4.8 0.9 - - - +
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Residues in contact with SER 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A ASP* 2.4 31.4 + - - -
516A ARG* 1.3 96.2 - - - +
518A PHE* 1.3 67.0 + - - +
520A ASP* 4.0 5.4 - - - +
521A LEU* 3.5 19.9 + - - +
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Residues in contact with PHE 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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514A TYR* 4.0 18.8 - + + -
515A ASP* 3.0 32.9 + - - +
517A SER* 1.3 88.7 + - - +
519A THR* 1.3 62.9 + - - +
521A LEU 3.4 0.9 + - - -
522A TYR* 3.0 24.5 + - - +
544A MSE 3.6 31.2 - - - +
603A PRO* 4.7 9.9 - - + -
605A GLU* 3.4 42.8 - - + -
606A THR* 3.4 26.5 - - - -
609A LEU* 4.2 12.1 - - + -
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Residues in contact with THR 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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479A LEU* 3.9 26.7 - - + +
480A PHE* 4.2 6.3 - - + -
483A HIS* 3.9 14.7 + - + -
514A TYR* 3.7 24.9 - - + +
515A ASP 3.2 14.9 + - - +
516A ARG* 3.4 10.4 + - - -
518A PHE* 1.3 74.1 - - + +
520A ASP* 1.3 65.0 + - - +
522A TYR* 3.8 6.5 - - - +
523A ILE* 3.0 26.5 + - - +
609A LEU* 5.8 2.9 - - + -
640A TYR* 3.0 28.6 + - - -
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Residues in contact with ASP 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A ARG* 2.7 44.4 + - - +
517A SER* 4.0 6.6 - - - +
519A THR* 1.3 72.1 - - - +
521A LEU* 1.3 62.2 + - - +
523A ILE* 3.4 4.8 - - - +
524A GLN* 3.2 38.3 + - - +
640A TYR* 2.3 31.2 + - - -
644A GLN* 3.1 27.2 + - - +
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Residues in contact with LEU 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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517A SER 3.5 13.8 + - - +
518A PHE 3.4 1.0 + - - -
519A THR 3.3 0.2 - - - -
520A ASP* 1.3 79.8 - - - +
522A TYR* 1.3 64.2 - - - +
524A GLN* 3.2 23.8 + - - +
525A ILE* 3.1 21.6 + - + +
540A LYS* 4.1 20.9 - - + +
543A GLU* 3.8 35.0 - - + +
544A MSE 3.6 51.6 - - + +
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Residues in contact with TYR 522 (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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479A LEU* 4.0 21.4 - - + +
480A PHE* 3.6 31.2 - + - -
518A PHE 3.0 17.5 + - - +
519A THR* 3.8 5.6 - - - +
521A LEU* 1.3 77.5 - - - +
523A ILE* 1.3 60.4 + - - +
525A ILE* 3.0 19.0 + - + +
526A ILE* 3.1 35.0 + - + +
544A MSE 3.7 8.9 - - + +
546A PHE* 3.8 36.6 - + - -
563A ILE* 5.9 4.5 - - + +
566A LEU* 5.0 1.6 - - - +
609A LEU* 4.0 26.6 + - + -
610A HIS* 5.7 1.2 + - - -
613A MSE 3.4 34.5 + - + +
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Residues in contact with ILE 523 (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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480A PHE* 3.7 39.5 - - + -
519A THR 3.0 16.3 + - - +
520A ASP 3.4 11.4 - - - +
522A TYR* 1.3 76.4 - - - +
524A GLN* 1.3 64.7 + - + +
526A ILE* 3.3 2.3 + - - +
527A ARG* 2.9 30.0 + - - +
633A PHE* 4.6 7.6 - - + -
637A TYR* 3.6 40.6 - - + -
640A TYR* 3.9 44.0 - - + -
644A GLN* 5.9 0.4 - - - +
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Residues in contact with GLN 524 (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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520A ASP* 3.2 32.5 + - - +
521A LEU* 3.2 18.9 + - - +
523A ILE* 1.3 80.5 - - + +
525A ILE* 1.3 55.9 + - - +
527A ARG* 3.7 7.0 - - - +
528A ALA* 3.0 30.0 + - - +
540A LYS* 3.1 38.4 + - + +
637A TYR* 5.8 2.5 - - + +
644A GLN* 5.1 6.3 - - - +
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Residues in contact with ILE 525 (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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521A LEU* 3.1 18.3 + - + +
522A TYR* 3.0 14.6 + - + +
524A GLN* 1.3 78.0 - - - +
526A ILE* 1.3 62.1 + - + +
528A ALA* 3.3 7.0 + - - +
529A ALA* 3.0 26.2 + - - +
537A VAL* 3.8 9.3 - - + +
540A LYS* 3.6 43.3 - - + +
541A SER* 4.0 15.5 - - - +
544A MSE 4.2 7.9 - - + -
546A PHE* 3.9 27.8 - - + -
563A ILE* 3.9 25.8 - - + -
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Residues in contact with ILE 526 (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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480A PHE* 4.7 1.6 - - + -
522A TYR* 3.1 50.9 + - + +
523A ILE* 3.9 6.7 - - - +
525A ILE* 1.3 80.7 - - + +
527A ARG* 1.3 65.2 + - - +
529A ALA* 3.2 7.1 + - + +
530A ALA* 2.9 22.3 + - - +
563A ILE* 4.7 8.1 - - + -
566A LEU* 4.4 20.2 - - + -
567A GLY* 4.8 0.8 - - - -
570A PHE* 3.8 24.9 - - + -
613A MSE 4.3 10.3 - - + -
633A PHE* 3.5 27.6 - - + -
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Residues in contact with ARG 527 (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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523A ILE 2.9 14.4 + - - +
524A GLN* 3.7 7.6 - - - +
526A ILE* 1.3 75.9 - - - +
528A ALA* 1.3 57.0 + - - +
530A ALA* 3.2 19.0 + - - +
531A ASP* 2.9 70.9 + - - +
570A PHE 5.7 0.4 + - - -
571A ALA* 6.2 0.4 - - - +
633A PHE* 3.8 18.7 - - + -
634A GLU* 3.3 36.2 + - - -
637A TYR* 3.1 60.3 - - + +
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Residues in contact with ALA 528 (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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524A GLN 3.0 19.1 + - - +
525A ILE* 3.6 5.6 - - - +
527A ARG* 1.3 76.2 - - - +
529A ALA* 1.3 61.1 + - - +
531A ASP* 3.1 8.3 + - - -
532A ARG 3.1 4.3 + - - -
533A ASP* 2.9 30.4 + - + +
536A THR* 3.8 30.3 - - + -
537A VAL* 3.7 15.3 - - + +
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Residues in contact with ALA 529 (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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525A ILE 3.0 13.8 + - - +
526A ILE* 3.2 10.1 + - + +
528A ALA* 1.3 75.9 - - - +
530A ALA* 1.3 59.7 + - - +
532A ARG* 3.0 24.6 + - - -
537A VAL* 3.5 10.0 - - + +
563A ILE* 3.5 38.1 - - + +
564A LEU* 3.9 12.2 - - - +
567A GLY* 3.6 12.9 - - - +
568A GLU 4.5 0.3 + - - -
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Residues in contact with ALA 530 (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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526A ILE 2.9 16.7 + - - +
527A ARG* 3.7 23.6 + - - +
529A ALA* 1.3 76.1 - - - +
531A ASP* 1.3 60.9 + - - +
532A ARG* 3.2 6.7 + - - +
567A GLY* 3.5 21.7 - - - +
570A PHE* 4.4 15.0 - - + -
571A ALA* 3.3 23.7 - - + +
633A PHE* 4.4 5.4 - - + -
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Residues in contact with ASP 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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527A ARG* 2.9 55.7 + - - +
528A ALA* 3.1 8.4 + - - +
530A ALA* 1.3 75.3 - - - +
532A ARG* 1.3 71.4 + - - +
533A ASP* 3.2 8.0 + - + +
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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