Contacts of the helix formed by residues 511 - 525 (chain B) in PDB entry 4PO2
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 511 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510B LEU* 1.3 73.1 - - - +
512B LYS* 1.3 64.2 + - - +
513B GLU* 3.5 9.7 + - - +
514B GLU* 3.0 33.6 + - - +
515B ILE* 3.2 25.0 + - - +
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Residues in contact with LYS 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510B LEU 4.1 0.8 + - - -
511B SER* 1.3 72.7 - - - +
513B GLU* 1.3 56.7 + - - +
515B ILE* 3.5 10.4 + - - +
516B GLU* 2.9 31.4 + - - +
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Residues in contact with GLU 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511B SER* 3.1 10.0 - - - +
512B LYS* 1.3 76.8 - - - +
514B GLU* 1.3 58.9 + - - +
516B GLU* 3.3 6.0 + - - +
517B ARG* 2.9 36.4 + - - +
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Residues in contact with GLU 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B ASN* 3.3 13.2 + - - -
510B LEU* 3.2 27.2 - - + +
511B SER* 3.0 25.2 + - - +
513B GLU* 1.3 74.8 - - - +
515B ILE* 1.3 58.6 + - - +
517B ARG* 3.2 37.6 + - - +
518B MET* 2.9 59.2 + - + +
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Residues in contact with ILE 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B PRO* 3.7 35.7 - - + +
399B LEU* 3.9 26.2 - - + -
416B ARG* 5.5 0.2 - - - +
510B LEU* 4.0 26.7 - - + +
511B SER 3.2 21.0 + - - +
512B LYS* 3.6 8.1 - - - +
514B GLU* 1.3 77.1 - - - +
516B GLU* 1.3 59.2 + - - +
518B MET* 3.0 11.8 + - - +
519B VAL* 2.9 34.8 + - + +
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Residues in contact with GLU 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B LYS 2.9 19.1 + - - +
513B GLU* 3.7 5.8 - - - +
515B ILE* 1.3 77.7 - - - +
517B ARG* 1.3 56.8 + - - +
519B VAL* 3.5 8.0 + - - +
520B GLN* 2.9 31.8 + - - +
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Residues in contact with ARG 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B GLU* 2.9 20.0 + - - +
514B GLU* 3.2 53.9 + - - +
516B GLU* 1.3 76.1 - - - +
518B MET* 1.3 60.5 + - + +
520B GLN* 3.4 5.9 + - - +
521B GLU* 2.9 49.2 + - + +
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Residues in contact with MET 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B LEU* 3.6 36.8 - - + -
444B GLU* 5.0 0.7 - - - +
445B GLY* 5.1 7.6 - - - -
446B GLU* 4.9 8.1 + - + +
447B ARG* 5.0 2.4 - - - +
453B ASN* 6.3 0.4 - - - -
454B ASN* 3.2 31.4 - - + +
510B LEU* 4.9 1.3 - - + -
514B GLU* 2.9 51.3 + - + +
515B ILE* 3.0 7.6 + - - +
517B ARG* 1.3 77.0 - - + +
519B VAL* 1.3 59.9 + - - +
521B GLU* 3.3 6.2 + - - +
522B ALA* 2.9 30.7 + - - +
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Residues in contact with VAL 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B LEU* 4.7 2.0 - - + -
416B ARG* 3.3 54.5 - - - +
446B GLU* 4.6 8.1 - - + -
515B ILE* 2.9 28.1 + - + +
516B GLU* 3.8 7.4 - - - +
518B MET* 1.3 73.9 - - - +
520B GLN* 1.3 59.5 + - - +
522B ALA* 3.3 6.0 + - - +
523B GLU* 2.9 34.8 + - + +
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Residues in contact with GLN 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B GLU 2.9 19.3 + - - +
517B ARG* 3.5 6.5 - - - +
519B VAL* 1.3 77.3 - - - +
521B GLU* 1.3 56.9 + - + +
523B GLU* 3.3 6.3 + - - +
524B LYS* 2.9 37.3 + - - +
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Residues in contact with GLU 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447B ARG* 4.4 15.6 + - - +
517B ARG* 2.9 42.8 + - + +
518B MET* 3.3 6.9 + - - +
520B GLN* 1.3 73.2 - - + +
522B ALA* 1.3 63.6 + - - +
524B LYS* 3.3 20.4 + - - +
525B TYR* 3.1 55.9 + - - +
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Residues in contact with ALA 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B GLU* 3.5 33.9 - - + +
447B ARG* 3.6 21.7 - - - +
518B MET 2.9 18.3 + - - +
519B VAL* 3.6 4.0 - - - +
521B GLU* 1.3 77.7 - - - +
523B GLU* 1.3 61.8 + - - +
525B TYR 3.4 2.4 + - - -
526B LYS* 3.1 25.5 + - - +
529B ASP* 4.8 2.2 - - - +
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Residues in contact with GLU 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B VAL* 2.9 21.6 + - + +
520B GLN* 3.3 6.7 + - - +
522B ALA* 1.3 76.6 - - - +
524B LYS* 1.3 62.5 + - - +
526B LYS* 3.3 39.4 - - - +
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Residues in contact with LYS 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B GLN* 2.9 23.3 + - - +
521B GLU* 3.4 25.7 + - - +
523B GLU* 1.3 77.6 - - - +
525B TYR* 1.3 92.8 + - + +
526B LYS* 3.6 1.3 + - - +
528B GLU* 4.0 5.7 - - - +
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Residues in contact with TYR 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447B ARG* 4.0 31.0 - - - +
521B GLU* 3.1 42.9 + - - +
522B ALA 3.6 3.6 - - - +
524B LYS* 1.3 108.3 + - + +
526B LYS* 1.3 57.4 + - - +
528B GLU* 3.2 25.7 - - + +
529B ASP* 3.0 31.0 + - - +
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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