Contacts of the helix formed by residues 512 - 523 (chain f) in PDB entry 5T0J
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 ALA 512 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501f ILE* 3.7 28.0 - - + -
505f GLU* 5.2 7.2 - - + -
510f GLU 2.7 15.0 + - - +
511f MET* 1.3 73.6 - - - +
513f LEU* 1.3 55.8 + - - +
514f ARG 3.1 3.6 - - - -
515f THR* 3.1 5.6 + - - +
516f PHE* 2.7 35.5 + - - +
538f ILE* 4.1 27.6 - - + -
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Residues in contact with LEU 513 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510f GLU* 4.2 29.8 - - + +
511f MET 3.4 2.9 - - - +
512f ALA* 1.3 79.2 - - - +
514f ARG* 1.3 59.4 + - - +
516f PHE* 4.1 13.9 - - + -
517f GLY* 3.3 17.7 + - - -
521f ARG* 5.8 0.2 + - - -
538f ILE* 5.1 11.2 - - + -
546f ASN* 5.2 16.2 - - + +
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Residues in contact with ARG 514 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511f MET* 3.8 34.9 + - - +
513f LEU* 1.3 79.9 - - - +
515f THR* 1.3 71.7 + - - +
517f GLY 4.3 0.2 - - - -
518f HIS* 3.2 23.2 + - - +
521f ARG* 4.8 2.6 + - - -
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Residues in contact with THR 515 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487f MET* 4.2 32.8 - - + -
500f LEU* 6.2 0.2 - - + -
501f ILE* 4.0 25.9 - - + +
512f ALA* 3.1 7.6 + - - -
514f ARG* 1.3 89.8 + - - +
516f PHE* 1.3 64.1 + - - +
518f HIS* 3.3 7.5 + - + +
519f LEU* 3.2 27.5 + - + +
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Residues in contact with PHE 516 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498f ILE* 5.5 0.2 - - + -
501f ILE* 4.8 13.4 - - + +
512f ALA* 2.7 26.1 + - + +
513f LEU* 4.4 13.0 - - + -
515f THR* 1.3 74.8 - - - +
517f GLY* 1.3 62.2 + - - +
519f LEU* 3.3 27.3 + - + +
520f LEU* 3.4 24.9 - - + +
531f VAL* 3.3 42.8 - - + -
532f PRO* 4.7 0.7 - - + -
534f ALA* 4.0 17.7 - - + -
535f LEU* 3.5 31.0 - - + -
538f ILE* 4.9 11.7 - - + -
550f THR* 6.5 1.3 - - + -
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Residues in contact with GLY 517 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513f LEU 3.3 16.8 + - - -
516f PHE* 1.3 80.9 - - - +
518f HIS* 1.3 62.3 + - - +
520f LEU* 3.3 26.0 - - - +
521f ARG* 3.0 34.8 + - - +
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Residues in contact with HIS 518 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487f MET* 6.0 5.8 - - + -
514f ARG 3.2 19.6 + - - +
515f THR* 3.3 9.3 + - + +
516f PHE 3.2 0.6 - - - -
517f GLY* 1.3 77.8 - - - +
519f LEU* 1.3 62.1 + - - +
521f ARG* 3.3 19.8 + - + +
522f TYR* 3.0 55.2 + + + +
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Residues in contact with LEU 519 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487f MET* 5.6 9.2 - - + -
490f HIS* 5.7 7.1 + - + +
497f GLY* 4.4 13.7 - - - +
498f ILE* 5.6 5.6 - - + -
501f ILE* 4.2 22.0 - - + -
515f THR* 3.2 21.9 + - + +
516f PHE* 3.3 25.4 - - + +
518f HIS* 1.3 81.6 - - + +
520f LEU* 1.3 61.6 + - - +
522f TYR* 5.1 2.9 - - - -
523f GLY* 3.0 27.3 + - - +
527f LEU* 3.8 14.9 - - + +
531f VAL* 3.7 29.6 - - + -
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Residues in contact with LEU 520 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516f PHE* 3.4 34.8 - - + +
517f GLY* 3.3 22.0 - - - +
519f LEU* 1.3 84.8 - - - +
521f ARG* 1.3 83.1 + - + +
523f GLY* 3.9 8.7 + - - +
524f GLU 5.6 0.2 - - - +
527f LEU* 5.6 0.7 - - - -
528f ARG* 3.3 39.7 + - + +
531f VAL* 4.1 28.0 - - + -
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Residues in contact with ARG 521 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514f ARG 4.8 2.6 + - - -
517f GLY* 3.0 38.1 + - - +
518f HIS* 3.3 30.5 + - - +
520f LEU* 1.3 92.4 - - + +
522f TYR* 1.3 64.0 + - + +
523f GLY 3.7 4.0 + - - +
528f ARG* 4.3 7.9 + - - +
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Residues in contact with TYR 522 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490f HIS* 4.6 24.5 - + - -
518f HIS* 3.0 41.6 + + + +
519f LEU* 5.1 2.2 - - - -
521f ARG* 1.3 76.4 - - + +
523f GLY* 1.3 70.5 + - - +
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Residues in contact with GLY 523 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490f HIS* 5.0 5.2 - - - -
519f LEU 3.0 23.4 + - - -
520f LEU 3.9 5.9 + - - +
521f ARG 3.4 6.9 - - - +
522f TYR* 1.3 86.2 - - - +
524f GLU* 1.3 68.4 + - - +
525f PRO* 4.6 0.9 - - - +
527f LEU* 3.7 12.8 - - - -
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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