Contacts of the helix formed by residues 511 - 518 (chain E) in PDB entry 6O81
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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507E ILE* 3.4 32.1 - - - +
508E PRO* 3.5 6.2 + - - +
509E CYS 3.1 0.6 - - - -
510E SER* 1.3 77.8 + - - +
512E VAL* 1.3 63.9 + - - +
513E PRO 3.4 3.1 - - - -
514E VAL* 3.1 28.6 + - - +
515E VAL* 3.2 15.8 + - - +
294G SER 5.0 2.2 - - - -
297G SER* 3.9 24.8 - - - -
301G ILE* 4.7 6.2 - - - +
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Residues in contact with VAL 512 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408E LEU* 4.0 31.9 - - + +
409E LEU 3.3 25.8 - - - +
412E GLY* 3.8 12.1 - - - -
443E PHE* 3.7 27.9 - - + -
500E VAL* 4.3 3.8 - - + -
507E ILE* 4.1 11.2 - - + -
508E PRO 3.8 13.2 - - - +
509E CYS* 3.0 24.8 + - - +
511E SER* 1.3 78.9 - - - +
513E PRO* 1.4 64.1 - - + +
515E VAL* 4.5 4.9 - - - -
516E LEU* 3.8 9.3 + - - +
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Residues in contact with PRO 513 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C ASN* 5.4 1.8 - - - +
332C ALA* 5.7 1.6 - - + +
335C TYR* 3.7 43.4 + - + -
410E ALA* 3.4 36.3 - - + +
412E GLY 5.2 0.2 - - - +
509E CYS 4.3 1.3 - - - +
510E SER 4.0 11.0 - - - +
511E SER 3.6 2.2 - - - -
512E VAL* 1.4 90.6 - - + +
514E VAL* 1.3 60.3 + - - +
516E LEU* 3.0 35.5 + - + +
517E ARG* 3.0 7.4 + - - +
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Residues in contact with VAL 514 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C TYR* 3.6 25.1 - - + -
337C TYR* 3.7 20.6 - - - +
510E SER 4.6 0.2 - - - +
511E SER* 3.1 24.4 + - - +
513E PRO* 1.3 76.7 - - - +
515E VAL* 1.3 55.9 + - - +
517E ARG* 2.9 38.9 + - - +
518E VAL* 3.2 13.2 + - + +
298G ASP* 3.3 27.8 - - + +
301G ILE* 3.7 20.0 - - + -
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Residues in contact with VAL 515 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440E THR* 3.7 26.0 - - + +
443E PHE* 3.7 15.0 - - + -
502E THR* 5.4 3.1 - - - +
504E LEU* 3.7 26.9 - - + -
507E ILE* 3.8 25.1 - - + -
511E SER 3.2 15.7 + - - +
512E VAL 4.2 0.4 - - - +
513E PRO 3.3 0.2 - - - -
514E VAL* 1.3 74.4 - - - +
516E LEU* 1.3 62.3 + - - +
518E VAL* 3.0 14.7 + - + +
519E LYS* 3.0 21.3 + - + +
301G ILE* 3.8 17.7 - - + -
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Residues in contact with LEU 516 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409E LEU 5.9 0.2 - - - +
410E ALA* 5.8 0.7 - - + -
440E THR* 5.2 2.7 - - + +
443E PHE* 3.8 29.8 - - + -
444E CYS 3.4 31.4 - - - +
445E GLU* 3.5 31.4 - - + +
512E VAL 3.8 12.2 + - - +
513E PRO* 3.0 20.9 + - + +
515E VAL* 1.3 78.1 - - - +
517E ARG* 1.3 54.1 + - - +
519E LYS* 3.0 8.6 + - + +
520E SER* 2.8 39.8 + - - -
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Residues in contact with ARG 517 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C TYR* 4.1 10.6 + - - +
338C ARG* 3.3 42.4 - - - +
342C GLU* 3.4 25.4 - - - +
513E PRO 3.0 8.6 + - - +
514E VAL* 2.9 41.5 + - - +
516E LEU* 1.3 77.0 - - - +
518E VAL* 1.3 66.4 + - - +
520E SER* 3.9 7.1 + - - +
522E ASP* 3.1 35.5 + - - +
298G ASP* 2.9 25.1 + - - -
302G LYS* 3.5 21.8 - - - +
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Residues in contact with VAL 518 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504E LEU* 4.5 8.1 - - + -
514E VAL* 3.2 10.5 + - + +
515E VAL* 3.0 30.6 + - + +
517E ARG* 1.3 95.0 - - - +
519E LYS* 1.3 67.0 + - + +
520E SER 3.8 0.7 - - - -
521E SER* 5.0 1.8 + - - -
522E ASP 3.8 13.6 - - - +
301G ILE* 5.4 8.7 - - + +
302G LYS* 5.0 9.2 - - + -
304G TYR* 3.7 28.1 + - + +
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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
------------------------------------------------------------
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