Contacts of the helix formed by residues 511 - 518 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507F ILE* 3.4 32.6 - - - +
508F PRO* 3.6 5.7 + - - +
509F CYS 3.0 0.8 + - - -
510F SER* 1.3 79.3 + - - +
512F VAL* 1.3 62.3 + - - +
513F PRO* 3.4 2.2 - - - -
514F VAL* 3.2 29.5 + - - -
515F VAL* 3.4 15.1 + - - +
294H SER 4.9 2.9 - - - -
297H SER* 3.9 24.6 - - - -
301H ILE* 4.7 4.0 - - - +
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Residues in contact with VAL 512 (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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408F LEU* 3.8 33.2 - - + +
409F LEU 3.3 25.8 - - - +
412F GLY* 3.8 12.3 - - - +
443F PHE* 4.2 8.8 - - + -
500F VAL* 4.0 9.6 - - + -
507F ILE* 4.4 4.3 - - + -
508F PRO 3.9 11.9 - - - +
509F CYS* 3.0 26.1 + - + +
511F SER* 1.3 78.1 - - - +
513F PRO* 1.4 65.7 - - + +
515F VAL* 3.4 19.4 - - + +
516F LEU* 3.7 14.4 - - - +
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Residues in contact with PRO 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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331D ASN* 5.4 2.0 - - - +
332D ALA* 5.8 1.3 - - + -
335D TYR* 3.9 43.8 + - + -
410F ALA* 3.3 34.3 - - + +
411F ASN 5.6 0.2 - - - -
412F GLY 5.2 0.2 - - - +
509F CYS 4.4 0.2 - - - +
510F SER* 4.0 11.4 - - - +
511F SER 3.6 1.8 - - - -
512F VAL* 1.4 91.4 - - + +
514F VAL* 1.3 60.1 + - - +
516F LEU* 2.9 35.5 + - + +
517F ARG* 3.0 8.8 + - - +
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Residues in contact with VAL 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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335D TYR* 3.6 25.4 - - + -
337D TYR* 3.6 20.9 - - - +
510F SER 4.7 0.7 - - - +
511F SER* 3.2 25.0 + - - +
513F PRO* 1.3 75.6 - - - +
515F VAL* 1.3 58.5 + - - +
517F ARG* 2.9 43.3 + - - +
518F VAL* 3.3 6.3 + - + +
298H ASP* 3.3 29.8 - - + +
301H ILE* 3.7 20.0 - - + -
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Residues in contact with VAL 515 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440F THR* 4.3 12.3 - - + -
443F PHE* 3.6 20.0 - - + -
502F THR* 5.5 0.4 - - - +
504F LEU* 3.7 33.9 - - + -
507F ILE* 4.3 13.0 - - + -
511F SER 3.4 10.9 + - - +
512F VAL* 3.4 19.1 - - - +
514F VAL* 1.3 75.0 - - - +
516F LEU* 1.3 67.6 + - - +
518F VAL* 3.0 19.4 + - + +
519F LYS* 3.0 22.8 + - + +
301H ILE* 4.3 12.1 - - + -
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Residues in contact with LEU 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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409F LEU 5.5 1.8 - - - +
410F ALA* 5.6 0.7 - - + -
440F THR* 5.3 2.0 - - + +
443F PHE* 3.9 29.8 - - + -
444F CYS 3.5 28.7 - - - +
445F GLU* 3.6 28.9 - - + +
512F VAL 3.7 15.9 - - - +
513F PRO* 2.9 21.7 + - + +
515F VAL* 1.3 83.3 - - - +
517F ARG* 1.3 55.1 - - - +
519F LYS* 3.0 9.8 + - + +
520F SER* 2.8 36.7 + - - -
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Residues in contact with ARG 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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335D TYR* 4.2 8.6 + - - +
338D ARG* 3.3 52.9 - - - +
342D GLU* 3.5 17.7 - - - +
513F PRO 3.0 8.6 + - - +
514F VAL* 2.9 41.1 + - - +
516F LEU* 1.3 76.6 - - - +
518F VAL* 1.3 65.7 + - - +
519F LYS 3.3 0.7 + - - -
520F SER* 3.7 7.0 + - - -
522F ASP* 3.2 41.5 + - + +
298H ASP* 2.8 25.9 + - - -
302H LYS* 3.5 23.0 - - - +
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Residues in contact with VAL 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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504F LEU* 4.8 6.3 - - + -
514F VAL* 3.3 10.4 + - + +
515F VAL* 3.0 31.4 + - + +
517F ARG* 1.3 95.9 - - - +
519F LYS* 1.3 66.6 + - + +
520F SER 3.8 0.2 - - - -
521F SER 5.0 1.4 + - - -
522F ASP 3.7 14.7 + - - +
301H ILE* 5.4 7.6 - - + +
302H LYS* 4.9 10.1 - - + -
304H TYR* 3.7 26.2 + - + +
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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