Contacts of the helix formed by residues 475 - 485 (chain F) in PDB entry 4CYM
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 GLN 475 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469F VAL* 5.8 0.2 - - - +
470F ALA* 3.1 10.2 + - - +
473F CYS* 3.3 32.5 - - + +
474F GLY* 1.3 75.3 - - - +
476F ALA* 1.3 63.6 + - - +
477F SER* 3.3 7.2 - - - +
478F LEU* 3.0 43.5 + - + +
479F ILE* 3.0 15.0 + - - +
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Residues in contact with ALA 476 (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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91C MET* 5.6 4.7 - - - -
474F GLY 2.8 12.0 + - - +
475F GLN* 1.3 71.2 - - - +
477F SER* 1.3 63.2 + - - +
479F ILE* 3.1 15.4 + - - +
480F ASP* 3.0 26.8 + - - +
510F SER* 4.8 13.5 - - - +
511F VAL* 4.8 6.3 - - + -
514F LEU* 3.7 16.2 - - + +
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Residues in contact with SER 477 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475F GLN* 4.4 4.5 - - - +
476F ALA* 1.3 76.1 + - - +
478F LEU* 1.3 58.4 + - - +
480F ASP* 3.4 14.8 - - - +
481F LEU* 3.1 25.8 + - - +
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Residues in contact with LEU 478 (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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469F VAL* 6.4 0.4 - - + -
470F ALA* 3.9 23.3 - - + +
475F GLN* 3.0 44.3 + - + +
477F SER* 1.3 79.7 + - - +
479F ILE* 1.3 60.0 + - - +
481F LEU* 3.1 23.8 + - + +
482F LEU* 2.8 46.1 + - + +
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Residues in contact with ILE 479 (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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467F LEU* 4.1 17.5 - - + -
470F ALA* 4.0 15.5 - - + +
471F ALA* 4.3 10.5 - - + -
475F GLN 3.0 13.8 + - - +
476F ALA* 3.3 10.8 - - - +
478F LEU* 1.3 71.8 - - - +
480F ASP* 1.3 68.2 + - - +
481F LEU 3.0 0.5 + - - -
482F LEU* 3.1 0.9 + - - -
483F VAL* 2.9 38.2 + - + +
511F VAL* 3.6 40.6 - - + -
514F LEU* 3.8 21.5 - - + -
515F LEU* 4.3 13.9 - - + -
518F TYR* 4.2 4.7 - - + -
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Residues in contact with ASP 480 (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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93C ARG* 3.3 29.4 + - - -
476F ALA* 3.0 19.7 + - - +
477F SER* 3.4 15.3 - - - +
479F ILE* 1.3 75.2 - - - +
481F LEU* 1.3 64.3 + - - +
483F VAL* 3.5 1.9 + - - +
484F SER* 3.0 24.4 + - - -
514F LEU* 3.7 6.0 - - - +
518F TYR* 2.5 40.5 + - - +
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Residues in contact with LEU 481 (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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454F VAL* 5.0 9.4 - - + -
477F SER 3.1 11.4 + - - +
478F LEU* 3.4 26.2 - - + +
479F ILE 3.0 1.2 - - - -
480F ASP* 1.3 80.6 - - - +
482F LEU* 1.3 67.8 + - + +
484F SER* 2.5 26.9 + - - +
485F LYS* 3.1 31.5 + - + +
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Residues in contact with LEU 482 (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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454F VAL* 3.9 30.3 - - + -
456F PRO* 4.3 10.2 - - + +
466F PRO* 3.6 22.2 - - + +
467F LEU* 3.4 38.6 - - + +
470F ALA* 3.9 15.0 - - + -
478F LEU* 2.8 33.0 + - + +
479F ILE 3.8 2.5 - - - +
481F LEU* 1.3 74.5 - - + +
483F VAL* 1.3 62.8 + - - +
485F LYS* 3.0 15.3 + - - +
486F GLY 3.3 0.5 + - - -
487F ALA* 3.0 28.7 + - + +
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Residues in contact with VAL 483 (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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467F LEU* 4.3 10.8 - - + -
479F ILE* 2.9 27.8 + - + +
480F ASP 3.8 3.1 - - - +
482F LEU* 1.3 75.0 - - - +
484F SER* 1.3 63.5 + - - +
486F GLY* 3.0 15.6 + - - -
487F ALA* 3.9 8.7 + - - +
489F VAL* 4.2 21.1 - - + -
515F LEU* 5.7 1.1 - - + -
518F TYR* 3.6 51.1 - - + -
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Residues in contact with SER 484 (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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480F ASP 3.0 14.2 + - - -
481F LEU* 2.5 26.4 + - - +
483F VAL* 1.3 76.7 - - - +
485F LYS* 1.3 68.3 + - - +
486F GLY 3.3 1.4 + - - -
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Residues in contact with LYS 485 (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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453F VAL* 3.5 27.5 - - + +
454F VAL* 3.5 26.2 - - + +
456F PRO* 3.3 20.3 - - + +
481F LEU* 3.1 29.6 + - + +
482F LEU* 3.0 11.9 + - - +
484F SER* 1.3 83.1 + - - +
486F GLY* 1.3 57.5 + - - +
487F ALA 3.5 2.0 - - - -
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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