Contacts of the helix formed by residues 519 - 526 (chain C) in PDB entry 6O0T
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 519 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517C ARG 3.8 1.7 + - - -
518C VAL* 1.3 79.8 - - - +
520C GLU* 1.3 65.2 + - - +
521C GLN* 3.9 6.3 + - - +
522C GLN* 3.1 45.6 + - - +
523C MSE 3.2 10.6 + - - +
539C LEU* 4.4 4.0 - - - -
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Residues in contact with GLU 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519C SER* 1.3 74.8 - - - +
521C GLN* 1.3 66.9 + - + +
523C MSE 3.2 11.3 + - - +
524C LEU* 3.1 21.8 + - - +
535C ARG* 3.7 21.5 + - + +
539C LEU* 3.5 31.3 - - + +
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Residues in contact with GLN 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519C SER* 3.3 6.8 + - - +
520C GLU* 1.3 81.0 - - + +
522C GLN* 1.3 61.5 + - + +
524C LEU* 3.2 9.5 + - + +
525C GLU* 2.8 64.6 + - + +
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Residues in contact with GLN 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517C ARG 3.9 5.5 + - - +
518C VAL* 3.3 14.3 - - + +
519C SER* 3.1 38.7 + - - +
521C GLN* 1.3 78.1 - - + +
523C MSE 1.3 58.3 + - - +
526C ASP* 3.0 44.2 + - - +
527C CYS* 3.2 6.2 + - - -
520D GLU* 5.5 2.4 + - - -
532D GLY* 4.0 8.7 + - - -
533D VAL* 3.5 31.7 - - + +
536D ALA* 3.5 29.7 - - - +
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Residues in contact with MSE 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C MSE 5.6 3.6 - - + -
515C LEU* 5.1 8.5 - - + +
518C VAL* 3.7 26.9 - - + -
519C SER 3.2 9.3 + - - +
520C GLU* 3.2 9.0 + - - +
522C GLN* 1.3 75.9 - - - +
524C LEU* 1.3 59.3 + - - +
527C CYS* 3.4 13.5 - - - +
528C GLY 3.1 10.2 + - - -
529C ILE* 3.0 42.3 + - + -
535C ARG* 4.1 24.0 - - - +
538C ILE* 3.7 31.4 - - + +
539C LEU* 3.6 40.6 - - + +
542C ALA* 5.2 2.0 - - + -
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Residues in contact with LEU 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520C GLU 3.1 14.0 + - - +
521C GLN* 3.2 10.1 + - + +
523C MSE 1.3 79.8 - - - +
525C GLU* 1.3 73.6 + - + +
528C GLY* 3.7 13.9 + - - -
529C ILE 3.8 9.2 - - - +
530C HIS* 4.1 23.4 - - + +
535C ARG* 3.6 34.9 - - - +
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Residues in contact with GLU 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521C GLN* 2.8 56.1 + - + +
522C GLN* 5.9 0.2 - - - -
524C LEU* 1.3 82.9 - - + +
526C ASP* 1.3 73.0 + - - +
528C GLY 4.8 0.9 + - - -
531D LEU* 5.5 0.5 - - - +
532D GLY* 6.0 1.4 + - - -
535D ARG* 5.3 6.2 + - - -
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Residues in contact with ASP 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504C GLY* 4.2 4.0 - - - +
508C CYS* 4.1 11.1 - - - +
522C GLN* 3.0 25.8 + - - +
525C GLU* 1.3 93.6 - - - +
527C CYS* 1.3 61.8 + - - +
528C GLY 3.5 0.9 - - - -
530D HIS 4.4 2.8 - - - +
531D LEU* 3.4 28.8 - - + +
532D GLY* 3.1 34.0 + - - -
533D VAL* 3.2 22.7 + - + -
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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