Contacts of the strand formed by residues 534 - 536 (chain D) in PDB entry 2O1S
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 PHE 534 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447D VAL* 4.0 17.0 - - + -
448D ILE 3.5 5.6 - - - +
449D MSE 3.4 39.3 - - + -
460D MSE 5.4 0.4 - - + -
463D THR* 4.8 0.2 - - + -
492D LEU* 4.4 17.9 - - + -
493D PRO 3.3 24.9 - - - -
494D ILE* 3.8 16.2 - - + -
495D GLY* 3.4 23.6 - - - -
496D LYS 3.6 13.0 - - - -
511D PHE* 3.4 10.1 - - - -
532D MSE 2.6 14.4 + - - +
533D ARG* 1.3 88.4 - - + +
535D VAL* 1.3 60.1 + - - +
536D LYS 4.2 4.3 - - - +
537D PRO* 3.1 19.6 - - + +
538D LEU* 3.2 20.0 - - - +
539D ASP 4.9 1.6 + - - +
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Residues in contact with VAL 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562C MSE 5.6 1.9 - - - +
437D LEU* 4.0 14.4 - - + +
441D ARG* 3.6 36.1 + - + +
448D ILE* 2.8 24.8 + - + +
450D THR* 3.4 29.8 - - + -
511D PHE* 3.7 19.1 - - + -
533D ARG 4.1 0.4 + - - -
534D PHE* 1.3 74.3 - - - +
536D LYS* 1.3 60.3 + - - +
538D LEU* 3.1 24.1 - - - +
565D ALA* 3.8 18.3 - - + -
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Residues in contact with LYS 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562C MSE 3.5 21.1 - - + +
589C ASP* 2.5 38.6 + - - -
440D LEU 4.8 0.2 - - - +
441D ARG* 3.3 29.2 - - + +
443D ILE 3.2 25.6 - - - -
444D PRO* 4.6 0.6 - - - +
445D GLU 4.8 1.4 - - - +
446D MSE 3.3 22.0 - - - +
447D VAL* 3.2 4.0 - - - +
448D ILE* 2.6 45.5 + - + +
534D PHE* 3.2 2.2 - - - -
535D VAL* 1.3 83.9 - - + +
537D PRO* 1.3 74.5 - - + +
538D LEU 3.7 0.9 - - - +
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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