Contacts of the strand formed by residues 838 - 842 (chain A) in PDB entry 2RD0
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 CYS 838 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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755A LEU* 3.7 3.8 - - - +
807A LEU* 3.9 35.4 - - - -
810A ASP* 4.4 3.8 - - - -
811A MET* 3.4 33.8 - - - +
814A LEU* 3.2 29.8 - - + -
818A ARG* 6.2 0.2 - - - +
836A TYR* 3.6 1.3 + - - -
837A GLY* 1.3 75.5 - - - +
839A LEU* 1.3 60.2 + - - +
847A LEU 3.3 6.1 - - - -
848A ILE* 4.2 12.8 - - + -
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Residues in contact with LEU 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666A PHE* 4.0 17.5 - - + -
669A TRP* 4.2 20.0 - - + -
670A HIS* 3.9 29.4 - - + +
754A PRO* 3.4 40.4 - - + +
755A LEU* 3.7 15.2 - - + +
807A LEU* 4.9 2.7 - - - -
811A MET* 4.2 0.7 - - + -
838A CYS* 1.3 74.7 - - - +
840A SER* 1.3 72.0 + - - +
841A ILE* 3.3 15.2 - - + +
846A GLY* 3.0 6.4 - - - -
847A LEU* 2.9 36.0 + - + +
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Residues in contact with SER 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A TRP 4.3 3.5 - - - +
670A HIS* 5.3 0.3 + - - -
673A SER* 3.2 28.8 + - - -
806A ASP* 5.3 0.5 + - - -
807A LEU* 4.2 17.3 + - - +
808A ARG* 4.1 19.4 + - - +
811A MET* 3.5 27.5 - - - +
839A LEU* 1.3 83.0 - - - +
841A ILE* 1.3 59.8 + - - +
842A GLY 3.4 12.3 + - - -
844A CYS* 5.2 0.7 + - - -
845A VAL 3.5 8.0 + - - -
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Residues in contact with ILE 841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A TRP* 3.7 29.6 - - + -
672A LYS* 4.6 6.6 - - - +
673A SER* 3.8 10.6 + - - -
709A MET* 3.3 53.8 - - + -
710A GLU* 6.0 0.7 - - - +
713A ILE* 3.9 20.6 - - + +
754A PRO* 5.4 0.4 - - + -
839A LEU* 3.3 36.6 - - + +
840A SER* 1.3 73.5 - - - +
842A GLY* 1.3 58.3 + - - +
845A VAL* 3.0 25.0 + - + +
846A GLY* 4.1 3.1 - - - +
847A LEU* 4.5 3.1 - - + +
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Residues in contact with GLY 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A LYS 4.9 1.3 - - - -
673A SER* 3.2 25.0 - - - +
676A HIS* 4.2 1.6 - - - -
713A ILE* 6.0 1.6 - - - -
840A SER* 3.4 15.2 + - - -
841A ILE* 1.3 81.5 - - - +
843A ASP* 1.3 60.9 + - - -
844A CYS 2.9 10.2 + - - -
845A VAL* 3.7 9.3 + - - -
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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