Contacts of the strand formed by residues 839 - 843 (chain A) in PDB entry 2X36
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 HIS 839 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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784A LEU* 3.5 9.9 - - - +
785A ARG* 3.0 33.3 + - + +
786A ARG* 4.0 42.2 + - + +
787A PRO 5.0 7.0 - - - -
788A GLN* 5.4 5.1 + - - -
797A ASP 3.1 29.6 + - - -
798A GLY 4.0 1.8 - - - -
799A SER* 2.7 31.6 + - - +
837A THR 4.1 7.7 + - - -
838A SER* 1.3 75.8 - - - +
840A ILE* 1.3 60.3 + - - +
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Residues in contact with ILE 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A THR* 4.3 5.6 - - - -
783A SER 3.3 10.8 - - - +
784A LEU* 4.5 3.1 - - + -
785A ARG* 4.3 3.7 - - - +
799A SER 2.9 11.9 + - - +
800A LEU* 3.3 17.3 - - + -
801A GLU* 2.8 25.8 + - - +
818A TYR* 5.7 4.3 - - + -
834A TYR* 3.5 31.0 - - + +
835A LEU* 4.0 22.9 - - + +
838A SER* 4.0 15.9 - - - +
839A HIS* 1.3 80.1 - - - +
841A HIS* 1.3 75.7 + - - +
864A LEU* 4.5 7.6 - - + -
867A LEU* 3.6 20.6 - - + -
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Residues in contact with HIS 841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A THR* 3.2 7.6 - - - -
783A SER 2.8 35.7 + - - +
785A ARG* 4.3 4.7 - - + -
800A LEU* 4.4 0.2 - - - -
801A GLU* 3.1 24.5 + - + -
802A VAL 4.4 0.4 - - - -
803A THR* 2.6 45.8 + - + +
840A ILE* 1.3 79.9 - - - +
842A LEU* 1.3 85.1 + - - +
843A HIS 4.4 0.2 - - - -
815B ARG 4.1 10.1 + - - -
816B ILE* 4.2 3.3 - - + +
819B THR* 3.0 45.1 - - + +
885B LEU* 3.5 21.7 - - + +
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Residues in contact with LEU 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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780A VAL* 3.7 27.8 - - + -
781A GLU 3.5 4.3 - - - +
782A THR* 4.0 11.4 - - + -
800A LEU* 3.9 22.2 - - + -
801A GLU 2.6 11.4 + - - +
802A VAL* 3.2 14.7 - - + -
803A THR 2.8 25.8 + - - +
814A ALA* 3.9 24.9 - - + -
841A HIS* 1.3 80.1 + - - +
843A HIS* 1.3 63.5 + - - +
844A VAL* 4.2 11.0 - - + -
860A ILE* 3.8 27.6 - - + -
864A LEU* 5.2 2.0 - - + -
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Residues in contact with HIS 843 (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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779A PHE 4.4 0.7 + - - +
780A VAL* 3.8 7.4 - - - +
781A GLU* 2.8 50.2 + - + +
803A THR* 2.8 40.2 - - - +
804A GLY* 3.7 12.5 + - - -
842A LEU* 1.3 75.4 - - - +
844A VAL* 1.3 59.7 + - - +
845A PRO* 3.6 30.4 - - + +
846A GLU 5.0 0.2 - - - -
812B GLU* 4.8 0.6 + - - -
816B ILE* 3.6 23.0 - - + +
885B LEU* 3.9 21.0 + - + +
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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