Contacts of the strand formed by residues 909 - 913 (chain F) 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 CYS 909 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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874F ARG* 3.4 41.5 - - - +
876F ASN 3.7 7.0 + - - +
877F LEU* 3.4 14.9 - - - +
878F ALA 3.3 21.3 + - - -
907F VAL* 3.4 7.0 - - - +
908F THR* 1.3 79.1 - - - +
910F ILE* 1.3 63.3 + - - +
911F VAL* 5.2 0.2 - - - -
932F GLU* 3.3 24.5 - - + +
934F HIS* 4.0 18.4 - - - -
945F ILE* 4.8 2.7 - - - -
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Residues in contact with ILE 910 (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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768F LEU* 4.1 17.7 - - + -
878F ALA* 3.6 10.5 - - + +
898F LYS 5.0 0.7 - - - +
899F THR* 4.3 17.3 - - - +
902F ALA* 4.6 13.7 - - + -
907F VAL* 5.0 4.3 - - + -
909F CYS* 1.3 75.3 - - - +
911F VAL* 1.3 64.9 + - - +
912F LEU* 3.8 25.5 + - + -
920F PHE* 4.6 4.7 - - + -
931F LEU* 4.4 17.3 - - + -
932F GLU 2.9 17.3 + - - +
933F VAL* 3.5 20.9 - - + -
934F HIS* 2.9 26.9 + - - +
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Residues in contact with VAL 911 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877F LEU* 4.2 14.1 - - + -
878F ALA 3.0 7.0 + - - +
879F MET* 3.5 22.7 - - + -
880F THR 3.4 25.1 + - - +
909F CYS* 5.2 0.9 - - - -
910F ILE* 1.3 76.0 - - - +
912F LEU* 1.3 64.7 + - - +
934F HIS* 3.4 9.2 - - + +
936F VAL* 4.0 11.4 - - + -
942F ILE* 3.7 37.7 - - + -
945F ILE* 4.2 36.1 - - + -
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Residues in contact with LEU 912 (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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768F LEU* 5.5 1.3 - - + -
880F THR* 3.9 20.0 - - + -
895F ILE* 4.6 15.5 - - + -
898F LYS* 5.8 4.5 - - + -
899F THR* 5.0 3.6 - - - +
910F ILE* 3.8 24.2 + - + -
911F VAL* 1.3 78.0 - - - +
913F PRO* 1.3 75.0 - - + +
916F ASN* 4.9 4.3 - - + +
920F PHE* 3.3 46.9 - - + -
933F VAL* 4.1 6.5 - - + -
934F HIS 2.8 11.6 + - - +
935F PHE* 3.3 15.7 - - + -
936F VAL* 3.0 30.8 + - - +
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Residues in contact with PRO 913 (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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880F THR* 3.6 24.0 - - + +
881F GLY* 4.1 3.6 - - - -
889F ILE* 3.9 14.8 - - + +
890F LEU 3.1 31.0 - - - +
891F PRO* 3.6 13.9 - - + -
892F VAL* 4.2 2.2 - - + +
912F LEU* 1.3 90.5 - - + +
914F ALA* 1.3 61.1 + - - +
915F GLU 4.3 3.4 - - - +
916F ASN* 3.0 41.5 + - + +
935F PHE* 3.7 8.0 - - - -
936F VAL 3.7 6.5 - - - +
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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