Contacts of the strand formed by residues 843 - 846 (chain A) in PDB entry 2IVF
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 843 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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842A PRO* 1.3 90.3 - - + +
844A LYS* 1.3 61.3 + - - +
845A ILE 4.0 0.2 - - - -
876A MET* 4.1 5.6 - - + -
880A ASP* 3.5 33.2 - - + -
884A LEU* 3.9 29.2 - - + -
914A LYS* 3.3 29.6 - - + +
915A GLN 3.9 9.6 - - - -
916A CYS* 4.1 6.1 - - + -
970A ARG* 3.3 10.4 - - - -
971A VAL* 2.9 54.4 + - + +
973A ILE* 3.7 35.9 - - + -
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Residues in contact with LYS 844 (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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299A ARG* 6.0 0.6 - - - +
300A VAL* 3.2 42.0 + - + +
833A ASP* 4.6 10.1 + - - +
834A THR* 3.1 37.6 + - - +
842A PRO 4.0 1.8 + - - +
843A PHE* 1.3 71.8 - - - +
845A ILE* 1.3 63.0 + - - +
846A THR* 3.7 1.4 + - - +
914A LYS 2.9 12.8 + - - +
915A GLN* 3.3 8.3 - - - +
916A CYS 3.1 20.5 + - - +
968A GLY* 3.6 19.3 - - - +
969A VAL 3.5 3.4 - - - -
970A ARG* 3.7 35.9 - - - +
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Residues in contact with ILE 845 (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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843A PHE 4.0 0.4 - - - -
844A LYS* 1.3 71.4 - - - +
846A THR* 1.3 64.0 + - - +
894A LEU* 3.6 26.7 - - + -
916A CYS* 3.2 26.9 - - - +
918A VAL* 4.0 5.8 - - + -
932A TYR* 3.5 32.8 - - + -
935A LEU* 4.9 1.3 - - + -
936A LEU* 3.7 25.4 - - + -
966A ASP 3.4 4.8 - - - +
968A GLY 2.8 27.9 + - - -
969A VAL* 2.9 27.9 + - + +
971A VAL* 4.0 17.5 - - + -
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Residues in contact with THR 846 (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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284A ASP* 4.9 0.2 + - - -
300A VAL* 3.6 41.7 - - + -
845A ILE* 1.3 82.4 - - - +
847A GLY* 1.3 60.6 + - - +
915A GLN* 3.0 26.1 + - + +
916A CYS 2.8 7.6 + - - +
917A ILE* 3.2 13.9 - - - +
918A VAL 2.9 24.3 + - - +
932A TYR* 4.2 5.6 + - - -
966A ASP* 5.3 0.4 - - - -
967A ARG* 4.1 6.5 - - - +
968A GLY 4.4 2.5 - - - +
1986A MGD 3.8 27.9 - - + +
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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
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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