Contacts of the strand formed by residues 843 - 847 (chain F) in PDB entry 3N1Q
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 ILE 843 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835F THR* 4.5 0.2 - - - -
836F GLU 3.5 12.3 - - - +
837F ALA* 4.3 7.0 - - - -
838F VAL* 4.2 2.9 - - - +
842F GLN* 1.3 79.7 - - - +
844F MET* 1.3 71.1 + - - +
845F LEU* 4.3 1.3 - - + +
889F HIS 3.8 0.5 - - - +
890F MET* 3.7 2.1 - - - -
891F ILE* 2.9 38.7 + - + +
894F LEU* 4.0 15.5 - - + +
900F TYR* 4.2 10.5 - - + -
902F ILE* 4.1 15.9 - - + -
921F CYS* 3.6 49.8 - - + +
923F THR* 3.7 25.6 - - + +
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Residues in contact with MET 844 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834F TYR* 4.0 20.7 - - + +
835F THR* 3.3 2.9 - - - -
836F GLU* 2.7 39.4 + - + +
838F VAL* 3.5 19.0 - - + +
843F ILE* 1.3 75.6 - - - +
845F LEU* 1.3 68.4 + - - +
888F TRP* 3.8 27.8 - - + -
889F HIS 3.2 28.5 - - - +
890F MET* 3.5 34.3 - - + -
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Residues in contact with LEU 845 (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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832F ILE* 4.3 14.8 - - + -
834F TYR* 3.3 5.4 - - - +
835F THR* 3.6 17.7 - - + -
843F ILE 4.3 2.5 - - - +
844F MET* 1.3 81.7 - - - +
846F LYS* 1.3 61.1 + - - +
847F TRP* 3.8 15.7 - - + -
864F ILE* 4.2 20.9 - - + -
888F TRP* 3.3 5.5 - - - +
889F HIS* 3.1 43.2 + - + +
891F ILE* 3.8 29.4 - - + -
902F ILE* 3.7 27.1 - - + -
904F MET* 4.9 2.7 - - + -
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Residues in contact with LYS 846 (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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832F ILE* 3.6 3.1 - - - -
833F ALA* 2.6 45.3 + - + +
834F TYR* 3.1 41.7 + - + +
845F LEU* 1.3 74.6 - - - +
847F TRP* 1.3 64.5 + - - +
848F THR* 4.5 8.7 - - - -
887F GLN* 3.1 41.9 + - - +
888F TRP* 4.5 9.3 - - + +
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Residues in contact with TRP 847 (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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830F PRO* 4.3 7.4 - - + -
831F HIS 3.1 19.5 - - - +
832F ILE* 4.0 2.2 - - + -
833F ALA 4.0 1.1 - - - +
845F LEU* 3.8 17.9 - - + -
846F LYS* 1.3 80.4 + - - +
848F THR* 1.3 79.2 + - - +
849F TYR* 4.4 3.6 - - + +
862F PHE* 3.7 30.8 - + - -
864F ILE* 4.3 9.0 - - + -
882F VAL* 4.7 3.8 - - + -
886F LYS* 2.9 29.8 + - + -
887F GLN* 3.1 33.3 + - + +
888F TRP* 3.5 33.2 - - - -
889F HIS* 3.8 16.2 - - + -
904F MET* 3.4 42.0 - - + -
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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