Contacts of the strand formed by residues 872 - 879 (chain F) in PDB entry 2QFD
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 ASP 872 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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861F LYS* 4.4 16.3 - - - +
862F ILE 3.3 9.7 - - - +
863F PHE* 3.8 22.6 - - + -
870F SER 3.7 1.0 + - - -
871F HIS* 1.3 84.0 + - + +
873F TRP* 1.3 58.5 + - - +
874F GLY 3.6 13.4 + - - +
888F LYS* 3.3 22.9 + - - +
891F SER* 2.7 31.4 + - - -
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Residues in contact with TRP 873 (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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810F CYS* 3.4 44.6 - - + +
815F ALA* 5.8 1.6 - - + -
816F LEU 5.1 1.8 - - - -
817F ALA* 3.9 17.9 - - + -
838F PHE* 3.9 31.4 - + - -
841F CYS* 3.5 31.6 - - + -
842F PHE* 4.0 11.4 - - + -
862F ILE* 3.0 22.5 + - + +
864F CYS* 3.5 26.2 - - + +
871F HIS* 3.5 16.2 - + - +
872F ASP* 1.3 80.9 - - - +
874F GLY* 1.3 58.7 + - - +
886F VAL 4.7 0.2 - - - -
887F ILE* 3.3 9.8 - - + +
888F LYS* 2.8 29.2 + - - +
891F SER* 4.0 5.6 - - - -
892F PHE* 3.6 29.2 - + + -
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Residues in contact with GLY 874 (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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861F LYS* 3.6 5.4 - - - +
862F ILE* 3.1 18.7 + - - +
872F ASP* 3.6 10.4 + - - +
873F TRP* 1.3 82.0 - - - +
875F ILE* 1.3 72.1 + - - +
886F VAL 3.5 7.6 - - - -
888F LYS* 3.4 20.8 - - - +
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Residues in contact with ILE 875 (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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853F PHE* 4.0 20.2 - - + -
856F PHE* 4.0 18.2 - - + -
858F LYS* 3.7 28.9 - - + +
860F ALA 3.1 11.7 - - - +
861F LYS* 4.5 4.9 - - + -
862F ILE* 3.2 12.7 - - - +
874F GLY* 1.3 81.5 - - - +
876F HIS* 1.3 59.5 + - - +
877F VAL* 3.4 26.5 - - + -
886F VAL* 2.8 42.4 + - + +
888F LYS* 6.2 0.2 - - + -
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Residues in contact with HIS 876 (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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842F PHE* 3.6 35.9 - + - -
844F SER* 4.5 15.5 - - - -
858F LYS* 4.0 0.2 - - - -
859F ARG* 2.9 27.3 + - + +
860F ALA* 2.7 21.1 + - + +
862F ILE* 3.6 13.2 - - + +
875F ILE* 1.3 73.6 - - - +
877F VAL* 1.3 64.9 + - - +
883F GLU* 3.6 21.5 - - + +
884F ILE* 3.1 43.3 + - - -
885F PRO* 3.9 3.0 - - - +
881H THR* 6.0 0.2 - - - -
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Residues in contact with VAL 877 (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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856F PHE* 3.5 39.3 - - + -
857F GLU 3.1 10.5 - - - +
858F LYS* 3.7 7.4 - - - -
859F ARG* 4.2 2.7 - - - +
875F ILE* 3.4 34.5 - - + -
876F HIS* 1.3 81.7 + - - +
878F LYS* 1.3 59.8 + - - +
883F GLU* 3.3 6.7 - - - +
884F ILE* 2.7 64.4 + - + +
886F VAL* 4.2 8.7 - - + -
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Residues in contact with LYS 878 (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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856F PHE* 3.1 6.0 - - - +
857F GLU* 2.6 64.6 + - + +
859F ARG* 3.5 28.0 - - - +
877F VAL* 1.3 72.2 - - - +
879F TYR* 1.3 61.2 + - - +
880F LYS 3.5 21.9 + - - +
881F THR* 5.4 2.7 - - - +
882F PHE 4.1 2.9 - - - +
883F GLU* 2.9 20.9 - - - +
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Residues in contact with TYR 879 (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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826F ILE* 3.8 22.6 - - + +
827F GLU* 2.7 43.8 + - - -
855F SER 3.2 22.9 - - - -
856F PHE* 4.1 5.8 - - + +
877F VAL* 3.9 0.8 + - + -
878F LYS* 1.3 72.9 - - - +
880F LYS* 1.3 104.5 + - + +
882F PHE* 2.6 37.9 + + + +
884F ILE* 3.5 21.8 - - + -
918F PHE* 3.7 38.7 - + - -
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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