Contacts of the strand formed by residues 872 - 879 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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861C LYS* 4.0 19.2 + - - +
862C ILE 3.8 5.3 - - - +
863C PHE* 3.5 25.2 - - + -
870C SER 3.8 1.0 + - - -
871C HIS* 1.3 79.6 + - + +
873C TRP* 1.3 53.3 + - - +
874C GLY* 4.4 7.1 + - - +
888C LYS* 2.5 38.7 + - - +
891C SER* 2.8 32.6 - - - -
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Residues in contact with TRP 873 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810C CYS* 3.9 31.1 - - + +
815C ALA* 5.3 2.2 - - + -
817C ALA* 3.7 17.7 - - + -
838C PHE* 3.8 25.4 - + - -
841C CYS* 3.2 34.3 - - + -
842C PHE* 3.6 22.7 - - + -
862C ILE* 2.8 22.5 + - + +
864C CYS* 3.8 30.9 - - + +
871C HIS* 3.3 14.3 + + - +
872C ASP* 1.3 78.8 - - - +
874C GLY* 1.3 59.2 + - - +
887C ILE* 3.3 6.9 - - + +
888C LYS* 2.8 28.2 + - - -
891C SER* 3.3 16.2 + - - -
892C PHE* 3.4 30.7 - + + -
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Residues in contact with GLY 874 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861C LYS* 3.5 5.6 + - - +
862C ILE* 2.6 35.7 + - - +
872C ASP* 3.7 7.1 + - - +
873C TRP* 1.3 82.1 - - - +
875C ILE* 1.3 61.4 + - - +
886C VAL 3.3 9.2 - - - -
887C ILE* 4.2 1.8 - - - -
888C LYS* 4.4 15.5 - - - -
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Residues in contact with ILE 875 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853C PHE* 3.2 34.1 - - + -
856C PHE* 3.8 10.1 - - + -
858C LYS* 3.9 22.2 - - + +
860C ALA 3.3 15.0 - - - +
861C LYS* 4.2 13.0 - - - +
862C ILE* 3.8 6.2 - - - +
874C GLY* 1.3 78.4 - - - +
876C HIS* 1.3 61.2 + - - +
877C VAL* 3.3 26.0 - - + -
885C PRO* 3.5 2.6 - - - +
886C VAL* 2.8 44.2 + - + +
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Residues in contact with HIS 876 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842C PHE* 3.8 32.0 - + - -
844C SER* 4.8 6.7 - - - -
859C ARG* 2.9 29.4 + - + +
860C ALA* 2.9 24.1 + - + +
862C ILE* 3.8 10.5 - - + -
875C ILE* 1.3 73.0 - - - +
877C VAL* 1.3 65.6 + - - +
883C GLU* 3.4 18.1 + - + +
884C ILE* 3.3 32.1 + - - -
885C PRO* 3.8 15.8 - - + +
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Residues in contact with VAL 877 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826C ILE* 6.0 0.2 - - + -
856C PHE* 3.7 28.9 - - + -
857C GLU 3.2 13.2 - - - +
858C LYS* 3.6 12.3 - - - -
859C ARG* 4.3 5.8 - - - +
875C ILE* 3.3 34.8 - - + -
876C HIS* 1.3 82.8 + - - +
878C LYS* 1.3 63.9 + - - +
879C TYR* 4.4 1.8 - - + +
882C PHE 3.6 0.2 - - - +
883C GLU* 3.3 4.3 - - - -
884C ILE* 2.8 50.9 + - + +
886C VAL* 4.1 13.9 - - + -
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Residues in contact with LYS 878 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856C PHE* 3.2 5.2 - - - +
857C GLU* 2.9 45.6 + - + +
859C ARG* 3.0 40.9 - - - +
877C VAL* 1.3 75.6 - - - +
879C TYR* 1.3 60.6 + - - +
880C LYS 4.0 19.3 + - - +
881C THR* 5.4 4.7 - - - +
882C PHE 3.2 11.9 - - - +
883C GLU* 4.6 2.7 - - + +
813G CYS* 4.5 16.4 + - - +
814G LYS* 5.7 3.8 - - - +
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Residues in contact with TYR 879 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826C ILE* 3.7 37.6 - - + +
827C GLU* 3.1 28.3 + - + +
855C SER 3.5 18.8 - - - -
856C PHE* 4.2 6.5 - - + -
877C VAL* 3.9 3.2 - - + -
878C LYS* 1.3 72.1 - - - +
880C LYS* 1.3 91.8 + - + +
881C THR 2.9 0.9 + - - -
882C PHE* 2.7 33.3 + + - +
884C ILE* 3.7 21.3 - - + -
918C PHE* 3.8 32.4 - + - +
909E LYS* 3.3 17.2 + - - -
868G ASN* 3.9 13.5 - - - -
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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