Contacts of the strand formed by residues 872 - 878 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840C GLU* 5.4 1.9 - - - +
861H LYS* 4.7 16.0 - - - +
862H ILE 3.7 1.4 - - - +
863H PHE* 3.6 24.9 - - + -
870H SER 3.8 0.6 + - - -
871H HIS* 1.3 83.5 + - + +
873H TRP* 1.3 64.3 + - - +
874H GLY* 2.7 24.2 + - - +
888H LYS* 3.2 24.9 + - - +
891H SER* 2.8 24.4 + - - -
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Residues in contact with TRP 873 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810H CYS* 3.7 23.6 - - + -
815H ALA* 5.7 0.9 - - + -
816H LEU 5.2 0.9 - - - -
817H ALA* 3.6 18.2 - - + -
838H PHE* 3.8 29.4 - + - -
841H CYS* 3.7 31.0 - - + -
842H PHE* 3.8 18.2 - + + -
862H ILE* 2.7 24.6 + - + +
864H CYS* 3.5 38.6 - - + +
871H HIS* 3.0 20.1 + - + -
872H ASP* 1.3 79.7 + - - +
874H GLY* 1.3 59.2 + - - +
887H ILE* 3.4 8.4 - - + +
888H LYS* 3.2 28.3 + - - +
891H SER* 4.0 9.7 + - - -
892H PHE* 3.6 32.9 - + + -
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Residues in contact with GLY 874 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861H LYS* 3.3 5.7 - - - +
862H ILE* 2.9 21.9 + - - -
872H ASP* 2.7 14.7 + - - +
873H TRP* 1.3 82.9 - - - +
875H ILE* 1.3 71.5 + - - +
886H VAL 3.5 8.1 - - - -
888H LYS* 4.4 11.9 - - - -
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Residues in contact with ILE 875 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856H PHE* 4.8 6.3 - - + -
858H LYS* 3.7 39.3 - - + +
860H ALA 3.2 11.0 - - - +
861H LYS* 4.1 10.1 - - + +
862H ILE* 3.7 8.1 - - - +
874H GLY* 1.3 82.3 - - - +
876H HIS* 1.3 58.6 + - - +
877H VAL* 3.4 26.5 - - + -
885H PRO* 3.4 3.3 - - - +
886H VAL* 2.7 52.5 + - + +
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Residues in contact with HIS 876 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839H LYS* 5.2 6.3 - - - -
842H PHE* 3.8 32.5 - + - -
844H SER* 4.3 9.2 + - - +
859H ARG* 2.9 30.9 + - + +
860H ALA* 2.8 24.4 + - + +
862H ILE* 4.0 9.5 - - + +
875H ILE* 1.3 72.7 - - - +
877H VAL* 1.3 64.5 + - - +
883H GLU* 3.5 42.7 + - + +
884H ILE* 3.6 19.7 + - - -
885H PRO* 4.3 2.6 - - + +
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Residues in contact with VAL 877 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856H PHE* 3.3 36.8 - - + -
857H GLU 3.1 9.2 - - - +
858H LYS* 3.5 16.6 - - + -
859H ARG* 4.2 4.5 - - - +
875H ILE* 3.4 35.4 - - + -
876H HIS* 1.3 73.3 - - - +
878H LYS* 1.3 59.8 + - - +
879H TYR 4.3 0.2 - - - +
883H GLU* 3.3 3.1 - - - +
884H ILE* 2.9 56.7 + - + +
886H VAL* 3.7 13.0 - - + -
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Residues in contact with LYS 878 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839F LYS* 2.9 37.0 + - - +
840F GLU* 4.2 11.9 - - - +
842F PHE 5.1 2.1 + - - -
856H PHE* 3.7 3.2 - - - +
857H GLU* 2.7 51.2 + - + +
859H ARG* 3.4 29.4 - - - +
877H VAL* 1.3 70.3 - - - +
879H TYR* 1.3 69.7 + - - +
881H THR* 3.0 31.6 + - - +
882H PHE 3.1 14.1 - - - +
883H GLU* 4.0 10.1 - - + +
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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
------------------------------------------------------------
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