Contacts of the strand formed by residues 857 - 864 (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 GLU 857 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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850H PRO* 4.2 19.7 - - + +
851H LYS 4.4 8.3 - - - +
852H GLN* 4.5 14.8 - - + +
856H PHE* 1.3 78.6 - - - +
858H LYS* 1.3 61.1 + - - +
859H ARG* 3.2 29.9 + - - +
877H VAL* 3.1 4.4 - - - +
878H LYS* 2.7 60.1 + - + +
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Residues in contact with LYS 858 (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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836C ASP* 5.0 6.5 + - - +
840C GLU* 6.0 0.2 + - - -
847H HIS* 3.2 38.1 + - + +
850H PRO* 3.5 25.0 - - + +
851H LYS* 4.1 18.6 + - + +
856H PHE* 4.3 1.0 + - - -
857H GLU* 1.3 74.0 - - - +
859H ARG* 1.3 74.9 + - - +
860H ALA 3.8 3.4 - - - +
861H LYS* 4.3 8.3 - - - +
875H ILE* 3.7 45.9 - - + +
876H HIS 4.0 0.9 - - - +
877H VAL* 3.5 13.5 - - + +
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Residues in contact with ARG 859 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840F GLU* 3.3 41.6 + - - +
846H PRO* 3.5 4.0 - - - +
847H HIS* 2.9 29.2 + - - +
849H LYS 5.2 2.7 - - - -
850H PRO* 5.4 1.9 - - + +
857H GLU* 3.2 28.5 + - - +
858H LYS* 1.3 80.6 - - - +
860H ALA* 1.3 66.8 + - + +
876H HIS* 2.9 13.4 + - + +
877H VAL 4.2 2.2 - - - -
878H LYS* 3.4 40.4 - - - +
883H GLU* 3.1 26.1 + - - -
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Residues in contact with ALA 860 (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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844H SER* 4.7 4.9 - - - -
845H ARG 3.5 7.0 - - - +
846H PRO* 3.3 28.3 - - + -
847H HIS* 3.2 20.3 - - - +
858H LYS* 3.8 0.5 - - - +
859H ARG* 1.3 85.0 - - + +
861H LYS* 1.3 59.1 + - - +
875H ILE* 3.2 8.8 - - - +
876H HIS* 2.8 37.1 + - + -
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Residues in contact with LYS 861 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836C ASP* 2.8 39.0 + - - +
839C LYS* 5.2 7.4 - - - -
840C GLU* 6.2 2.0 - - - -
844H SER* 3.7 2.6 - - - -
845H ARG 3.1 31.1 + - - +
847H HIS* 2.9 38.6 + - + +
858H LYS* 4.3 6.2 - - - +
860H ALA* 1.3 76.2 - - - +
862H ILE* 1.3 62.9 + - - +
863H PHE* 3.5 29.9 - - + -
872H ASP* 4.7 15.7 - - - +
874H GLY 3.3 11.7 - - - +
875H ILE* 4.4 5.8 - - + -
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Residues in contact with ILE 862 (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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838H PHE* 5.1 0.7 - - + -
842H PHE* 3.5 38.4 - - + -
843H VAL 3.4 4.5 - - - +
844H SER* 4.2 4.0 - - - +
861H LYS* 1.3 77.3 - - - +
863H PHE* 1.3 61.3 + - - +
872H ASP* 3.7 2.6 - - - +
873H TRP* 2.7 44.4 + - + -
874H GLY 2.9 26.1 + - - +
875H ILE 3.9 15.5 - - - +
876H HIS* 4.0 24.0 - - + +
885H PRO* 3.9 18.2 - - + -
886H VAL 4.4 0.4 - - - +
887H ILE* 4.3 12.1 - - + -
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Residues in contact with PHE 863 (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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842H PHE* 3.2 9.1 - - - -
843H VAL* 3.0 33.8 + - + +
845H ARG* 3.7 47.3 - - + -
861H LYS* 3.5 46.0 - - + -
862H ILE* 1.3 76.7 - - - +
864H CYS* 1.3 66.0 + - - +
870H SER* 3.7 28.9 - - - -
871H HIS 3.0 8.7 - - - +
872H ASP* 3.6 30.3 - - + -
873H TRP* 4.1 3.6 - - - +
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Residues in contact with CYS 864 (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* 3.8 0.7 - - - -
813H CYS* 3.7 18.4 - - - -
815H ALA* 5.2 0.9 - - - -
841H CYS 4.0 0.7 - - - -
843H VAL* 4.4 3.3 - - - +
863H PHE* 1.3 71.1 - - - +
865H ALA* 1.3 65.3 + - - +
866H ARG* 3.3 35.7 + - - +
869H CYS* 3.8 10.8 - - - -
870H SER* 3.3 19.6 + - - -
871H HIS 3.0 20.9 + - - +
873H TRP* 3.5 41.8 - - - +
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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