Contacts of the strand formed by residues 805 - 812 (chain A) in PDB entry 4C48
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 SER 805 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729A ILE* 3.7 23.5 - - - +
730A ASP 3.3 7.6 - - - -
731A ILE* 4.0 9.6 - - - -
786A ILE* 4.7 6.1 - - - +
801A PHE* 2.8 32.7 + - - +
802A SER* 3.5 12.5 - - - +
804A PHE* 1.3 80.2 - - - +
806A SER* 1.3 66.3 + - - +
807A SER* 5.5 1.2 + - - -
112B ASN* 4.0 0.3 + - - -
144B LYS* 3.6 8.1 + - - -
145B PHE* 3.4 10.5 - - - -
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Residues in contact with SER 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728A LYS 3.8 0.2 - - - +
729A ILE* 3.4 2.7 - - - -
730A ASP* 2.8 47.2 + - - +
805A SER* 1.3 79.4 - - - +
807A SER* 1.3 61.0 + - - +
808A ARG* 5.6 2.0 + - - -
112B ASN* 3.5 25.4 - - - +
114B ILE* 5.5 7.3 - - - +
145B PHE* 3.9 19.8 - - - -
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Residues in contact with SER 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A PHE* 3.3 34.7 - - - -
728A LYS 3.1 10.8 - - - -
729A ILE* 4.6 4.7 - - - -
783A PRO 5.6 0.2 + - - -
786A ILE* 5.7 3.3 - - - +
805A SER* 5.5 1.5 + - - -
806A SER* 1.3 75.3 - - - +
808A ARG* 1.3 68.1 + - - +
79B LEU* 3.9 22.6 - - - +
110B ASP* 4.2 6.9 - - - +
112B ASN* 2.8 26.6 + - - +
114B ILE* 6.0 0.5 - - - +
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Residues in contact with ARG 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727A PHE* 3.9 2.0 - - - -
728A LYS* 2.9 64.1 + - + +
730A ASP* 2.7 25.6 + - - +
806A SER* 5.6 2.2 + - - -
807A SER* 1.3 81.7 - - - +
809A TRP* 1.3 68.7 + - - +
810A GLU* 4.4 12.7 + - - +
79B LEU* 4.0 9.8 - - - +
81B SER* 6.2 4.3 - - - -
89B HIS* 5.3 17.5 + - - -
110B ASP* 5.0 7.0 - - - +
114B ILE* 6.0 7.7 - - + +
119B LEU* 5.8 11.6 - - - +
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Residues in contact with TRP 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725A PRO* 3.9 14.6 - - + -
726A GLN* 3.4 45.3 - - - -
727A PHE* 3.8 25.3 - + + -
783A PRO* 4.1 15.6 - - + +
808A ARG* 1.3 80.1 - - - +
810A GLU* 1.3 62.9 + - - +
811A TYR* 6.3 0.2 - - + -
45B VAL 5.9 0.7 - - - -
46B VAL* 3.1 31.0 - - + -
48B TRP* 3.4 39.7 - - + +
56B TYR* 4.6 1.6 - - - -
77B ASP* 4.9 1.3 + - - +
78B THR* 3.3 28.2 - - + +
79B LEU* 3.7 21.7 - - + +
81B SER* 6.3 1.4 - - - -
86B LEU* 5.5 1.4 - - - +
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Residues in contact with GLU 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725A PRO* 3.3 5.4 - - - +
726A GLN* 2.7 59.6 + - + +
728A LYS* 4.1 32.3 + - + +
808A ARG* 4.4 14.6 + - - +
809A TRP* 1.3 77.0 - - - +
811A TYR* 1.3 67.7 + - - +
56B TYR* 3.6 20.4 - - + +
90B PHE* 5.5 2.6 - - + -
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Residues in contact with TYR 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723A ASP* 4.3 14.8 - - + +
724A THR* 3.5 9.6 - - - -
725A PRO* 3.6 39.7 - - + +
726A GLN* 3.0 10.7 - - - +
809A TRP* 6.3 0.4 - - + -
810A GLU* 1.3 88.3 - - - +
812A GLY* 1.3 57.3 + - - +
23B ARG* 4.3 22.7 - - - -
44B ASP* 4.3 10.9 + - - -
46B VAL* 4.5 2.0 - - + +
48B TRP* 3.4 38.2 - + - -
53B LEU* 3.1 27.1 - - + +
56B TYR* 3.1 30.2 + + + +
57B TRP* 4.4 9.9 - - + +
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Residues in contact with GLY 812 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692A HIS* 5.0 3.8 - - - -
723A ASP* 3.8 12.9 - - - +
724A THR* 2.8 30.7 + - - +
726A GLN* 3.0 17.3 + - - +
811A TYR* 1.3 78.1 - - - +
813A SER* 1.3 62.5 + - - -
814A PRO* 3.6 1.4 - - - +
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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