Contacts of the strand formed by residues 68 - 76 (chain F) in PDB entry 5IJ7
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 PHE 68 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67F SER* 1.4 95.8 - - - +
69F LYS* 1.3 60.0 + - - +
362F MET* 5.3 0.7 - - - -
374F VAL* 4.0 23.1 - - + -
388F THR* 4.9 0.9 - - - -
390F LEU* 3.7 38.6 - - + +
404F PHE* 4.0 16.2 - + - -
408F SER 4.2 5.2 - - - -
409F SER 4.6 0.7 - - - -
411F LEU* 4.1 13.5 - - + -
423F TRP* 3.6 32.5 - - + -
424F ASP 3.2 2.9 - - - -
425F ARG* 3.5 60.8 - - + -
426F LEU 4.9 1.6 - - - +
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Residues in contact with LYS 69 (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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68F PHE* 1.3 74.6 - - - +
70F CYS* 1.4 71.7 + - - +
71F VAL* 3.1 17.9 + - + +
423F TRP* 3.4 3.8 - - - -
424F ASP* 2.8 37.6 + - + +
426F LEU* 5.7 6.2 + - + +
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Residues in contact with CYS 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 4.3 11.5 - - - +
69F LYS* 1.4 79.8 - - - +
71F VAL* 1.3 62.3 + - - +
72F ASN 4.0 10.8 - - - -
392F HIS* 4.0 23.2 - - + -
421F TRP* 3.7 30.7 - - - -
422F ARG 3.4 12.6 - - - -
423F TRP* 3.4 35.5 - - + -
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Residues in contact with VAL 71 (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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89B LEU* 3.7 11.2 - - - +
91B PHE* 3.8 9.4 - - - -
69F LYS* 3.7 17.5 - - + +
70F CYS* 1.3 75.1 - - - +
72F ASN* 1.4 63.4 + - - +
115F GLN* 4.6 3.3 - - - +
116F GLY* 3.5 37.3 - - - +
422F ARG* 2.9 19.4 + - + +
424F ASP* 3.3 36.1 - - + +
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Residues in contact with ASN 72 (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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87B SER* 3.1 13.7 + - - -
89B LEU* 3.7 11.7 - - - +
91B PHE* 3.6 23.9 - - - +
70F CYS* 3.7 5.5 - - - -
71F VAL* 1.4 75.9 - - - +
73F SER* 1.3 82.8 + - - +
74F LEU* 3.5 18.5 - - - +
116F GLY 2.7 29.9 + - - +
118F ILE* 3.7 26.4 + - + +
421F TRP* 3.6 2.1 - - - -
422F ARG* 2.8 33.9 + - + +
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Residues in contact with SER 73 (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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87B SER* 3.3 4.2 - - - -
88B ASP* 3.1 46.8 + - - -
89B LEU* 4.1 9.6 - - - +
72F ASN* 1.3 86.9 + - - +
74F LEU* 1.3 62.6 + - - +
419F SER* 4.7 0.5 - - - -
420F ILE 3.1 6.0 + - - -
421F TRP* 3.2 44.5 + - - -
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Residues in contact with LEU 74 (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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85B VAL* 3.4 28.5 - - + -
86B THR 3.2 7.9 - - - +
87B SER* 4.5 5.8 - - - -
88B ASP* 4.6 1.7 - - - +
91B PHE* 5.8 0.4 - - + -
94B GLN* 5.8 0.9 - - - +
72F ASN* 3.5 27.8 - - - +
73F SER* 1.3 80.9 + - - +
75F LYS* 1.3 59.7 + - - +
110F TYR* 3.6 23.8 - - + -
118F ILE* 3.8 34.5 - - + +
419F SER* 3.1 7.6 - - - -
420F ILE* 2.8 49.4 + - + +
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Residues in contact with LYS 75 (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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84B SER 4.1 0.2 - - - +
85B VAL* 3.5 7.4 - - - -
86B THR* 2.9 51.4 + - + -
88B ASP* 4.6 19.8 + - - +
74F LEU* 1.3 74.3 - - - +
76F GLU* 1.4 72.2 + - - +
77F ASP* 3.8 1.0 + - - -
79F ASN* 3.7 21.3 - - - +
417F ASP* 3.5 30.8 + - - +
418F ALA 3.4 6.1 - - - +
419F SER* 4.3 16.1 - - - -
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Residues in contact with GLU 76 (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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84B SER 4.2 5.2 - - - -
85B VAL* 4.5 2.5 - - + -
75F LYS* 1.4 78.6 - - - +
77F ASP* 1.4 63.9 + - - +
78F HIS* 2.9 42.1 + - + +
79F ASN* 3.4 11.1 + - - +
82F LEU* 3.4 11.8 - - + +
101F THR* 3.0 29.3 - - - +
103F GLY 5.3 0.3 + - - +
106F ARG* 4.7 7.9 - - - +
108F THR* 3.3 20.6 + - - -
110F TYR* 2.5 30.1 + - - +
418F ALA* 2.9 23.5 + - - +
420F ILE* 3.8 8.0 - - + +
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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