Contacts of the strand formed by residues 82 - 90 (chain B) in PDB entry 5LS6
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 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B TYR* 3.1 28.3 - - + -
81B SER* 1.3 76.8 - - - +
83B LYS* 1.3 63.4 + - - +
376B MET* 4.2 7.4 - - + -
388B VAL* 4.5 15.5 - - + -
402B THR* 5.5 0.2 - - - +
404B LEU* 3.6 31.6 - - + +
418B PHE* 4.1 20.6 - + - -
422B SER 4.5 1.1 - - - -
423B SER 4.5 2.2 - - - -
425B LEU* 3.9 23.3 - - + -
437B TRP* 3.5 25.1 - - + -
438B ASP 2.9 24.9 - - - +
439B ARG* 3.3 26.2 - - + +
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Residues in contact with LYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 1.3 78.5 - - - +
84B CYS* 1.3 65.0 + - - +
85B VAL* 3.0 45.9 - - + +
129B GLN* 4.5 14.1 + - - -
437B TRP* 4.2 6.5 - - - -
438B ASP 3.0 13.1 + - - +
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Residues in contact with CYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LYS* 1.3 75.2 - - - +
85B VAL* 1.3 58.6 + - - +
86B ASN 3.1 28.3 - - - -
87B SER* 4.9 0.2 - - - -
406B HIS* 4.6 20.0 - - + +
435B TRP* 3.7 26.5 - - - -
436B ARG 3.5 8.5 - - - -
437B TRP* 3.7 34.6 - - + -
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 3.7 16.7 - - - +
83B LYS* 3.0 41.1 - - + +
84B CYS* 1.3 72.8 - - - +
86B ASN* 1.3 64.2 + - - +
129B GLN* 4.1 11.2 - - + +
130B GLY* 3.3 33.6 - - - +
436B ARG* 2.8 9.0 + - - +
438B ASP* 3.4 35.7 - - + +
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Residues in contact with ASN 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A SER* 3.3 15.9 + - - -
88A ASP* 6.0 0.7 - - - -
89A LEU* 3.5 22.6 + - - +
84B CYS* 3.1 25.5 - - - -
85B VAL* 1.3 79.4 - - - +
87B SER* 1.3 91.9 + - - +
88B LEU* 4.0 13.2 - - - +
130B GLY 2.7 27.2 + - - +
131B GLU* 4.3 0.2 - - - +
132B ILE* 3.8 13.3 - - + +
436B ARG* 3.5 26.0 + - + -
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER* 3.8 0.2 - - - -
88A ASP* 3.1 47.4 + - - +
84B CYS* 4.9 0.2 - - - -
86B ASN* 1.3 91.4 + - - +
88B LEU* 1.3 64.0 + - - +
132B ILE* 6.1 0.4 - - - -
406B HIS* 5.3 0.5 - - - -
433B SER* 6.0 0.2 - - - -
434B ILE 3.3 10.3 - - - -
435B TRP* 3.2 41.4 - - - -
436B ARG 4.9 0.2 - - - +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A VAL* 3.5 23.6 - - + -
86A THR 3.1 18.6 - - - +
87A SER* 4.4 4.9 - - - +
88A ASP 5.0 0.2 - - - +
94A GLN* 5.4 2.5 - - - +
86B ASN* 4.0 14.8 - - - +
87B SER* 1.3 73.0 - - - +
89B LYS* 1.3 58.8 + - - +
124B TYR* 4.3 9.9 - - + -
132B ILE* 3.6 45.1 - - + +
433B SER* 3.2 6.1 - - - -
434B ILE* 2.8 72.4 + - + +
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Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A VAL* 3.5 7.6 - - - +
86A THR* 3.1 37.5 + - - +
88B LEU* 1.3 79.0 - - - +
90B GLU* 1.3 77.0 + - - +
93B ASN* 4.3 11.0 - - - +
431B ASP* 3.5 41.4 + - - +
432B ALA* 3.4 11.9 - - + +
433B SER* 4.4 7.4 - - - -
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A CYS* 4.3 6.2 - - - -
84A SER 4.0 6.1 - - - +
85A VAL* 4.4 2.9 - - + -
89B LYS* 1.3 90.3 - - - +
91B ASP* 1.3 64.1 + - - +
92B HIS* 3.5 34.6 + - + +
93B ASN* 4.1 5.5 - - - +
96B LEU* 3.2 15.8 - - + +
115B THR* 2.9 26.2 + - - +
117B GLY 5.7 0.2 + - - -
120B ARG* 4.2 5.4 - - - +
122B THR* 2.9 19.3 + - - +
124B TYR* 3.0 23.8 + - - +
432B ALA* 3.0 21.4 + - + +
434B ILE* 4.3 5.6 - - + -
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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