Contacts of the strand formed by residues 82 - 89 (chain A) in PDB entry 5H15
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A TYR* 4.1 22.2 - - + -
81A SER* 1.3 77.1 - - - +
83A LYS* 1.3 60.3 + - - +
376A MET* 3.9 18.8 - - - -
388A VAL* 4.6 12.6 - - + -
401A CYS* 6.4 0.2 - - + -
404A LEU* 3.8 40.6 - - + +
418A PHE* 4.1 9.2 - + - -
422A SER 4.4 4.7 - - - -
425A LEU* 4.0 20.6 - - + -
437A TRP* 3.8 29.5 - - + -
438A ASP 3.2 8.3 - - - +
439A ARG* 3.4 43.7 - - + -
440A LEU* 4.3 8.4 - - - +
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Residues in contact with LYS 83 (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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82A PHE* 1.3 73.9 - - - +
84A CYS* 1.3 74.4 + - - +
85A VAL* 3.2 27.4 + - + +
437A TRP* 3.7 3.8 - - - -
438A ASP* 2.9 30.7 + - + +
440A LEU* 3.7 26.2 - - + +
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Residues in contact with CYS 84 (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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83A LYS* 1.3 80.8 - - - +
85A VAL* 1.3 59.8 + - - +
86A ASN 3.9 10.5 - - - -
406A HIS* 4.2 20.5 - - + -
435A TRP* 3.8 29.4 - - - -
436A ARG 3.5 12.8 - - - -
437A TRP* 3.3 39.8 - - + -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LYS* 3.2 39.0 + - + +
84A CYS* 1.3 74.0 - - - +
86A ASN* 1.3 64.9 + - - +
129A GLN* 5.0 4.6 - - - +
130A GLY* 3.5 30.8 - - - +
436A ARG* 2.9 15.3 + - + +
438A ASP* 3.5 36.1 - - + +
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Residues in contact with ASN 86 (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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84A CYS* 3.7 9.5 - - - -
85A VAL* 1.3 80.7 - - - +
87A SER* 1.3 82.7 + - - +
88A LEU* 5.7 0.8 - - - +
130A GLY 2.8 32.2 + - - +
131A GLU* 4.1 2.4 - - - +
132A ILE* 3.6 30.3 + - + +
436A ARG* 3.0 29.6 + - + +
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Residues in contact with SER 87 (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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84A CYS* 5.6 0.2 - - - -
86A ASN* 1.3 89.6 + - - +
88A LEU* 1.3 69.5 + - - +
132A ILE* 4.9 0.2 - - - -
406A HIS* 5.8 0.5 - - - -
408A LYS* 5.6 3.8 - - - -
434A ILE 3.1 15.5 - - - -
435A TRP* 3.5 37.5 - - - -
436A ARG 4.9 0.2 - - - +
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Residues in contact with LEU 88 (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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86A ASN* 5.7 0.9 - - - +
87A SER* 1.3 76.1 - - - +
89A LYS* 1.3 67.9 + - - +
90A GLU* 5.0 0.4 - - + -
124A TYR* 3.6 34.3 - - + +
132A ILE* 3.7 44.2 - - + +
432A ALA 4.7 0.2 - - - -
433A SER* 3.2 7.8 - - - -
434A ILE* 2.9 51.1 + - + +
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Residues in contact with LYS 89 (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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88A LEU* 1.3 82.9 - - - +
90A GLU* 1.3 73.8 + - - +
91A ASP* 3.7 2.4 + - - -
93A ASN* 3.4 26.0 + - - -
431A ASP* 3.4 38.2 + - - +
432A ALA 3.5 6.1 - - - +
433A SER* 4.4 8.1 - - - +
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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
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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