Contacts of the strand formed by residues 80 - 86 (chain L) in PDB entry 4R2G
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 ASP 80 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30L ASN* 4.5 9.6 - - - +
31L SER* 2.9 37.9 + - - -
32L ASN* 5.4 0.7 + - - -
77L GLU 5.2 2.2 - - - +
78L ASP 3.1 10.6 + - - +
79L SER* 1.3 75.6 - - - +
81L THR* 1.3 80.5 + - - +
82L TYR* 3.9 18.2 - - + +
94L GLN* 3.7 5.1 - - - +
95L LEU* 3.0 29.7 + - - +
96L LEU* 5.5 0.2 - - - +
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Residues in contact with THR 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L ASN 3.3 2.1 - - - -
31L SER* 3.0 31.9 + - - -
80L ASP* 1.3 86.7 + - - +
82L TYR* 1.3 67.4 + - - +
83L ILE* 4.4 3.6 - - + +
92L GLU* 4.0 30.5 - - + +
93L VAL 3.7 11.2 - - - +
94L GLN* 3.5 22.2 + - + +
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Residues in contact with TYR 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L LEU* 3.7 19.3 - - + -
28L TRP* 3.8 22.0 - - + -
29L LYS 3.4 13.9 - - - +
30L ASN* 3.9 14.4 - - + -
36L ILE* 3.7 15.5 - - + -
51L LEU* 3.6 32.8 - - + +
69L LEU* 4.8 5.2 - - + -
71L ILE* 4.5 3.1 - - + +
78L ASP* 2.6 37.0 + - - +
80L ASP* 3.9 23.9 - - + +
81L THR* 1.3 71.3 - - - +
83L ILE* 1.3 64.2 + - - +
92L GLU* 3.5 2.8 - - - +
93L VAL* 2.9 38.5 + - - +
95L LEU* 4.0 17.5 - - + -
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Residues in contact with ILE 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L HIS 3.2 4.5 - - - +
28L TRP* 3.2 4.5 - - - -
29L LYS* 2.9 36.1 + - + +
30L ASN 3.1 31.0 - - - +
31L SER* 4.8 2.7 - - - -
33L GLN* 3.5 17.3 - - - +
81L THR* 4.4 4.5 - - + +
82L TYR* 1.3 79.7 - - - +
84L CYS* 1.3 62.1 + - - +
85L GLU* 3.9 5.4 - - + +
90L LYS* 4.3 24.7 - - + -
91L GLU 3.3 17.7 - - - +
92L GLU* 3.8 28.5 - - + +
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Residues in contact with CYS 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L CYS* 2.0 50.4 - - + -
26L PHE* 4.9 7.2 - - - -
27L HIS 3.4 4.9 - - - -
28L TRP* 3.6 35.6 - - + -
67L PHE 4.5 0.4 - - - -
83L ILE* 1.3 75.0 - - - +
85L GLU* 1.3 58.6 + - - +
86L VAL* 3.5 9.4 + - - +
89L GLN* 3.5 9.2 - - - +
91L GLU* 3.0 26.7 + - - +
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Residues in contact with GLU 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ASP* 4.3 13.4 - - - +
281A ALA* 4.6 5.5 - - - +
282A LYS* 6.0 1.0 - - - -
516A NAG 4.7 5.0 - - - +
25L GLN 4.2 1.2 - - - +
26L PHE* 3.4 3.6 - - - -
27L HIS* 2.9 51.8 + - + +
29L LYS* 3.1 34.6 + - + +
83L ILE* 3.9 5.4 - - + +
84L CYS* 1.3 69.8 - - - +
86L VAL* 1.3 58.8 + - - +
88L ASP 5.3 0.4 - - - -
89L GLN 3.2 6.5 - - - -
90L LYS* 3.4 40.0 + - + +
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Residues in contact with VAL 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L CYS* 3.8 28.0 - - - -
17L THR 3.9 15.0 - - - +
18L ALA* 3.8 24.4 - - + +
24L ILE* 4.3 10.1 - - + -
25L GLN 4.1 14.6 - - - +
26L PHE* 4.0 10.5 - - + -
67L PHE* 3.9 15.9 - - + -
84L CYS 4.2 3.1 - - - +
85L GLU* 1.3 73.3 - - - +
87L GLU* 1.3 73.1 + - + +
88L ASP 3.2 1.6 - - - +
89L GLN* 3.2 22.5 + - + +
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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