Contacts of the strand formed by residues 81 - 89 (chain W) in PDB entry 4N3E
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 TYR 81 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20W PHE* 3.5 10.2 - - - -
74W GLU* 3.3 41.7 + - + -
75W ILE* 3.5 3.2 - - - -
76W ASP* 2.8 56.0 + - + +
79W ASN* 4.6 2.0 - - + +
80W PHE* 1.3 73.1 - - - +
82W CYS* 1.3 69.6 + - - +
83W LYS* 4.1 4.5 - - - +
102W GLU* 2.3 47.6 + - + +
103W VAL 3.4 7.2 - - - -
104W LYS* 4.1 25.6 - - + -
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Residues in contact with CYS 82 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20W PHE* 4.5 0.9 - - + -
24W VAL* 3.6 32.5 - - + -
72W PHE* 3.9 19.5 - - - -
74W GLU 3.4 13.0 - - - -
75W ILE* 4.1 8.5 - - - -
81W TYR* 1.3 79.4 - - - +
83W LYS* 1.3 63.8 + - - +
84W TYR* 3.8 20.2 - - + -
101W TYR 4.4 0.2 - - - -
102W GLU* 3.2 9.8 - - - +
103W VAL* 2.9 40.3 + - + +
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Residues in contact with LYS 83 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72W PHE* 3.9 0.7 - - - -
73W ASP* 2.9 39.0 + - + +
74W GLU* 3.0 43.8 + - + +
81W TYR* 4.1 4.5 - - - +
82W CYS* 1.3 74.4 - - - +
84W TYR* 1.3 62.7 + - - +
100W VAL* 4.2 20.6 - - + +
101W TYR 3.4 3.6 - - - -
102W GLU* 3.7 30.4 + - + -
115X LYS* 5.1 13.9 - - - +
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Residues in contact with TYR 84 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23W LEU 4.4 0.6 + - - -
24W VAL* 4.7 11.9 - - + -
27W ARG* 3.8 28.3 + - - -
70W HIS* 3.7 31.0 - + + -
71W LYS 3.0 18.4 - - - +
72W PHE* 4.2 22.9 - + + -
73W ASP* 3.6 0.9 - - - -
82W CYS* 3.8 20.6 - - + -
83W LYS* 1.3 73.3 - - - +
85W THR* 1.3 60.1 + - - +
100W VAL* 3.5 3.2 - - - +
101W TYR* 2.8 76.0 + + + +
103W VAL* 4.3 15.0 - - + -
202W 2AN 3.7 21.5 - - - -
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Residues in contact with THR 85 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70W HIS* 3.1 7.6 - - - -
71W LYS* 2.6 44.6 + - + -
73W ASP* 3.0 22.3 + - - -
84W TYR* 1.3 73.4 + - - +
86W LEU* 1.3 74.9 + - - +
87W PHE* 3.4 14.0 + - + +
98W LYS* 3.8 25.8 + - + +
99W VAL 3.3 7.9 - - - +
100W VAL* 3.7 16.0 - - + +
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Residues in contact with LEU 86 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68W MET* 3.7 28.5 - - + -
69W LEU 3.7 16.2 - - - +
70W HIS* 3.7 23.6 - - + +
84W TYR 4.3 0.4 - - - -
85W THR* 1.3 68.1 - - - +
87W PHE* 1.3 58.2 + - - +
88W GLU 4.0 7.2 - - - +
91W VAL* 4.0 21.1 - - + -
92W LEU* 4.1 14.6 - - + +
98W LYS* 3.2 7.4 - - - -
99W VAL* 2.6 59.1 + - + +
101W TYR* 4.2 14.7 - - + +
203W 2AN 4.6 11.4 - - + -
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Residues in contact with PHE 87 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54W VAL* 3.5 23.1 - - + -
69W LEU* 3.3 31.3 + - + -
70W HIS 3.6 14.6 - - - -
71W LYS* 3.6 52.5 - - + -
85W THR* 3.4 13.4 + - + -
86W LEU* 1.3 73.2 - - - +
88W GLU* 1.3 74.4 + - + +
92W LEU* 3.1 13.9 - - - +
97W GLU 3.4 10.9 - - - +
98W LYS* 4.3 6.7 - - + -
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Residues in contact with GLU 88 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67W TYR* 2.5 32.1 + - - +
68W MET* 3.5 1.7 - - - -
69W LEU* 2.8 47.3 + - + +
86W LEU* 3.8 4.0 - - - +
87W PHE* 1.3 101.1 - - + +
89W GLY* 1.4 60.3 + - - +
92W LEU* 3.5 9.7 - - - +
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Residues in contact with GLY 89 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67W TYR* 3.3 31.2 - - - -
68W MET* 4.3 1.1 - - - -
88W GLU* 1.4 78.1 - - - +
90W ASP* 1.3 59.6 + - - -
91W VAL* 3.2 4.0 - - - -
92W LEU* 3.1 24.7 + - - +
93W ARG 4.7 0.3 + - - -
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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