Contacts of the strand formed by residues 72 - 77 (chain R) in PDB entry 1U8F
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 ASN 72 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23R PHE* 3.4 26.9 - - + -
29R ASP* 6.6 0.2 - - - -
30R ILE 5.5 2.5 - - - +
67R LEU 3.5 1.6 - - - +
68R VAL* 3.4 3.9 - - - +
69R ILE 2.9 38.7 + - - +
70R ASN* 3.4 13.3 + - - +
71R GLY* 1.3 80.3 - - - +
73R PRO* 1.3 71.1 - - + +
74R ILE* 3.6 6.1 + - + +
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Residues in contact with PRO 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R ILE 4.9 1.0 - - - +
31R VAL* 4.5 8.8 - - - +
66R LYS* 4.1 23.0 + - + +
67R LEU 3.8 3.6 - - - +
68R VAL* 4.3 17.5 - - + -
71R GLY 3.3 9.9 - - - +
72R ASN* 1.3 85.6 - - + +
74R ILE* 1.3 61.9 + - - +
75R THR 4.3 0.3 + - - -
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Residues in contact with ILE 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R THR* 5.1 0.2 - - + -
23R PHE* 3.9 20.2 - - + -
30R ILE* 3.6 23.8 - - + +
31R VAL 3.7 2.5 - - - -
32R ALA* 3.5 26.7 - - - +
33R ILE* 3.8 23.6 - - + -
66R LYS* 3.3 9.2 - - - +
67R LEU* 2.8 42.0 + - + +
69R ILE* 3.8 29.8 - - + -
72R ASN* 3.7 6.3 - - + +
73R PRO* 1.3 76.1 - - - +
75R THR* 1.3 70.2 + - - +
76R ILE* 3.5 4.5 + - + +
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Residues in contact with THR 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R VAL 3.0 16.7 + - - -
32R ALA* 3.1 7.9 - - - +
33R ILE 2.9 25.8 + - - +
66R LYS* 3.7 27.6 + - - +
73R PRO 4.3 0.8 + - - -
74R ILE* 1.3 70.9 - - - +
76R ILE* 1.3 64.8 + - - +
77R PHE* 3.6 32.9 + - + -
90R ALA* 4.4 12.4 + - + +
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Residues in contact with ILE 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R ILE* 3.4 17.0 - - + +
40R LEU* 3.9 30.7 - - + +
43R MET* 3.7 29.8 - - + -
65R GLY 4.5 13.0 + - - +
66R LYS* 5.1 0.2 - - - +
67R LEU* 3.8 18.2 - - + +
74R ILE* 3.5 13.0 + - + +
75R THR* 1.3 84.0 - - - +
77R PHE* 1.3 70.2 + - - +
78R GLN* 3.7 27.1 - - + +
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Residues in contact with PHE 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R ALA* 4.1 12.8 - - + -
33R ILE 2.8 13.3 + - - +
34R ASN* 3.0 22.4 - - + +
35R ASP 3.1 15.1 + - - -
75R THR* 3.6 26.7 - - + -
76R ILE* 1.3 78.1 - - - +
78R GLN* 1.3 78.3 + - - +
79R GLU* 4.5 9.4 - - + +
85R ILE* 3.5 27.4 - - + -
86R LYS* 3.5 38.4 - - + -
87R TRP* 4.5 3.6 - + - -
90R ALA* 4.0 16.6 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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