Contacts of the strand formed by residues 60 - 66 (chain F) in PDB entry 3V5I
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 ILE 60 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28F ARG* 3.6 35.2 - - - +
30F ILE* 4.1 15.9 - - + -
48F LEU* 4.3 12.3 - - + +
51F LEU* 3.8 35.9 - - + -
59F ASP* 1.3 73.7 - - - +
61F TYR* 1.3 66.7 + - - +
62F LEU* 5.4 0.2 - - + -
84F ILE* 3.8 28.9 - - + -
86F PRO* 3.9 10.1 - - + -
87F ASP 2.8 8.9 + - - +
88F VAL* 3.4 9.9 - - + -
89F GLN* 2.7 35.5 + - - +
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Residues in contact with TYR 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F ASP 4.4 8.1 - - - -
28F ARG* 2.9 17.8 + - + +
29F ILE* 3.4 23.7 - - + +
30F ILE* 2.7 34.0 + - - +
59F ASP* 3.7 27.8 + - - -
60F ILE* 1.3 73.3 - - - +
62F LEU* 1.3 57.3 + - - +
63F TYR* 4.0 6.0 + + + -
89F GLN* 3.4 41.2 + - + -
91F ILE* 4.2 17.7 - - + -
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Residues in contact with LEU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ILE* 3.5 38.1 - - + +
32F LEU* 4.4 14.1 - - + -
44F ILE* 4.6 9.9 - - + -
48F LEU* 5.9 2.5 - - + -
60F ILE* 5.4 1.1 - - + -
61F TYR* 1.3 72.0 - - - +
63F TYR* 1.3 65.9 + - - +
64F ILE* 3.8 17.1 + - + +
77F ILE* 5.0 8.5 - - + -
81F ILE* 4.1 26.5 - - + -
88F VAL* 3.9 12.6 - - + -
89F GLN 2.8 15.5 + - - +
90F THR* 3.3 15.5 - - + -
91F ILE* 2.9 25.1 + - - +
103F LEU* 5.4 3.8 - - + -
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Residues in contact with TYR 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E VAL* 5.5 1.1 - - + -
49E LEU* 3.5 38.0 - - + +
80E THR* 6.1 0.2 - - - -
83E HIS* 5.4 3.8 - - - -
29F ILE* 3.8 31.3 - - + +
30F ILE 3.0 6.5 + - - +
31F MET* 3.8 26.9 - - + -
32F LEU* 2.9 32.0 + - - +
61F TYR* 4.5 8.8 - + + -
62F LEU* 1.3 73.5 - - - +
64F ILE* 1.3 60.7 + - - +
65F ASN 4.1 0.2 - - - -
91F ILE* 3.3 50.0 - - + +
93F ILE* 4.1 25.1 - - + -
115F LEU* 6.0 1.3 - - + -
190F MET* 5.3 6.9 - - + +
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Residues in contact with ILE 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F LEU* 3.6 21.1 - - + -
62F LEU* 3.8 19.1 - - + +
63F TYR* 1.3 80.7 - - - +
65F ASN* 1.3 62.1 + - - +
66F SER* 4.2 11.2 - - - +
90F THR* 4.0 18.8 - - + -
91F ILE 2.8 12.5 + - - +
92F CYS* 3.5 10.2 - - + -
93F ILE* 3.1 24.3 + - - +
95F MET 4.0 0.2 - - - +
96F ALA* 4.2 11.4 - - + -
100F GLY 4.0 14.6 - - - +
103F LEU* 4.0 11.0 - - + -
104F LEU* 3.7 37.2 - - + +
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Residues in contact with ASN 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ASP* 3.5 36.5 + - - +
41E ALA* 4.5 5.3 - - - +
42E ASN* 5.5 3.6 - - - +
72E THR* 4.8 2.8 + - - -
73E ALA* 4.5 6.5 - - - +
76E ALA* 4.2 14.1 - - - +
32F LEU 2.8 17.8 + - - +
33F GLY* 3.3 21.1 + - - +
63F TYR 4.1 0.2 - - - -
64F ILE* 1.3 71.6 - - - +
66F SER* 1.3 59.1 + - - +
93F ILE* 3.1 27.6 - - + +
94F GLY* 3.9 2.0 - - - -
95F MET* 3.1 26.5 + - - +
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Residues in contact with SER 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ASP* 5.2 0.2 - - - -
32F LEU* 4.2 17.0 - - - -
34F SER 3.0 20.4 + - - -
36F ILE* 3.8 8.8 - - - +
64F ILE* 4.0 10.8 - - - +
65F ASN* 1.3 75.6 + - - +
67F PRO* 1.3 64.0 - - - +
68F GLY* 3.0 20.1 + - - -
95F MET* 2.8 15.4 + - - +
96F ALA* 3.6 0.9 - - - -
97F ALA* 2.9 25.5 + - - +
100F GLY* 4.3 4.7 - - - -
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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