Contacts of the strand formed by residues 18 - 25 (chain F) in PDB entry 3IT8
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 18 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8F THR 4.3 0.4 - - - -
9F VAL* 2.9 7.8 - - - +
10F THR* 2.8 38.5 + - - +
12F LYS* 2.9 40.6 - - + +
16F LEU* 4.0 1.9 + - - -
17F TYR* 1.3 75.5 - - - +
19F GLY* 1.3 59.1 + - - +
20F VAL* 5.9 2.0 - - + -
35F TYR 4.7 3.5 - - - +
37F HIS* 3.0 26.7 + - - -
70F TYR* 4.0 1.1 - - - -
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Residues in contact with GLY 19 (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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8F THR 3.2 6.7 - - - -
9F VAL* 4.2 0.7 - - - -
18F ASP* 1.3 79.2 + - - +
20F VAL* 1.3 67.1 + - - +
34F SER* 3.1 4.7 - - - -
35F TYR* 2.9 29.2 + - - +
66F PHE* 3.9 7.2 - - - -
70F TYR* 3.8 25.3 - - - -
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Residues in contact with VAL 20 (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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6F ASN 3.7 0.7 - - - +
7F TYR* 3.5 2.4 - - - +
8F THR* 2.8 51.2 + - + +
10F THR* 5.7 2.7 - - - +
18F ASP* 5.9 1.6 - - + -
19F GLY* 1.3 79.7 - - - +
21F PHE* 1.3 62.5 + - - +
22F TYR* 4.2 24.0 - - + +
32F LYS* 4.5 15.0 - - - -
33F ILE 3.1 10.5 - - - +
34F SER* 4.0 11.7 - - - -
66F PHE* 3.9 5.8 - - - -
325F NAG 4.6 6.7 - - - +
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Residues in contact with PHE 21 (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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5F TYR* 3.9 16.4 - + + -
6F ASN 3.1 15.5 - - - -
7F TYR* 3.4 42.6 - + + -
20F VAL* 1.3 76.2 - - - +
22F TYR* 1.3 82.1 + - - +
23F ASP* 3.9 14.1 - - + -
31F THR* 4.3 3.4 - - + -
32F LYS* 3.3 7.1 - - - +
33F ILE* 2.7 52.5 + - + +
64F TYR* 3.2 46.4 - + + -
66F PHE* 3.7 21.3 - + + -
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Residues in contact with TYR 22 (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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4F LYS 3.5 1.7 - - - +
5F TYR* 3.5 5.2 - - - -
6F ASN* 2.9 45.1 + - + +
20F VAL* 4.2 20.9 - - + +
21F PHE* 1.3 85.1 - - - +
23F ASP* 1.3 60.2 + - - +
24F HIS* 3.9 23.7 - + + +
29F LEU* 3.9 21.8 - - + -
31F THR 3.4 1.6 - - - -
32F LYS* 3.6 42.1 + - + -
325F NAG 3.2 34.6 + - - -
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Residues in contact with ASP 23 (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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3F LEU* 3.6 4.3 - - - +
4F LYS 3.6 2.7 - - - -
5F TYR* 3.2 17.4 - - - -
21F PHE* 3.9 9.6 - - + -
22F TYR* 1.3 73.3 - - - +
24F HIS* 1.3 60.5 + - - +
29F LEU* 3.6 3.5 - - - +
30F VAL* 2.7 42.0 + - - +
31F THR* 2.9 27.4 + - - +
64F TYR* 2.9 23.1 + - - -
170F TYR* 2.7 36.1 + - - -
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Residues in contact with HIS 24 (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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2F THR* 3.7 0.7 - - - +
3F LEU* 3.4 4.2 - - - +
4F LYS* 2.8 69.3 + - + +
6F ASN* 5.9 0.4 - - + -
22F TYR* 3.9 31.3 - + + +
23F ASP* 1.3 74.9 + - - +
25F TYR* 1.3 60.7 + - - +
26F ASN 3.8 12.3 + - - +
27F ASP* 4.4 9.1 + - - -
28F GLN 3.4 2.7 + - - -
29F LEU* 3.4 41.4 + - + +
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Residues in contact with TYR 25 (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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1F ILE* 3.1 30.1 - - + +
2F THR 3.2 16.4 - - - -
3F LEU* 4.4 2.5 - - + -
24F HIS* 1.3 71.4 - - - +
26F ASN* 1.3 87.9 + - - +
28F GLN* 2.8 25.5 + - + +
30F VAL* 3.8 20.4 - - + +
50F TRP* 4.0 9.6 - + + -
167F ILE* 4.1 18.2 - - + -
170F TYR* 3.6 30.3 - + + -
171F GLN* 3.3 27.6 - - - +
174F ALA* 3.7 28.3 - - + -
178F ILE* 3.9 9.2 - - + -
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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