Contacts of the strand formed by residues 22 - 28 (chain F) in PDB entry 4IHB
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 ALA 22 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12F VAL* 4.2 20.4 - - + -
20F SER* 3.6 3.1 + - - -
21F ASP* 1.3 75.6 - - - +
23F TYR* 1.3 60.3 + - - +
37F VAL* 3.3 1.7 - - - -
38F ILE* 3.0 31.0 + - - +
41F SER 5.3 1.1 + - - +
44F PRO* 4.1 13.9 - - + -
46F TRP* 3.1 22.7 + - + -
69F VAL* 4.2 8.5 - - + -
70F LYS 3.2 9.9 - - - +
71F ASP* 4.4 0.4 - - - +
81F LEU* 4.6 3.1 - - + -
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Residues in contact with TYR 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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22F ALA* 1.3 73.2 - - - +
24F CYS* 1.3 66.5 + - - +
25F SER* 4.8 6.5 - - - -
32F LYS* 5.9 2.2 + - - -
34F ARG* 3.4 34.8 - - + -
35F THR* 3.6 8.5 - - - +
36F LYS 3.2 20.4 - - - +
37F VAL* 3.5 20.9 - - + -
46F TRP* 3.6 7.6 - - - +
68F VAL 3.9 0.3 - - - +
69F VAL* 3.5 2.4 - - - +
70F LYS* 2.9 83.8 + - + +
71F ASP 4.4 0.2 - - - -
72F HIS* 3.0 39.4 + + + -
74F THR 4.8 0.2 - - - -
75F MET 5.2 0.5 + - - -
77F ARG 5.4 0.9 + - - -
78F ASN 4.6 2.3 + - - -
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Residues in contact with CYS 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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6F ILE* 3.9 32.3 - - + +
23F TYR* 1.3 76.1 - - - +
25F SER* 1.3 71.7 + - - +
26F ALA 4.1 0.3 + - - -
34F ARG* 3.4 2.8 - - - +
35F THR* 2.8 49.6 + - + +
46F TRP* 4.0 13.6 - - + -
67F VAL* 4.2 6.5 - - - -
68F VAL 3.5 6.7 - - - -
69F VAL* 4.4 6.1 - - + +
117F LEU* 4.2 21.5 - - - -
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Residues in contact with SER 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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23F TYR* 4.1 4.9 + - - -
24F CYS* 1.3 76.4 - - - +
26F ALA* 1.3 60.9 + - - +
27F VAL* 4.7 3.1 - - - +
32F LYS* 3.1 40.2 + - - +
33F LYS 3.6 4.6 + - - -
34F ARG* 4.4 5.8 - - - +
66F HIS 3.8 0.5 - - - +
67F VAL* 3.3 3.8 - - - -
68F VAL* 2.6 52.9 + - - +
70F LYS* 4.6 11.4 - - - -
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Residues in contact with ALA 26 (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 VAL* 5.7 0.7 - - + -
6F ILE* 4.0 24.2 - - + -
24F CYS 4.1 0.4 + - - -
25F SER* 1.3 74.6 + - - +
27F VAL* 1.3 63.6 + - - +
31F VAL 3.7 1.9 - - - +
32F LYS* 3.4 2.3 - - - -
33F LYS* 2.8 39.5 + - + +
50F PHE* 5.6 0.4 - - + -
52F TRP* 3.8 22.3 - - + -
65F LEU* 4.4 4.7 - - + -
66F HIS 3.4 3.8 - - - +
67F VAL* 4.2 12.6 - - + +
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Residues in contact with VAL 27 (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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207A FMT 6.1 1.8 - - - -
25F SER* 4.7 3.6 - - - +
26F ALA* 1.3 78.8 - - - +
28F PHE* 1.3 65.7 + - - +
30F GLY* 4.5 10.1 - - - +
31F VAL 3.6 16.2 - - - +
32F LYS* 3.8 27.8 - - + +
64F GLU 4.4 1.7 - - - +
65F LEU* 3.7 3.6 - - - +
66F HIS* 2.8 51.8 + - + +
68F VAL* 6.6 0.2 - - + -
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Residues in contact with PHE 28 (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 LEU* 3.6 21.8 - - + -
27F VAL* 1.3 74.8 - - - +
29F ALA* 1.3 72.9 + - + +
30F GLY 3.0 2.5 - - - -
31F VAL 2.8 27.8 + - - -
52F TRP* 3.2 45.5 - - + +
53F ASP 5.3 0.7 - - - -
54F LEU* 3.6 31.2 - - + -
57F ILE* 4.0 18.8 - - + -
59F LEU* 5.1 6.1 - - + -
63F SER* 4.9 8.1 - - - -
64F GLU 4.0 13.7 - - - -
65F LEU* 3.9 11.4 - - + -
88F LEU* 3.3 31.6 - - + -
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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
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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