Contacts of the strand formed by residues 23 - 28 (chain E) in PDB entry 1I8F
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 GLN 23 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E LYS* 1.3 76.2 - - - +
24E VAL* 1.3 66.3 + - - +
35E ARG* 4.1 22.5 + - - +
36E GLY* 3.2 23.1 + - - +
37E ILE* 3.6 15.4 - - + +
51E ASP* 5.3 6.4 - - - +
53E GLU* 4.2 11.1 - - - +
78E PRO* 3.6 3.5 - - - +
79E VAL* 2.9 54.5 + - + +
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Residues in contact with VAL 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E SER* 4.0 25.4 - - - +
22E LYS* 4.2 6.3 - - + +
23E GLN* 1.3 80.6 - - - +
25E LEU* 1.3 59.7 + - - +
26E VAL* 4.0 19.4 - - + +
35E ARG* 3.2 9.4 - - - +
36E GLY 2.8 39.7 + - - +
38E LEU* 4.3 11.2 - - + -
49E LEU* 4.1 14.4 - - + -
76E ILE* 3.9 19.3 - - + -
77E SER 3.3 7.9 - - - +
78E PRO* 3.9 13.0 - - + -
79E VAL* 4.2 3.1 - - - +
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Residues in contact with LEU 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E VAL* 1.3 72.7 - - - +
26E VAL* 1.3 65.1 + - - +
27E LYS* 4.5 2.2 - - + -
33E GLU* 3.6 31.4 - - + +
34E ILE 3.4 17.5 - - - +
35E ARG* 4.0 16.2 - - + -
75E PHE* 4.0 16.8 - - + -
76E ILE* 3.3 5.2 - - - +
77E SER* 2.8 43.1 + - - +
79E VAL* 4.7 6.9 - - + +
54F GLU* 4.3 2.0 - - - +
63F ARG* 3.4 50.5 - - - +
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Residues in contact with VAL 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E VAL* 4.0 19.7 - - + +
25E LEU* 1.3 80.1 - - - +
27E LYS* 1.3 64.2 + - - +
28E LEU* 3.5 27.3 + - + +
32E HIS 4.0 0.3 - - - +
33E GLU* 3.7 1.4 - - - -
34E ILE* 2.8 45.6 + - + +
47E LEU* 4.0 30.1 - - + -
49E LEU* 4.5 12.1 - - + -
68E VAL* 4.7 3.1 - - + -
73E VAL* 4.2 6.1 - - + -
75E PHE 3.4 11.9 - - - +
76E ILE* 4.0 7.0 - - + -
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Residues in contact with LYS 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LEU* 4.5 4.3 - - + -
26E VAL* 1.3 78.1 - - - +
28E LEU* 1.3 64.5 + - - +
32E HIS 3.3 10.1 - - - +
33E GLU* 3.7 36.6 + - + -
74E LEU* 2.9 34.5 + - + +
75E PHE* 3.2 36.7 + - + +
32F HIS* 4.3 16.1 - - + -
54F GLU* 2.8 39.4 + - - +
56F ILE* 3.7 16.2 - - - +
63F ARG* 4.3 3.7 - - - +
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Residues in contact with LEU 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D LEU* 4.3 35.2 - - + +
75D PHE* 4.5 1.8 - - + -
26E VAL* 3.5 26.7 - - + +
27E LYS* 1.3 77.2 - - - +
29E ARG* 1.3 72.6 + - - +
30E ASP 3.7 0.5 + - - -
31E SER* 3.7 3.8 + - - -
32E HIS* 2.9 33.0 + - + +
34E ILE* 3.6 29.8 - - + -
68E VAL* 3.8 9.0 - - + -
69E ARG 5.2 0.2 - - - +
72E ASN* 3.2 9.9 - - + +
73E VAL* 3.6 23.3 - - + +
74E LEU* 3.7 14.8 - - - +
32F HIS* 4.7 0.5 + - - -
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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