Contacts of the strand formed by residues 53 - 58 (chain E) in PDB entry 2IFG
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 PHE 53 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E TRP* 3.4 8.2 - - - -
22E VAL* 2.7 48.2 + - + +
25E LYS* 3.6 39.9 - - + -
38E VAL* 3.9 13.7 - - + -
51E GLN* 3.8 24.0 - - + -
52E TYR* 1.3 83.9 - - - +
54E PHE* 1.3 62.6 + - - +
55E GLU* 3.5 19.7 + - + +
87E VAL* 4.8 11.9 - - + -
88E LYS 4.2 8.1 - - - -
89E ALA* 3.6 22.4 - - + -
102E ILE* 3.6 20.4 - - + -
104E ILE* 4.8 6.3 - - + -
101F PHE* 5.2 0.7 - - - -
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Residues in contact with PHE 54 (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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350A GLN* 5.1 10.5 - - + -
351A PRO 5.5 0.9 - - - -
352A THR* 3.9 11.0 - - + -
379A MET* 3.5 36.8 - - + -
19E SER* 3.9 11.4 - - - -
20E VAL 3.8 5.2 - - - -
21E TRP* 3.8 33.5 - + + -
53E PHE* 1.3 70.8 - - - +
55E GLU* 1.3 63.3 + - - +
56E THR* 4.0 16.1 + - - -
104E ILE* 4.9 6.1 - - - +
105E ASP 4.0 5.4 - - - +
106E THR* 5.5 0.2 - - - -
84F HIS 4.7 3.8 - - - -
85F THR* 3.6 23.0 + - - -
86F PHE* 3.4 59.5 + + + +
101F PHE* 5.0 1.0 - - - -
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Residues in contact with GLU 55 (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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18E VAL 3.8 0.7 - - - +
19E SER* 3.1 3.9 - - - -
20E VAL* 2.8 44.5 + - + +
22E VAL* 3.4 32.6 - - + +
25E LYS* 3.6 19.2 + - - -
53E PHE* 3.8 9.8 - - - +
54E PHE* 1.3 77.3 - - - +
56E THR* 1.3 64.4 + - - +
57E LYS* 4.3 5.5 + - - +
104E ILE* 2.8 39.5 - - - +
105E ASP* 3.5 28.1 + - + +
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Residues in contact with THR 56 (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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350A GLN* 5.2 7.9 + - - +
17E SER* 3.8 25.1 - - - +
18E VAL 3.3 8.5 - - - +
19E SER* 3.1 26.6 + - - +
54E PHE* 4.0 12.1 - - - -
55E GLU* 1.3 75.0 - - - +
57E LYS* 1.3 63.5 + - - +
105E ASP* 3.3 8.9 + - - +
106E THR* 3.1 30.5 + - - +
107E ALA* 3.0 24.3 + - - +
84F HIS 5.3 1.0 + - - -
85F THR* 5.4 0.9 + - - -
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Residues in contact with LYS 57 (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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17E SER* 3.2 5.5 - - - -
18E VAL* 3.0 38.6 + - + +
20E VAL* 4.5 20.2 - - - +
22E VAL* 6.0 1.4 - - - +
55E GLU* 4.3 6.1 + - - +
56E THR* 1.3 74.2 - - - +
58E CYS* 1.3 76.4 + - - +
82E THR* 3.6 19.3 - - + +
105E ASP* 3.8 20.3 + - - +
107E ALA 4.2 0.4 - - - -
108E CYS* 4.1 5.6 - - - -
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Residues in contact with CYS 58 (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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16E ASP 4.2 0.2 - - - +
18E VAL* 4.2 0.3 - - - +
57E LYS* 1.3 89.6 - - - +
59E ARG* 1.3 66.1 + - - +
60E ASP 3.6 2.3 + - - -
80E CYS* 4.1 5.2 - - + -
81E THR* 3.1 35.4 - - - -
82E THR* 3.1 14.5 + - - +
108E CYS* 2.0 48.9 - - - -
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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