Contacts of the strand formed by residues 53 - 58 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101E PHE* 5.2 1.3 - + - -
21F TRP* 3.3 10.5 - - - -
22F VAL 2.7 44.8 + - - +
25F LYS* 3.8 36.6 - - + -
38F VAL* 4.1 12.6 - - + -
51F GLN* 3.6 31.2 - - + -
52F TYR* 1.3 88.5 - - - +
54F PHE* 1.3 61.6 + - - +
55F GLU* 3.5 20.0 + - + +
87F VAL* 4.8 9.6 - - + -
88F LYS 4.4 7.9 - - - -
89F ALA* 3.8 26.9 - - + -
102F ILE* 3.9 8.3 - - + -
104F ILE* 4.5 17.5 - - + -
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Residues in contact with PHE 54 (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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350B GLN* 4.7 16.2 - - + -
351B PRO 5.6 0.2 - - - -
352B THR* 3.9 13.0 - - + -
379B MET* 3.7 26.9 - - + -
85E THR* 3.5 22.1 + - - -
86E PHE* 3.2 60.7 + + + +
101E PHE* 5.2 0.4 - - - -
19F SER* 3.9 18.8 - - - -
20F VAL 3.8 3.8 - - - -
21F TRP* 3.5 34.9 - + + -
53F PHE* 1.3 71.3 - - - +
55F GLU* 1.3 61.7 + - - +
56F THR* 4.1 15.2 + - - -
85F THR* 6.0 0.3 - - - +
104F ILE* 4.5 10.0 - - - +
105F ASP 3.9 5.9 - - - +
106F THR* 5.5 0.2 - - - -
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Residues in contact with GLU 55 (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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18F VAL 3.9 0.9 - - - +
19F SER* 3.4 3.4 - - - -
20F VAL* 2.9 37.4 + - + +
22F VAL* 3.2 36.7 - - + +
25F LYS* 3.0 31.7 + - - -
53F PHE* 3.6 13.1 - - + +
54F PHE* 1.3 81.0 - - - +
56F THR* 1.3 63.1 + - - +
57F LYS* 5.6 5.9 + - - +
104F ILE* 3.4 21.8 - - + +
105F ASP* 3.3 29.7 - - + +
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Residues in contact with THR 56 (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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350B GLN* 5.0 9.1 + - - +
84E HIS 5.4 0.3 + - - -
85E THR* 5.2 1.0 + - - -
17F SER* 3.8 22.7 - - - +
18F VAL 3.3 10.5 - - - +
19F SER* 3.2 23.0 + - - +
54F PHE* 4.1 14.4 - - - -
55F GLU* 1.3 76.5 - - - +
57F LYS* 1.3 61.2 + - - +
82F THR* 3.7 1.4 - - - +
105F ASP* 3.2 21.6 + - - +
106F THR* 3.3 32.1 + - - +
107F ALA* 3.4 10.9 + - - -
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Residues in contact with LYS 57 (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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17F SER* 3.3 6.7 - - - -
18F VAL* 3.0 41.0 + - + +
20F VAL* 4.7 17.6 - - + +
22F VAL* 5.9 2.2 - - - +
55F GLU* 5.6 6.2 + - - +
56F THR* 1.3 76.1 - - - +
58F CYS* 1.3 77.0 + - - +
82F THR* 3.6 20.2 - - + +
105F ASP* 4.3 15.8 + - + +
107F ALA 4.5 1.1 - - - -
108F CYS* 4.2 2.5 - - - -
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Residues in contact with CYS 58 (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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16F ASP 3.6 1.3 - - - +
18F VAL* 4.4 0.9 - - - +
57F LYS* 1.3 89.1 - - - +
59F ARG* 1.3 58.8 + - - +
60F ASP* 2.9 18.5 + - - +
80F CYS* 3.8 6.7 - - + +
81F THR* 3.0 36.8 - - - -
82F THR* 3.2 12.2 + - - +
108F CYS* 2.0 49.0 - - - +
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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