Contacts of the strand formed by residues 253 - 257 (chain E) in PDB entry 1G3I
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 ILE 253 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LEU* 5.4 7.0 - - + -
34E ARG* 3.0 33.4 - - - +
67E ALA 5.1 1.1 - - - +
70E LEU* 4.8 10.3 - - + -
71E ALA* 3.9 25.6 - - + +
74E ALA* 5.9 0.9 - - + -
76E ALA* 4.1 15.5 - - + -
77E PRO 3.0 5.3 + - - +
78E PHE* 3.4 22.2 - - + -
79E ILE* 3.3 21.1 + - - +
103E LEU* 3.9 0.2 - - - +
252E GLY* 1.3 75.8 - - - +
254E VAL* 1.3 69.7 + - - +
255E PHE 4.1 0.4 - - - -
304E LEU* 3.3 21.8 - - + +
306E ILE* 3.6 31.9 - - + -
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Residues in contact with VAL 254 (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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79E ILE* 3.4 21.1 - - + +
81E VAL* 4.9 1.8 - - + -
99E ILE* 3.7 27.4 - - + -
100E ILE* 4.8 2.2 - - + -
103E LEU* 3.9 10.8 - - + -
253E ILE* 1.3 81.0 - - - +
255E PHE* 1.3 63.4 + - - +
256E ILE* 3.8 15.2 + - + -
303E ILE* 3.6 19.5 - - + -
304E LEU 2.9 7.2 + - - +
305E PHE* 3.5 28.6 - - + +
306E ILE* 2.8 26.5 + - - +
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Residues in contact with PHE 255 (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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55E MET* 4.4 1.1 - - + -
63E LYS* 3.7 22.0 - - + -
64E THR* 3.3 30.3 - - + -
67E ALA* 3.6 10.3 - - + -
78E PHE* 3.5 24.7 - + + -
79E ILE 2.8 10.1 + - - +
80E LYS* 3.3 23.2 - - + -
81E VAL* 3.0 26.7 + - - +
253E ILE 4.1 0.4 - - - -
254E VAL* 1.3 74.2 - - - +
256E ILE* 1.3 59.4 + - - +
257E ASP* 3.7 17.3 - - + -
306E ILE* 3.2 36.3 - - + -
308E SER* 3.5 29.2 - - - -
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Residues in contact with ILE 256 (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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81E VAL* 3.6 14.1 - - + +
83E ALA* 3.9 24.2 - - + -
99E ILE* 5.3 1.3 - - + -
254E VAL* 4.1 13.5 - - + -
255E PHE* 1.3 74.1 - - - +
257E ASP* 1.3 60.2 + - - +
259E ILE* 3.6 26.4 + - + -
282E LEU* 3.5 36.6 - - + -
286E VAL* 5.3 4.7 - - + -
305E PHE* 4.2 22.0 - - + -
306E ILE 2.8 12.7 + - - +
307E ALA* 3.3 7.4 - - + +
308E SER* 2.9 26.7 + - - +
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Residues in contact with ASP 257 (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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80E LYS* 3.7 30.8 + - - -
81E VAL 2.8 17.2 + - - +
82E GLU* 4.0 16.7 - - - +
83E ALA* 3.1 22.4 + - - +
255E PHE* 3.6 6.0 + - + -
256E ILE* 1.3 72.0 - - - +
258E GLU* 1.3 85.1 + - - +
259E ILE 2.9 4.3 + - - -
308E SER* 2.3 31.5 + - - -
454E ATP 2.7 33.4 + - - -
322F GLU* 5.5 0.9 - - - +
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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