Contacts of the strand formed by residues 92 - 98 (chain F) in PDB entry 3E2A
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 HIS 92 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MET* 3.3 44.8 - - + +
3D LYS* 4.1 12.2 - - + +
4D ILE* 3.8 17.0 - - + +
36F HIS 4.0 5.8 + - - +
37F TYR* 3.4 33.7 - + + -
38F LEU 3.0 23.0 + - - -
90F ILE* 3.0 9.5 - - - +
91F GLU* 1.3 89.2 + - + +
93F ILE* 1.3 63.9 + - - +
94F ILE* 5.1 0.9 - - + -
175F SER* 2.7 30.4 + - - -
177F HIS* 3.0 14.5 + + + +
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Residues in contact with ILE 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F LEU* 3.4 34.1 - - + +
40F ILE* 4.1 11.2 - - + -
81F VAL* 4.2 16.4 - - + -
84F ALA* 5.6 0.4 - - + -
85F VAL* 3.7 29.6 - - + -
90F ILE* 5.0 2.7 - - + -
92F HIS* 1.3 80.2 - - - +
94F ILE* 1.3 61.0 + - - +
158F LEU* 3.5 25.6 - - + +
164F VAL* 4.7 0.9 - - + -
174F LEU* 3.9 12.1 - - + -
175F SER 3.0 6.3 + - - -
176F LEU* 3.3 21.7 - - + +
177F HIS* 2.8 32.9 + - - +
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Residues in contact with ILE 94 (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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4D ILE* 4.6 2.2 - - + -
7D LEU* 3.9 12.8 - - + -
37F TYR* 4.1 26.7 - - + -
38F LEU 2.8 11.7 + - - +
39F TRP* 3.4 33.4 - - + -
40F ILE* 2.7 33.6 + - - +
92F HIS* 5.1 0.2 - - + -
93F ILE* 1.3 78.5 - - - +
95F ILE* 1.3 68.9 + - - +
96F CYS* 4.1 0.6 + - + -
177F HIS* 3.6 16.8 - - + +
179F TRP* 3.6 51.6 - - + -
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Residues in contact with ILE 95 (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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40F ILE* 3.3 20.2 - - + +
68F ASN* 3.8 31.4 - - - +
70F VAL* 3.8 13.2 - - + -
94F ILE* 1.3 76.6 - - - +
96F CYS* 1.3 62.4 + - - +
97F GLY 4.1 0.2 - - - -
151F VAL* 4.1 9.6 - - + +
154F GLN* 3.3 45.5 - - + +
155F VAL* 3.4 13.9 - - + +
158F LEU* 4.1 16.8 - - + -
177F HIS 2.9 13.2 + - - +
178F GLY* 3.3 1.0 - - - -
179F TRP 2.9 26.5 + - - +
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Residues in contact with CYS 96 (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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39F TRP* 3.3 47.6 - - + +
40F ILE 2.8 9.5 + - - -
41F GLY* 3.5 18.9 - - - -
42F CYS* 3.9 2.9 + - - +
52F LEU* 5.3 0.9 - - - -
68F ASN* 3.7 8.8 - - - +
94F ILE* 4.0 2.7 - - + -
95F ILE* 1.3 74.4 - - - +
97F GLY* 1.3 74.9 - - - +
98F HIS* 5.1 0.7 - - - -
179F TRP* 3.4 8.7 - - + -
181F PHE* 4.0 10.3 - - - -
188F LEU* 4.0 20.4 - - - -
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Residues in contact with GLY 97 (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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68F ASN* 3.5 16.8 - - - -
96F CYS* 1.3 81.7 - - - +
98F HIS* 1.3 65.1 + - - +
147F THR* 5.1 3.1 - - - -
151F VAL* 3.5 20.7 - - - +
179F TRP 2.9 10.1 + - - -
180F VAL* 3.9 4.9 - - - -
181F PHE 2.9 21.0 + - - -
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Residues in contact with HIS 98 (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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42F CYS* 3.6 10.5 - - + +
44F ASP* 3.5 15.5 - - + +
45F SER* 3.7 18.5 + - - +
68F ASN* 4.7 0.2 - - - -
96F CYS 5.1 0.4 - - - -
97F GLY* 1.3 77.7 - - - +
99F THR* 1.3 65.5 + - - +
100F ASN 4.0 2.2 - - - -
101F CYS* 3.5 25.3 - - - +
147F THR* 3.3 21.5 - - - +
180F VAL* 4.0 1.3 - - - -
181F PHE* 3.1 21.8 - - + +
230F ZN 2.1 37.0 - - - -
231F SO4 2.5 47.1 + - - +
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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