Contacts of the strand formed by residues 92 - 98 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C MET* 3.6 37.2 - - - +
3C LYS* 4.1 14.7 - - + +
4C ILE* 3.7 17.9 - - + +
36E HIS* 3.9 9.6 + - - +
37E TYR* 3.4 24.4 - + + +
38E LEU 2.9 10.6 + - - +
90E ILE* 2.4 27.2 - - - +
91E GLU* 1.3 89.8 + - + +
93E ILE* 1.3 59.1 + - - +
94E ILE* 4.1 1.1 - - + -
173E LYS* 4.2 10.7 + - - -
175E SER* 2.8 29.3 + - - -
177E HIS* 3.3 16.6 - - + +
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Residues in contact with ILE 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E LEU* 3.3 35.0 - - + +
40E ILE* 4.0 12.3 - - + -
81E VAL* 4.0 17.0 - - + -
85E VAL* 3.7 28.7 - - + -
90E ILE* 4.5 3.1 - - + -
92E HIS* 1.3 77.2 - - - +
94E ILE* 1.3 58.4 + - - +
158E LEU* 3.4 27.8 - - + +
164E VAL* 4.5 1.1 - - + -
174E LEU* 3.8 13.0 - - + -
175E SER 2.9 6.7 + - - -
176E LEU* 3.3 21.3 - - + +
177E HIS* 2.8 32.2 + - - +
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Residues in contact with ILE 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 4.5 2.5 - - + -
7C LEU* 5.1 2.5 - - + -
37E TYR* 3.9 33.4 - - + -
38E LEU 2.8 10.3 + - - +
39E TRP* 3.4 29.3 - - + -
40E ILE* 2.7 32.9 + - - +
60E LEU* 5.2 0.7 - - + -
92E HIS 5.0 0.2 - - - -
93E ILE* 1.3 78.6 - - - +
95E ILE* 1.3 66.8 - - - +
96E CYS* 3.8 2.0 + - + +
177E HIS* 3.5 16.8 - - + +
179E TRP* 3.5 56.8 - - + -
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Residues in contact with ILE 95 (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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40E ILE* 3.3 24.5 - - + +
68E ASN* 3.9 29.8 - - - +
70E VAL* 3.6 13.5 - - + -
94E ILE* 1.3 73.3 - - - +
96E CYS* 1.3 61.6 + - - +
151E VAL* 4.0 11.8 - - + +
154E GLN* 3.3 46.2 - - + +
155E VAL* 3.4 13.5 - - + +
158E LEU* 4.1 11.7 - - + -
177E HIS 2.8 14.3 + - - +
178E GLY* 3.4 1.0 - - - -
179E TRP 2.9 26.9 + - - +
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Residues in contact with CYS 96 (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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39E TRP* 3.3 46.4 - - + +
40E ILE 2.7 9.7 + - - -
41E GLY* 3.5 18.9 - - - -
42E CYS* 4.1 2.8 + - - +
52E LEU* 4.6 1.6 - - - -
68E ASN* 3.7 8.6 - - - +
94E ILE* 3.8 3.7 + - + -
95E ILE* 1.3 72.1 - - - +
97E GLY* 1.3 74.9 + - - +
98E HIS* 5.1 0.6 - - - -
179E TRP* 3.3 7.4 - - - -
181E PHE* 3.9 12.1 - - - -
188E LEU* 3.8 22.0 - - - -
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Residues in contact with GLY 97 (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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68E ASN* 3.7 21.7 - - - +
96E CYS* 1.3 80.6 - - - +
98E HIS* 1.3 62.4 + - - +
147E THR* 4.9 3.4 - - - -
151E VAL* 3.6 16.3 - - - +
179E TRP 2.8 9.7 + - - -
180E VAL* 3.9 5.4 - - - -
181E PHE 2.8 22.3 + - - -
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Residues in contact with HIS 98 (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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42E CYS* 3.4 18.4 - - + +
44E ASP* 2.9 13.9 - - - -
45E SER* 3.4 22.7 - - - -
68E ASN* 4.5 0.7 - - - -
96E CYS* 5.1 0.9 - - - -
97E GLY* 1.3 77.1 - - - +
99E THR* 1.3 69.9 + - - +
100E ASN 4.3 2.2 - - - -
101E CYS* 3.4 23.8 - - + +
147E THR* 3.3 23.0 - - - +
180E VAL* 4.0 3.4 - - - -
181E PHE* 3.2 15.7 - - + +
230E ZN 2.1 37.0 - - - -
233E SO4 3.2 35.4 + - - +
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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