Contacts of the strand formed by residues 145 - 151 (chain E) in PDB entry 3SDI
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 GLY 145 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43E ASN 4.7 3.6 - - - -
141E TYR* 3.4 27.1 - - - -
142E ASP 3.1 20.0 + - - -
143E LYS 3.6 0.8 - - - -
144E SER* 1.3 79.3 - - - +
146E ALA* 1.3 62.4 + - - -
147E HIS* 3.1 17.0 - - - -
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Residues in contact with ALA 146 (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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41E ARG* 3.4 22.9 + - + +
42E SER 3.6 23.8 - - - +
43E ASN 4.1 6.8 + - - +
45E HIS 3.6 31.2 - - - +
46E ALA* 4.3 2.5 - - + -
140E GLY 3.5 6.1 - - - +
141E TYR* 3.5 10.9 - - + -
144E SER 4.8 0.7 - - - +
145E GLY* 1.3 74.2 - - - -
147E HIS* 1.3 70.0 + - - +
159E GLU* 4.7 0.2 - - - +
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Residues in contact with HIS 147 (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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41E ARG* 3.9 6.7 - - - +
46E ALA* 3.8 7.2 - - - +
109E VAL* 3.9 26.7 - - + -
110E GLU* 5.5 5.8 + - + -
138E ILE 4.3 0.9 - - - -
139E ILE* 3.3 5.2 - - - -
140E GLY 2.9 27.5 + - - +
142E ASP* 2.9 36.9 + - - -
144E SER* 3.0 23.3 + - - -
145E GLY 3.1 25.1 + - - -
146E ALA* 1.3 78.4 + - - +
148E LEU* 1.3 62.0 + - - +
149E LEU* 5.3 0.7 - - + -
159E GLU* 2.8 34.6 + - - +
63F LYS* 4.8 10.1 - - - -
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Residues in contact with LEU 148 (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 GLY* 3.3 42.0 - - - +
40E LEU 3.8 1.6 - - - +
41E ARG* 4.2 10.8 - - + +
137E LEU* 4.3 9.9 - - + -
138E ILE 3.2 13.7 - - - +
139E ILE* 3.8 18.2 - - + -
147E HIS* 1.3 76.0 - - - +
149E LEU* 1.3 88.7 + - - +
159E GLU* 3.4 3.5 - - - +
160E LEU* 3.2 36.2 + - + +
161E TYR 3.9 1.8 - - - +
162E GLY* 3.5 24.0 - - - +
163E THR* 3.8 11.7 - - + +
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Residues in contact with LEU 149 (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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109E VAL* 3.3 43.5 - - + +
110E GLU* 4.6 6.5 - - - +
112E ALA 5.0 0.4 - - - -
113E GLY* 3.8 18.4 - - - +
137E LEU* 3.3 6.1 - - - +
138E ILE* 2.7 53.8 + - + +
147E HIS* 5.3 0.4 - - + -
148E LEU* 1.3 93.0 - - - +
150E GLU* 1.3 60.2 + - - +
151E PHE 4.2 0.2 - - - -
157E VAL* 3.6 17.5 - - + -
158E THR 3.3 3.1 - - - +
159E GLU* 3.8 32.5 - - + +
160E LEU* 5.2 0.7 - - - -
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Residues in contact with GLU 150 (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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136E LEU 3.5 2.9 - - - +
137E LEU* 3.7 18.2 - - + -
149E LEU* 1.3 75.1 - - - +
151E PHE* 1.3 63.4 + - - +
152E GLN* 2.9 35.5 + - + +
156E ASN 3.4 2.3 - - - +
157E VAL* 3.2 9.0 - - - +
158E THR* 3.0 34.3 + - - +
160E LEU* 3.7 20.2 - - + +
163E THR* 2.9 28.1 + - + +
164E ALA 4.6 0.2 - - - +
165E ILE* 3.8 12.0 - - + +
173E LYS* 4.2 10.6 + - - -
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Residues in contact with PHE 151 (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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88E LEU* 4.0 26.5 - - + -
116E LEU* 3.7 35.7 - - + -
117E CYS 4.5 0.4 - - - -
120E ALA* 3.8 18.6 - - + -
132E TYR* 5.0 2.2 - - + -
134E VAL 3.5 21.3 - - - -
135E GLY* 3.4 6.2 - - - -
136E LEU* 2.8 50.9 + - + +
138E ILE* 4.4 11.7 - - + -
149E LEU 4.2 0.4 - - - -
150E GLU* 1.3 73.7 - - - +
152E GLN* 1.3 86.5 + - - +
153E PRO* 3.8 5.8 - - + -
155E GLY* 4.7 2.2 - - - -
156E ASN 3.7 2.2 - - - -
157E VAL* 3.8 22.4 - - + -
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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