Contacts of the strand formed by residues 150 - 156 (chain E) in PDB entry 3DBL
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 LEU 150 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125E VAL* 5.3 1.1 - - - -
126E VAL* 3.5 17.9 - - + +
128E ALA* 4.5 2.5 - - + -
139E LEU* 4.3 10.5 - - + -
140E ALA* 3.5 39.7 - - + +
143E LEU* 3.8 23.6 - - + -
148E ILE 4.1 5.4 - - - +
149E PRO* 1.3 75.0 - - - +
151E LEU* 1.3 74.7 + - - +
152E ILE* 3.9 25.4 - - + -
164E ILE* 3.6 4.0 - - - +
165E ILE* 2.7 54.6 + - + +
166E ILE* 4.9 0.4 - - - +
508E ILE* 5.6 1.5 - - - +
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Residues in contact with LEU 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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45E ILE* 6.0 0.2 - - + -
125E VAL* 5.0 5.2 - - + -
126E VAL 2.9 11.4 + - - +
127E VAL* 3.4 12.9 - - + +
128E ALA 3.0 24.6 + - - +
150E LEU* 1.3 75.9 - - - +
152E ILE* 1.3 61.6 + - - +
153E CYS* 3.8 14.7 + - - -
162E MET* 3.7 25.8 - - + -
163E ARG 3.5 7.4 - - - +
164E ILE* 3.8 34.1 - - + +
501E ALA* 3.8 24.9 - - + +
504E GLU* 4.5 5.4 - - + -
505E VAL* 3.8 17.5 - - + -
508E ILE* 5.3 4.7 - - + -
516E PHE* 4.1 3.4 - - + -
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Residues in contact with ILE 152 (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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128E ALA* 3.7 15.5 - - + +
131E LEU* 5.3 4.9 - - + +
136E SER* 4.1 25.6 - - - +
139E LEU* 5.9 1.6 - - + -
140E ALA* 4.8 1.3 - - + -
150E LEU* 3.9 31.2 - - + -
151E LEU* 1.3 73.9 - - - +
153E CYS* 1.3 67.7 + - - +
154E ARG* 5.8 1.3 - - + -
161E TYR* 3.9 13.4 - - + +
162E MET* 3.5 2.3 - - - -
163E ARG* 2.9 45.2 + - + +
165E ILE* 4.2 8.7 - - + -
398E LEU* 4.0 27.4 - - + -
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Residues in contact with CYS 153 (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 THR* 4.3 19.5 - - + -
45E ILE* 3.9 21.5 - - + -
127E VAL* 4.5 1.6 - - - -
128E ALA 2.8 14.0 + - - +
129E THR* 3.3 6.0 - - + -
130E GLN* 3.2 20.4 + - - +
131E LEU 4.9 0.5 + - - -
151E LEU* 3.9 26.0 - - - -
152E ILE* 1.3 83.4 - - - +
154E ARG* 1.3 65.1 + - - +
161E TYR 3.3 6.5 - - - +
162E MET* 4.0 9.2 - - - -
497E LEU* 4.4 4.9 - - + -
501E ALA* 4.0 11.7 - - - -
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Residues in contact with ARG 154 (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 THR* 5.4 0.2 - - - -
130E GLN* 3.3 17.6 - - - +
131E LEU 4.7 16.2 + - - +
152E ILE* 5.8 1.8 - - + -
153E CYS* 1.3 78.4 - - - +
155E THR* 1.3 69.2 + - - +
156E TYR* 4.1 12.7 + - - +
159E VAL* 3.7 1.2 - - - +
160E GLY* 3.7 1.6 - - - -
161E TYR* 2.8 57.2 + - + +
429E LEU* 3.9 33.0 + - + +
432E VAL* 4.2 9.7 - - - +
433E ASP* 2.8 44.0 + - - -
442E TYR* 3.5 28.3 + - - -
497E LEU* 3.4 8.1 - - - +
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Residues in contact with THR 155 (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 THR* 2.9 24.9 + - - -
130E GLN* 2.9 27.2 + - - +
154E ARG* 1.3 75.6 + - - +
156E TYR* 1.3 69.4 + - - +
157E GLY 4.0 5.8 - - - +
159E VAL 3.6 3.8 - - - -
487E ALA 5.3 1.0 - - - +
488E ALA 4.4 2.4 - - - +
489E GLU* 3.8 29.6 - - + +
490E PRO* 4.3 0.2 - - + -
493E ILE* 3.8 23.6 - - + +
494E ALA* 3.7 11.7 + - - +
497E LEU* 3.5 14.7 - - - +
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Residues in contact with TYR 156 (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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154E ARG* 4.1 18.8 - - + +
155E THR* 1.3 76.3 - - - +
157E GLY* 1.3 60.3 + - - +
158E LEU 3.1 0.5 + - - -
159E VAL* 2.8 40.0 + - + +
429E LEU* 3.9 21.8 - - + -
432E VAL* 3.8 19.7 - - + -
442E TYR* 4.4 7.6 - + - -
443E PRO* 3.6 32.4 + - - +
482E PHE* 3.8 44.5 + + - -
485E TYR* 4.2 6.8 - + + -
487E ALA* 3.5 42.5 + - + +
488E ALA 3.8 2.2 - - - -
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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