Contacts of the strand formed by residues 136 - 141 (chain E) in PDB entry 1EFX
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 MET 136 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E TYR* 3.9 1.6 - - - +
135E ASP* 1.3 89.3 - - + +
137E TYR* 1.3 67.3 + - - +
138E HIS* 4.7 4.4 - - - +
149E ARG* 2.8 52.3 - - + +
150E PHE 3.4 6.3 - - - +
151E SER* 4.8 0.4 - - - -
152E ALA 4.1 0.9 - - - +
179E GLY* 3.5 3.3 - - - -
180E SER* 2.8 60.0 + - - +
181E PHE 3.5 33.7 - - - +
182E ARG* 3.7 11.0 - - + +
185E PRO* 4.8 12.6 - - + -
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Residues in contact with TYR 137 (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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108E PRO* 4.4 7.4 - - + -
128E CYS* 3.6 24.9 - - + -
130E SER* 3.5 17.4 - - - -
132E SER 4.2 3.3 + - - -
134E TYR* 3.3 36.3 - + + +
136E MET* 1.3 75.8 - - - +
138E HIS* 1.3 63.8 + - - +
149E ARG* 3.3 26.3 - - - +
150E PHE 2.9 10.5 + - - -
152E ALA* 4.4 11.4 - - + -
160E PHE* 2.8 31.5 + - - +
161E GLN 3.4 10.3 - - - -
162E ALA* 3.0 31.6 - - + -
164E PHE* 3.6 11.2 - - + -
177E CYS* 4.1 6.1 - - - -
178E PHE 3.1 17.0 - - - -
179E GLY* 3.7 2.2 - - - -
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Residues in contact with HIS 138 (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 MET* 4.7 5.4 - - + +
137E TYR* 1.3 76.4 - - - +
139E LEU* 1.3 58.9 + - - +
140E SER 4.1 0.6 + - - -
147E GLU* 4.2 5.5 + - - +
148E CYS 3.4 6.7 + - - +
149E ARG* 3.3 35.9 - - + +
164E PHE* 4.2 2.5 - - - -
176E ARG 3.5 1.2 - - - +
177E CYS* 3.1 8.6 - - - -
178E PHE* 2.6 55.7 + - + +
180E SER* 3.2 20.1 + - - -
185E PRO 5.0 1.5 + - - -
188E TRP* 3.1 62.0 + + + -
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Residues in contact with LEU 139 (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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110E LEU* 4.0 26.5 - - + -
126E LEU* 4.1 13.2 - - + -
138E HIS* 1.3 72.7 - - - +
140E SER* 1.3 61.3 + - - +
146E HIS* 3.5 14.5 + - - +
147E GLU* 3.7 2.1 - - - +
148E CYS* 3.1 31.8 + - + -
164E PHE* 3.4 50.8 - - + -
166E LEU* 4.4 10.3 - - + -
175E TYR* 4.0 33.2 - - + -
176E ARG 3.6 10.8 - - - +
177E CYS* 4.9 1.8 - - + -
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Residues in contact with SER 140 (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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138E HIS 4.1 0.2 + - - -
139E LEU* 1.3 74.3 - - - +
141E ARG* 1.3 61.4 + - - +
142E GLU 3.8 0.9 + - - -
143E GLY* 2.9 31.0 + - - -
146E HIS* 3.3 13.0 + - - -
147E GLU* 3.4 25.7 + - - -
175E TYR* 3.3 7.0 - - - +
176E ARG* 2.9 41.9 + - - +
178E PHE* 5.1 7.6 - - - -
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Residues in contact with ARG 141 (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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140E SER* 1.3 72.4 + - - +
142E GLU* 1.3 91.7 + - - +
143E GLY 2.9 4.2 + - - -
145E ALA* 2.9 37.7 + - + +
146E HIS* 3.3 33.7 + - + +
171E HIS* 4.3 16.3 - - - +
172E GLY 3.2 24.4 + - - -
174E THR 3.5 7.9 - - - +
175E TYR* 3.7 33.1 + - + -
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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