Contacts of the strand formed by residues 137 - 141 (chain A) in PDB entry 1EJI
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 ARG 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A VAL* 4.0 0.6 - - - +
135A HIS 4.4 2.5 - - - +
136A GLY* 1.3 74.1 - - - -
138A ILE* 1.3 64.1 + - - +
168A GLU* 3.1 13.1 - - + +
192A LEU 4.6 0.8 + - - -
193A PHE* 2.7 79.2 + - + +
194A HIS* 3.9 15.3 - - - +
195A PRO* 4.1 0.9 - - + -
196A LYS* 2.9 35.2 + - + +
197A LEU 3.5 1.7 + - - -
154C MSE 3.2 22.6 - - - +
159C LYS* 5.6 2.4 - - - +
168C GLU* 3.3 27.5 + - - +
169C SER 2.8 47.3 + - - +
193C PHE* 4.7 1.0 - - - -
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Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A TYR* 3.7 34.1 - - + -
132A VAL* 3.8 21.1 - - + -
136A GLY 4.4 1.6 - - - +
137A ARG* 1.3 80.7 - - - +
139A MSE 1.3 70.5 + - - +
140A GLY 4.8 0.4 - - - +
151A HIS 4.9 6.3 - - - +
163A THR* 4.3 6.3 - - + -
167A PHE* 3.9 25.1 - - + -
168A GLU 2.9 9.2 + - - +
169A SER* 3.3 10.0 - - - -
170A MSE 3.2 23.9 + - - +
193A PHE* 3.9 0.5 - - - -
197A LEU* 3.4 14.8 - - + +
199A ILE* 3.7 28.3 - - + -
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Residues in contact with MSE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 1.3 80.3 - - - +
140A GLY* 1.3 55.2 + - - +
170A MSE 3.2 45.5 - - + +
171A PRO 4.1 12.6 - - - +
172A TYR* 4.1 10.9 - - + -
186A LEU* 3.7 24.2 - - + -
189A ASN* 4.2 9.2 - - + -
190A ALA* 3.9 25.4 - - - -
193A PHE* 3.8 10.3 - - + -
195A PRO* 3.6 27.1 - - + -
197A LEU 3.1 5.3 + - - -
198A ILE* 3.5 10.2 - - + +
199A ILE* 2.7 33.6 + - - +
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Residues in contact with GLY 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ILE 4.2 0.4 + - - -
139A MSE 1.3 74.1 - - - +
141A LEU* 1.3 62.2 + - - -
151A HIS* 3.7 23.3 + - - -
152A GLY 5.7 0.2 - - - -
169A SER* 6.1 0.2 - - - -
170A MSE 3.7 4.9 + - - -
171A PRO* 3.1 8.4 - - - +
172A TYR* 2.9 33.7 + - - -
199A ILE* 4.3 12.8 - - - -
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLY* 1.3 71.4 - - - -
142A ASP* 1.3 69.8 - - - +
143A LEU 3.3 1.0 + - - -
145A ASP* 3.6 27.4 - - + +
146A GLY* 3.6 5.4 - - - -
147A GLY* 3.0 41.3 - - - +
148A HIS 4.2 1.4 + - - +
151A HIS* 4.8 9.5 + - - +
152A GLY 5.5 1.4 - - - +
171A PRO* 4.5 0.2 - - - -
172A TYR* 3.5 47.2 + - + +
173A LYS* 4.3 1.3 - - - -
174A VAL* 4.2 11.7 - - + -
181A ILE* 4.2 15.9 - - + -
199A ILE 4.6 1.2 + - - -
201A GLY 4.5 5.8 + - - +
202A THR* 3.8 20.4 - - + -
205A TYR* 4.9 2.5 - - + -
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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