Contacts of the helix formed by residues 161 - 167 (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 SER 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A LEU* 3.1 39.2 + - - +
150A THR* 3.8 4.2 - - - +
153A PHE* 3.4 20.9 + - - -
160A ILE* 1.3 78.3 - - - +
162A ALA* 1.3 68.3 + - - +
163A THR* 3.3 16.5 + - - -
164A SER* 3.0 15.5 + - - -
165A ILE* 3.2 14.0 - - - +
298B PRO 4.4 3.2 + - - -
299B GLY 3.9 5.3 + - - -
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Residues in contact with ALA 162 (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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125A PHE* 4.0 13.5 - - + -
161A SER* 1.3 72.4 + - - +
163A THR* 1.3 63.8 + - - +
165A ILE* 2.9 25.1 + - + +
166A PHE* 3.0 23.6 + - + +
129B THR* 5.6 0.9 - - + -
299B GLY* 2.7 24.7 + - - +
300B LEU* 3.4 32.8 - - + -
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Residues in contact with THR 163 (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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125A PHE* 4.6 5.3 - - - -
128A TYR* 3.5 30.4 - - + -
138A ILE* 4.3 14.1 - - + -
150A THR* 3.3 18.5 + - - +
151A HIS 4.3 0.7 - - - -
152A GLY* 3.3 30.5 - - - +
161A SER* 3.0 13.3 + - - -
162A ALA* 1.3 79.5 - - - +
164A SER* 1.3 58.5 + - - +
167A PHE* 3.0 43.2 + - + +
169A SER* 5.2 1.7 - - - -
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Residues in contact with SER 164 (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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152A GLY* 4.3 0.4 - - - -
153A PHE 3.2 27.4 + - - -
154A MSE 4.0 14.8 - - - +
159A LYS* 3.4 31.2 + - - +
161A SER* 3.0 14.9 + - - -
163A THR* 1.3 78.9 - - - +
165A ILE* 1.3 57.8 + - - +
167A PHE 2.9 17.5 - - - +
168A GLU* 5.1 0.2 - - - -
169A SER* 3.5 25.2 + - - -
137C ARG* 5.9 0.5 + - - -
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Residues in contact with ILE 165 (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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135A HIS* 4.9 6.9 + - - -
159A LYS* 4.1 37.0 + - + +
160A ILE 4.9 2.7 - - - +
161A SER 3.2 18.4 - - - +
162A ALA* 2.9 17.4 + - - +
164A SER* 1.3 80.8 - - - +
166A PHE* 1.3 73.5 + - + +
167A PHE 3.4 1.3 + - - +
168A GLU* 5.6 1.2 - - - +
129B THR* 4.8 15.7 - - + -
134B PRO* 3.7 34.2 - - + +
299B GLY* 5.8 3.1 - - - -
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Residues in contact with PHE 166 (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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125A PHE* 3.8 13.7 - + - -
134A PRO* 3.6 6.6 - - - +
135A HIS* 2.9 28.1 + - - -
162A ALA* 3.0 25.1 + - + +
165A ILE* 1.3 84.6 - - + +
167A PHE* 1.3 73.1 + - + +
125B PHE* 3.8 18.2 - + - -
129B THR* 3.7 31.4 - - + -
134B PRO* 3.8 27.1 - - + -
166B PHE* 3.3 48.4 - + + -
167B PHE* 3.9 17.7 - + - -
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Residues in contact with PHE 167 (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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125A PHE* 3.9 23.8 - + - -
128A TYR* 3.5 45.1 - + + -
129A THR* 3.8 4.7 - - - -
132A VAL* 3.7 11.0 - - + -
133A GLU* 3.4 36.3 - - - -
134A PRO* 4.0 3.1 - - + -
135A HIS 4.0 3.1 - - - +
136A GLY 3.6 6.7 - - - +
138A ILE* 3.9 15.9 - - + -
163A THR* 3.0 28.6 + - + +
164A SER* 2.9 24.8 - - - +
165A ILE 4.2 0.9 - - - +
166A PHE* 1.3 87.1 - - + +
168A GLU* 1.3 71.6 + - - +
169A SER* 5.2 0.7 - - - +
166B PHE* 3.9 18.8 - + - -
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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