Contacts of the helix formed by residues 170 - 181 (chain A) in PDB entry 1EJ0
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 170 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A MET* 4.1 19.3 - - - +
168A GLY 3.3 0.6 + - - -
169A GLU* 1.3 78.1 - - - +
171A PHE* 1.3 62.1 - - - +
172A ASP 3.4 2.6 - - - +
173A GLU* 3.5 11.8 + - - +
174A TYR* 3.2 24.8 + - - +
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Residues in contact with PHE 171 (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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141A MET* 4.4 0.8 - - - -
165A VAL* 3.9 21.5 - - + -
166A PHE 3.8 17.7 - - - +
167A GLN* 4.7 8.1 - - + -
168A GLY 3.1 21.2 + - - +
169A GLU 3.3 2.6 + - - -
170A GLY* 1.3 75.7 - - - +
172A ASP* 1.3 68.8 + - + +
174A TYR* 3.3 5.1 + - - +
175A LEU* 2.9 50.0 + - + +
187A VAL* 4.1 19.3 - - + -
200A VAL* 3.8 23.1 - - + -
202A ILE* 4.1 17.7 - - + -
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Residues in contact with ASP 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLY 4.6 1.6 + - - -
170A GLY 3.4 0.8 - - - +
171A PHE* 1.3 86.7 - - + +
173A GLU* 1.3 64.9 + - - +
175A LEU* 3.8 4.5 - - - +
176A ARG* 3.0 55.8 + - - +
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Residues in contact with GLU 173 (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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145A GLU* 6.0 1.8 - - - +
170A GLY* 3.5 11.6 + - - +
171A PHE 3.3 0.6 - - - -
172A ASP* 1.3 83.1 + - - +
174A TYR* 1.3 59.0 + - - +
176A ARG* 3.4 9.6 + - + +
177A GLU* 3.0 27.8 + - + +
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Residues in contact with TYR 174 (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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141A MET* 4.0 11.7 - - + -
144A VAL* 2.7 43.5 + - + +
145A GLU* 3.5 34.3 + - - +
148A LEU* 3.7 15.9 - - + +
161A PHE* 3.5 22.9 - - - -
163A VAL* 3.8 2.6 - - + +
165A VAL* 3.8 27.1 - - + -
170A GLY 3.2 18.8 + - - +
171A PHE* 3.8 3.8 - - - +
173A GLU* 1.3 75.5 - - - +
175A LEU* 1.3 63.6 + - - +
177A GLU* 3.2 5.5 + - + +
178A ILE* 3.0 50.2 + - + +
202A ILE* 4.0 10.8 - - + -
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Residues in contact with LEU 175 (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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171A PHE* 2.9 41.9 + - + +
172A ASP* 3.8 4.3 - - - +
174A TYR* 1.3 77.7 - - - +
176A ARG* 1.3 56.9 + - - +
178A ILE* 3.2 3.0 + - - -
179A ARG* 2.8 66.2 + - - +
185A VAL* 3.7 28.3 - - + -
187A VAL* 4.0 19.1 - - + -
202A ILE* 4.1 20.4 - - + -
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Residues in contact with ARG 176 (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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172A ASP* 3.0 43.5 + - - +
173A GLU* 3.6 9.0 - - + +
175A LEU* 1.3 76.4 - - - +
177A GLU* 1.3 62.7 + - - +
179A ARG* 3.3 21.4 + - - +
180A SER* 3.0 22.5 + - - -
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Residues in contact with GLU 177 (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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145A GLU* 5.8 0.9 - - - +
148A LEU* 3.8 11.9 - - + -
152A ARG* 3.0 34.0 + - - +
173A GLU* 3.0 17.5 + - + +
174A TYR* 3.6 7.6 - - + +
175A LEU 3.2 0.2 - - - -
176A ARG* 1.3 76.9 - - - +
178A ILE* 1.3 64.6 + - - +
180A SER* 2.7 29.6 + - - -
181A LEU* 3.3 20.1 + - + +
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Residues in contact with ILE 178 (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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148A LEU* 4.1 21.1 - - + -
161A PHE* 3.9 15.3 - - + -
163A VAL* 4.2 0.7 - - + -
174A TYR* 3.0 47.7 + - + +
175A LEU* 3.6 6.7 - - - +
177A GLU* 1.3 76.8 - - - +
179A ARG* 1.3 62.7 + - - +
181A LEU* 3.0 14.1 + - - -
182A PHE* 3.2 23.6 + - + +
185A VAL* 4.0 12.6 - - + -
202A ILE* 4.0 19.7 - - + -
204A ALA* 3.6 29.2 - - + -
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Residues in contact with ARG 179 (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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175A LEU* 2.8 58.2 + - + +
176A ARG* 3.6 18.9 - - - +
177A GLU 3.3 0.2 - - - -
178A ILE* 1.3 72.9 - - - +
180A SER* 1.3 61.6 + - - +
182A PHE 3.1 17.8 - - - +
185A VAL* 3.9 31.8 + - + +
187A VAL* 5.4 3.6 - - - +
208A LYS* 3.2 6.2 + - - -
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Residues in contact with SER 180 (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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176A ARG 3.0 12.7 + - - -
177A GLU* 2.7 29.3 + - - -
179A ARG* 1.3 77.2 - - - +
181A LEU* 1.3 66.4 + - - +
208A LYS* 3.2 20.3 + - - +
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Residues in contact with LEU 181 (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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148A LEU* 4.1 25.4 - - + -
152A ARG* 4.1 21.8 - - + +
177A GLU* 3.4 34.3 - - + +
178A ILE* 3.0 3.7 + - - +
180A SER* 1.3 84.3 - - - +
182A PHE* 1.3 78.2 + - + +
207A ARG* 3.7 15.6 + - + +
208A LYS* 2.9 31.1 + - - +
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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