Contacts of the helix formed by residues 165 - 175 (chain A) in PDB entry 1E5E
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 ASP 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A ALA* 5.2 1.2 - - - +
163A ILE 4.2 0.4 + - - -
164A ILE* 1.3 70.9 - - - +
166A MET* 1.3 56.6 + - - +
167A GLU* 3.2 10.9 + - - +
168A ARG* 3.0 56.4 + - + +
169A VAL* 3.1 28.3 + - - +
300A ILE* 3.6 39.8 - - + +
304A GLN* 4.3 1.6 - - - +
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Residues in contact with MET 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A PHE* 3.4 41.1 - - + -
155A THR* 3.9 11.4 - - + -
164A ILE* 3.1 11.2 + - - +
165A ASP* 1.3 69.6 - - - +
167A GLU* 1.3 62.0 + - - +
169A VAL* 3.2 2.0 + - - +
170A CYS* 2.8 34.7 + - - -
183A ALA* 4.5 1.3 - - - -
193A THR* 3.8 23.3 - - + -
195A PRO* 3.8 22.2 - - + -
198A PHE* 3.7 36.1 - - + -
200A VAL* 4.3 4.5 - - + -
304A GLN* 3.0 30.1 + - + +
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Residues in contact with GLU 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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165A ASP* 3.2 7.7 + - - +
166A MET* 1.3 78.5 - - - +
168A ARG* 1.3 57.7 + - - +
170A CYS* 3.3 2.1 + - - +
171A LYS* 2.9 63.2 + - + +
198A PHE* 3.5 39.9 - - + +
304A GLN* 4.3 2.0 + - - +
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Residues in contact with ARG 168 (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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134A THR 4.1 6.5 + - - -
135A ALA* 2.8 33.7 + - - +
136A ILE 3.9 0.8 - - - -
137A PRO* 3.4 39.8 - - - +
138A GLY 5.7 0.2 - - - +
165A ASP* 3.0 53.3 + - - +
167A GLU* 1.3 75.3 - - - +
169A VAL* 1.3 66.8 + - - +
171A LYS* 3.3 8.6 + - + +
172A ASP* 3.1 39.2 + - - +
300A ILE* 5.9 0.2 - - - +
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Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A THR* 3.6 23.1 - - - +
140A VAL* 4.2 11.5 - - + +
151A VAL* 3.9 23.3 - - + -
153A PHE* 3.7 26.9 - - + -
164A ILE* 3.6 22.2 - - + -
165A ASP 3.1 16.6 + - - +
166A MET 3.2 4.2 + - - +
168A ARG* 1.3 81.5 - - + +
170A CYS* 1.3 58.7 + - - +
172A ASP* 3.4 6.7 + - - +
173A ALA* 2.9 27.4 + - - +
181A VAL* 4.6 3.6 - - + -
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Residues in contact with CYS 170 (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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153A PHE* 5.2 0.7 - - - -
166A MET* 2.8 20.1 + - - +
167A GLU 3.7 3.8 - - - +
169A VAL* 1.3 78.4 - - - +
171A LYS* 1.3 59.9 + - + +
174A HIS* 2.8 42.1 + - - +
181A VAL* 3.7 23.1 - - - -
198A PHE 3.7 11.2 - - - +
199A GLY* 3.5 33.2 - - - +
200A VAL* 3.6 20.6 - - - -
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Residues in contact with LYS 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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167A GLU* 2.9 53.8 + - + +
168A ARG* 3.3 7.1 + - + +
170A CYS* 1.3 73.7 - - + +
172A ASP* 1.3 67.4 + - - +
174A HIS* 3.6 3.9 - - - -
175A SER* 3.0 23.4 + - - -
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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
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138A GLY* 4.5 14.2 + - - -
140A VAL* 4.0 20.0 - - + +
141A LYS* 4.2 23.0 + - + +
144A MET* 3.4 11.0 - - - +
168A ARG* 3.1 32.3 + - - +
169A VAL* 3.7 4.3 - - - +
171A LYS* 1.3 80.5 - - - +
173A ALA* 1.3 60.0 + - - +
175A SER* 2.7 25.8 + - - -
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Residues in contact with ALA 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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140A VAL* 4.1 3.7 - - + +
144A MET* 3.1 31.6 - - - +
151A VAL* 3.9 20.2 - - + -
169A VAL 2.9 16.5 + - - +
170A CYS 3.8 0.7 - - - +
172A ASP* 1.3 71.7 - - - +
174A HIS* 1.3 60.9 + - - +
175A SER 3.1 2.5 + - - -
176A GLN 3.4 7.3 - - - +
179A VAL* 3.5 11.4 - - + +
181A VAL* 3.4 33.0 - - + -
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Residues in contact with HIS 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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170A CYS* 2.8 33.9 + - + +
171A LYS* 3.6 4.9 - - - +
173A ALA* 1.3 71.4 - - - +
175A SER* 1.3 63.9 + - - +
176A GLN 3.1 11.7 + - - +
177A GLU* 6.0 0.9 - - - -
179A VAL* 3.4 20.4 + - + -
181A VAL* 3.9 8.6 - - + +
199A GLY* 3.2 28.8 - - - -
201A ASP* 2.7 30.0 + - - -
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Residues in contact with SER 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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141A LYS* 3.5 32.1 + - - +
144A MET* 4.5 1.0 - - - +
171A LYS 3.0 11.9 + - - -
172A ASP* 2.7 22.3 + - - -
173A ALA 3.1 0.4 - - - -
174A HIS* 1.3 78.8 - - - +
176A GLN* 1.3 57.9 + - - +
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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