Contacts of the helix formed by residues 160 - 171 (chain A) in PDB entry 1EE8
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 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A GLU* 2.6 33.0 + - - +
52A LYS* 3.9 9.6 - - - -
151A LEU* 3.8 11.0 - - - -
159A VAL* 1.3 74.1 - - - +
161A ASN* 1.3 64.2 + - - -
164A ALA* 3.0 25.1 + - - +
253A ARG* 5.7 1.1 - - - -
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Residues in contact with ASN 161 (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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2A GLU* 3.4 3.3 + - - +
147A LYS* 3.0 30.3 + - - +
151A LEU* 3.8 2.6 - - - +
160A GLY* 1.3 70.8 - - - -
162A ILE* 1.3 65.1 + - + +
165A ASP* 2.9 31.5 + - - +
231A TYR* 4.4 14.6 - - + +
253A ARG* 3.1 48.3 + - - +
254A GLY 3.8 9.0 - - - +
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Residues in contact with ILE 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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2A GLU* 2.9 24.4 + - + +
5A GLU* 5.4 3.4 - - - +
161A ASN* 1.3 73.9 - - + +
163A TYR* 1.3 84.3 + - + +
165A ASP* 3.6 2.1 - - - +
166A GLU* 2.9 34.1 + - + +
207A SER* 4.5 9.9 - - - +
209A LEU* 3.6 36.1 - - + -
228A HIS* 4.0 20.4 - - + +
231A TYR* 3.6 32.2 - - + +
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Residues in contact with TYR 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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2A GLU* 3.0 30.5 + - + +
4A PRO* 3.4 35.1 - - + +
5A GLU* 2.5 33.4 + - - -
158A GLY 5.5 0.2 - - - -
159A VAL* 4.4 8.7 - - + -
162A ILE* 1.3 88.1 - - + +
164A ALA* 1.3 60.5 + - - +
166A GLU* 3.8 2.9 - - + +
167A ALA* 2.9 31.4 + - - +
194A LEU* 4.2 2.2 - - + +
197A VAL* 3.6 21.9 - - + +
198A LEU* 3.8 20.6 - - + -
201A ALA* 3.3 22.2 - - + +
207A SER* 2.8 19.0 + - - -
224A PHE* 3.8 16.4 - + - -
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Residues in contact with ALA 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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147A LYS* 4.2 10.3 - - + -
150A LEU* 4.1 17.9 - - + -
151A LEU* 3.5 22.2 - - + -
159A VAL* 3.9 11.1 - - + +
160A GLY 3.0 21.2 + - - +
161A ASN 3.9 2.5 - - - +
163A TYR* 1.3 77.1 - - - +
165A ASP* 1.3 65.3 + - - +
167A ALA* 3.2 2.3 + - - +
168A LEU* 2.9 31.8 + - - +
194A LEU* 5.1 0.4 - - - -
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Residues in contact with ASP 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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147A LYS* 2.6 33.8 + - - +
161A ASN 2.9 18.4 + - - +
162A ILE 3.6 4.0 - - - +
164A ALA* 1.3 75.2 - - - +
166A GLU* 1.3 62.0 + - - +
168A LEU* 3.4 7.5 + - - +
169A PHE* 3.1 22.7 + - - +
175A PRO* 6.1 0.2 - - - -
230A VAL* 3.9 11.6 - - + +
231A TYR* 3.7 12.2 - - + -
254A GLY 4.4 0.7 - - - +
255A THR* 3.6 6.8 - - - +
256A HIS* 2.8 52.1 + - - +
262A GLN* 4.5 0.5 + - - -
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Residues in contact with GLU 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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162A ILE* 2.9 24.5 + - + +
163A TYR* 4.2 1.3 - - - +
165A ASP* 1.3 76.3 - - - +
167A ALA* 1.3 62.7 + - - +
169A PHE* 3.4 4.5 + - - +
170A ARG* 3.0 25.3 + - - +
197A VAL* 4.0 23.2 - - + +
224A PHE* 4.6 7.3 - - + -
227A ARG 3.8 4.0 - - - +
228A HIS* 3.3 22.0 - - + -
229A ALA* 2.7 30.2 + - - +
230A VAL* 3.0 12.8 + - - +
231A TYR* 2.8 36.8 + - + +
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Residues in contact with ALA 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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150A LEU* 5.1 0.7 - - + -
163A TYR 2.9 19.9 + - - +
164A ALA* 3.7 3.1 - - - +
166A GLU* 1.3 76.7 - - - +
168A LEU* 1.3 58.4 + - - +
170A ARG 3.2 0.7 + - - -
171A ALA* 2.9 31.2 + - - +
190A LEU* 4.3 8.7 - - + -
193A ALA* 3.4 6.5 - - - +
194A LEU* 3.6 40.6 - - + +
197A VAL* 4.1 12.2 - - + +
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Residues in contact with LEU 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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146A LEU* 3.6 31.9 - - + -
147A LYS* 3.9 15.0 - - + -
150A LEU* 3.6 19.1 - - + -
164A ALA 2.9 24.3 + - - +
165A ASP* 3.7 7.2 - - - +
167A ALA* 1.3 76.5 - - - +
169A PHE* 1.3 56.5 + - - +
171A ALA* 3.4 1.1 + - - -
172A ARG 2.9 6.8 + - - -
173A LEU* 2.9 39.2 + - + +
174A SER 4.6 1.1 - - - +
175A PRO* 3.7 29.4 - - + -
190A LEU* 3.7 17.5 - - + -
262A GLN* 3.1 11.5 + - - +
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Residues in contact with PHE 169 (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 3.1 16.7 + - - +
166A GLU* 3.8 5.2 - - - +
167A ALA 3.2 0.2 - - - -
168A LEU* 1.3 73.4 - - - +
170A ARG* 1.3 72.2 + - - +
172A ARG* 2.9 54.7 + - - -
229A ALA* 3.3 24.9 - - + -
230A VAL* 3.6 28.7 - - + -
238A CYS* 3.6 32.8 - - - -
239A PRO* 3.9 13.5 - - + -
240A ALA* 4.1 2.0 - - + -
258A CYS* 4.2 6.1 - - + -
261A CYS* 4.2 9.0 - - + -
262A GLN* 3.1 27.3 - - + +
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Residues in contact with ARG 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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166A GLU* 3.0 17.9 + - - +
167A ALA 3.7 4.5 - - - +
169A PHE* 1.3 83.3 - - + +
171A ALA* 1.3 59.3 + - - +
172A ARG* 3.4 17.8 + - - +
193A ALA* 3.9 18.4 - - + +
196A GLU* 3.7 24.3 + - - +
197A VAL* 3.5 24.4 - - + +
200A GLU* 2.5 46.0 + - - -
224A PHE* 4.5 10.3 - - - -
227A ARG* 5.1 8.9 + - - +
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Residues in contact with ALA 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 ALA 2.9 17.3 + - - +
168A LEU 4.0 3.4 - - - +
170A ARG* 1.3 75.1 - - - +
172A ARG* 1.3 68.3 + - - +
173A LEU* 3.4 10.4 + - + +
189A ARG* 3.0 58.2 + - + +
190A LEU* 3.7 16.4 - - + +
193A ALA* 3.8 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