Contacts of the helix formed by residues 183 - 194 (chain A) in PDB entry 3EDH
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 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ASP* 2.6 28.1 + - - -
144A ASP* 3.3 37.9 - - - -
145A SER* 3.7 0.2 - - - -
175A GLN* 4.3 0.2 - - - +
181A ARG* 3.4 10.3 + - - +
182A LEU* 1.3 75.7 - - - +
184A LYS* 1.3 65.4 + - - +
185A GLY 3.9 0.7 - - - -
186A ASP* 2.8 23.3 + - - -
187A ILE* 3.0 24.7 + - - +
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Residues in contact with LYS 184 (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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144A ASP* 5.0 0.6 + - - -
181A ARG* 5.8 0.6 - - - +
183A SER* 1.3 73.4 - - - +
185A GLY* 1.3 58.3 + - - +
187A ILE* 3.4 9.8 + - + +
188A ALA* 2.9 29.4 + - - +
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Residues in contact with GLY 185 (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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139A GLU* 4.4 7.2 - - - +
142A ASP* 3.4 21.1 + - - -
183A SER* 3.1 3.8 + - - -
184A LYS* 1.3 78.0 - - - +
186A ASP* 1.3 63.4 + - - +
188A ALA* 3.9 6.3 - - - +
189A GLN* 2.9 30.4 + - - +
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Residues in contact with ASP 186 (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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37A TRP* 5.2 3.3 - - + -
100A PHE* 4.4 9.1 - - + -
103A GLU* 5.0 0.7 - - - +
142A ASP* 3.4 1.1 + - - +
145A SER* 2.6 27.5 + - - -
146A ILE* 2.8 36.9 + - - +
147A MET* 4.5 4.3 - - - +
182A LEU* 3.8 15.2 - - + -
183A SER* 2.8 41.3 + - - +
185A GLY* 1.3 72.0 - - - +
187A ILE* 1.3 58.4 + - - +
189A GLN* 3.8 8.6 + - - +
190A ALA* 2.9 33.0 + - - +
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Residues in contact with ILE 187 (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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40A HIS* 3.4 47.8 - - + +
41A THR* 4.6 2.5 - - + -
182A LEU* 3.9 27.8 - - + +
183A SER 3.0 18.5 + - - +
184A LYS* 3.7 7.9 - - + +
186A ASP* 1.3 74.1 - - - +
188A ALA* 1.3 65.2 + - - +
190A ALA* 3.3 5.2 + - - +
191A ARG* 3.0 65.5 + - - +
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Residues in contact with ALA 188 (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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139A GLU* 3.7 22.2 - - - +
184A LYS 2.9 17.4 + - - +
185A GLY* 3.9 2.7 - - - +
187A ILE* 1.3 78.0 - - - +
189A GLN* 1.3 62.8 + - - +
191A ARG* 3.4 11.5 + - - +
192A LYS* 3.2 25.9 + - - +
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Residues in contact with GLN 189 (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 ALA* 4.3 1.3 - - + +
100A PHE* 3.5 25.0 - - + -
106A ARG* 4.0 0.2 + - - -
136A SER* 3.0 24.2 - - - +
137A LEU* 3.9 8.6 - - + +
139A GLU* 3.7 27.2 - - + +
185A GLY 2.9 17.3 + - - +
186A ASP* 4.0 3.4 + - - +
188A ALA* 1.3 76.2 - - - +
190A ALA* 1.3 61.0 + - - +
192A LYS* 3.2 5.0 + - - +
193A LEU* 2.9 27.4 + - - +
201A ACE 3.0 23.7 + - - +
211A ZN 2.4 33.5 - - - -
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Residues in contact with ALA 190 (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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37A TRP* 3.8 27.6 - - + -
41A THR* 4.0 11.9 - - + -
43A VAL* 5.7 0.7 - - + -
98A VAL* 4.7 3.6 - - + -
100A PHE* 3.8 17.6 - - + -
186A ASP 2.9 18.9 + - - +
187A ILE 3.9 3.1 - - - +
189A GLN* 1.3 76.7 - - - +
191A ARG* 1.3 62.7 + - - +
193A LEU* 3.2 4.3 + - - +
194A TYR* 3.0 30.9 + - + +
198A CYS* 4.4 0.6 - - - -
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Residues in contact with ARG 191 (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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39A LYS 5.4 0.2 + - - -
40A HIS* 2.9 39.5 + - - +
41A THR* 4.4 6.2 - - - +
187A ILE* 3.0 37.9 + - - +
188A ALA* 3.6 9.2 - - - +
189A GLN 3.2 0.2 - - - -
190A ALA* 1.3 77.2 - - - +
192A LYS* 1.3 60.4 + - + +
194A TYR 3.5 0.2 + - - -
195A LYS* 3.0 3.8 + - - -
198A CYS* 2.9 55.9 + - + +
199A PRO 6.2 0.2 - - - -
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Residues in contact with LYS 192 (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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137A LEU* 2.9 47.6 + - + +
138A GLY* 4.3 7.1 + - - -
139A GLU* 2.7 33.5 + - + +
188A ALA* 3.2 12.1 + - - +
189A GLN 3.2 7.1 + - - +
191A ARG* 1.3 76.0 - - + +
193A LEU* 1.3 63.7 + - - +
195A LYS* 3.1 19.2 + - - +
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Residues in contact with LEU 193 (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 ALA* 4.4 8.3 - - + -
3A THR* 3.9 23.6 - - + +
9A VAL* 3.9 28.2 - - + +
98A VAL 3.9 11.7 - - - +
99A GLY* 4.5 9.4 - - - +
100A PHE* 4.2 22.0 - - + -
137A LEU* 3.6 21.0 - - + +
189A GLN 2.9 17.0 + - - +
190A ALA 3.2 4.9 + - - +
192A LYS* 1.3 77.2 - - - +
194A TYR* 1.3 82.2 + - + +
195A LYS* 3.6 7.1 + - - +
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Residues in contact with TYR 194 (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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9A VAL* 3.3 25.6 - - + -
10A TRP* 3.2 42.7 + + + -
13A GLY* 3.6 26.5 - - - -
15A ILE* 5.6 0.7 - - + -
42A CYS* 3.8 10.2 - - - -
43A VAL* 4.2 17.3 - - + -
98A VAL* 2.7 47.1 + - + -
190A ALA* 3.0 20.4 + - - +
193A LEU* 1.3 87.6 - - + +
195A LYS* 1.3 71.4 + - - +
198A CYS* 3.2 17.0 + - - -
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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