Contacts of the helix formed by residues 173 - 187 (chain A) in PDB entry 1D7K
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 THR 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ILE* 5.9 0.2 - - - -
156A ALA* 4.6 13.0 - - + -
171A GLY 5.3 1.3 - - - +
172A ALA* 1.3 72.6 - - - +
174A LEU* 1.3 66.1 + - - +
175A ARG* 3.4 28.6 - - - +
176A THR* 3.2 25.8 + - - +
177A SER* 2.8 24.5 + - - -
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Residues in contact with LEU 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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155A ILE* 5.4 4.3 - - + -
173A THR* 1.3 73.8 - - - +
175A ARG* 1.3 88.5 + - - +
177A SER* 3.1 5.9 + - - +
178A ARG* 3.1 18.9 + - - +
214A ASP* 4.2 36.8 - - + +
217A CYS* 4.0 24.7 - - + -
218A VAL* 3.8 26.7 - - + -
221A MET* 3.8 10.0 - - - +
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Residues in contact with ARG 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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173A THR* 3.4 28.0 - - - +
174A LEU* 1.3 103.4 - - - +
176A THR* 1.4 70.1 + - - +
177A SER 3.3 0.3 + - - -
178A ARG* 3.3 11.9 + - - +
179A LEU* 3.5 19.7 + - + +
300B GLN* 5.9 7.0 - - - +
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Residues in contact with THR 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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134A ASP 4.8 4.0 - - - +
135A SER* 5.9 1.1 - - - -
172A ALA* 4.2 6.5 - - + -
173A THR* 3.2 27.6 + - - +
175A ARG* 1.4 80.4 - - - +
177A SER* 1.3 63.1 + - - +
179A LEU* 3.1 16.5 + - + +
180A LEU* 3.0 41.4 + - + +
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Residues in contact with SER 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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153A LEU* 3.6 29.2 - - - +
155A ILE* 4.0 8.8 - - - +
172A ALA* 3.8 5.0 - - - +
173A THR 2.8 18.3 + - - -
174A LEU 3.1 11.8 + - - -
176A THR* 1.3 76.6 - - - +
178A ARG* 1.4 63.5 + - - +
180A LEU* 3.3 6.9 + - - +
181A LEU* 3.1 27.5 + - - +
218A VAL* 4.1 6.8 - - - +
221A MET* 3.6 18.4 - - - -
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Residues in contact with ARG 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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174A LEU 3.1 9.6 + - - +
175A ARG* 3.3 8.0 + - - +
176A THR 3.1 0.8 + - - -
177A SER* 1.4 78.0 - - - +
179A LEU* 1.3 61.4 + - + +
181A LEU* 3.4 8.2 + - - +
182A GLU* 3.3 42.6 + - - +
221A MET* 3.0 63.6 + - - +
224A GLU* 3.4 29.3 + - - +
225A VAL* 3.7 28.1 - - - +
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Residues in contact with LEU 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 ARG* 3.5 16.6 - - + +
176A THR* 3.5 14.1 - - + +
178A ARG* 1.3 73.3 - - + +
180A LEU* 1.3 62.6 + - + +
182A GLU* 3.5 18.4 + - - +
183A ARG* 2.9 32.2 + - - +
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Residues in contact with LEU 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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133A PHE* 4.1 15.8 - - + -
134A ASP* 3.7 28.5 - - - +
135A SER* 3.5 30.1 - - - +
136A GLU* 3.6 15.0 - - + +
139A LEU* 3.6 15.2 - - + +
153A LEU* 4.3 9.6 - - + -
172A ALA* 3.9 19.7 - - + -
176A THR* 3.0 24.8 + - + +
177A SER* 3.3 9.6 + - - +
179A LEU* 1.3 76.4 - - + +
181A LEU* 1.3 59.1 + - - +
183A ARG* 3.5 2.1 + - + -
184A ALA* 2.9 26.7 + - - +
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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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153A LEU* 4.1 12.3 - - + -
177A SER 3.1 14.5 + - - +
178A ARG* 3.9 5.8 - - - +
179A LEU 3.3 0.2 - - - -
180A LEU* 1.3 76.4 - - - +
182A GLU* 1.3 64.6 + - + +
184A ALA* 3.3 2.4 + - - +
185A LYS* 3.0 25.3 + - - +
191A VAL* 3.8 22.0 - - + -
218A VAL* 4.1 6.3 - - + +
221A MET* 3.6 36.1 - - + -
222A GLY* 3.7 22.7 - - - +
225A VAL* 4.4 13.0 - - + -
227A PHE* 3.5 14.8 - - + -
229A MET* 3.4 24.7 - - + -
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Residues in contact with GLU 182 (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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178A ARG* 3.3 42.2 + - + +
179A LEU* 3.6 25.9 + - - +
181A LEU* 1.3 76.5 - - + +
183A ARG* 1.4 59.4 + - - +
185A LYS* 3.5 7.3 + - - +
186A GLU* 3.0 28.9 + - - +
225A VAL* 4.3 20.7 - - + +
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Residues in contact with ARG 183 (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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136A GLU* 4.6 25.0 + - + +
139A LEU* 4.0 16.4 - - + -
140A MET* 5.6 11.9 - - - +
179A LEU 2.9 19.4 + - - +
180A LEU* 3.7 5.8 - - + +
182A GLU* 1.4 75.5 - - - +
184A ALA* 1.3 65.2 + - - +
186A GLU* 3.1 40.0 + - - +
187A LEU* 3.1 55.3 + - + +
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Residues in contact with ALA 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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133A PHE* 5.4 0.2 - - + -
139A LEU* 3.8 21.4 - - + +
180A LEU 2.9 20.1 + - - +
181A LEU 3.7 4.3 - - - +
183A ARG* 1.3 72.8 - - - +
185A LYS* 1.3 65.1 + - - +
187A LEU* 3.0 5.0 + - - +
188A ASN 3.0 5.4 + - - -
189A ILE* 2.9 35.6 + - + +
191A VAL* 3.6 30.7 - - + -
227A PHE* 4.1 0.9 - - + -
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Residues in contact with LYS 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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181A LEU 3.0 15.0 + - - +
182A GLU* 3.7 8.5 - - - +
184A ALA* 1.3 77.4 - - - +
186A GLU* 1.3 58.6 + - - +
188A ASN* 3.2 21.1 + - - +
189A ILE 4.8 1.1 - - - +
225A VAL* 3.7 28.7 - - + +
226A GLY* 3.1 25.6 + - - -
227A PHE* 3.4 32.6 - - + -
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Residues in contact with GLU 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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182A GLU 3.0 16.2 + - - +
183A ARG* 3.1 41.2 + - - +
184A ALA 3.1 0.4 - - - -
185A LYS* 1.3 76.5 - - - +
187A LEU* 1.3 60.0 + - + +
188A ASN* 3.4 10.7 + - - -
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Residues in contact with LEU 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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136A GLU 5.9 0.2 - - - +
139A LEU* 4.3 32.8 - - + +
140A MET* 4.7 4.5 - - - +
143A ALA* 4.6 14.8 - - + +
183A ARG* 3.1 53.2 + - + +
184A ALA* 3.0 5.9 + - - +
186A GLU* 1.3 76.0 - - + +
188A ASN* 1.3 71.6 + - - +
189A ILE* 3.2 18.5 + - + +
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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