Contacts of the helix formed by residues 173 - 188 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ALA* 4.5 5.0 - - - +
171B GLY 3.7 3.8 + - - +
172B ALA* 1.3 72.0 - - - +
174B LEU* 1.3 60.8 + - - +
175B ARG* 3.3 24.7 - - + +
176B THR* 2.4 44.7 + - - +
177B SER* 2.7 31.5 + - - -
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ILE* 6.0 2.9 - - + -
172B ALA 5.4 0.7 - - - +
173B THR* 1.3 73.8 - - - +
175B ARG* 1.3 82.3 + - - +
177B SER* 2.7 13.3 + - - -
178B ARG* 2.6 33.8 + - - +
214B ASP* 4.1 36.8 - - + +
217B CYS* 3.9 24.0 - - + -
218B VAL* 4.5 7.4 - - + -
221B MET* 3.8 17.8 - - + +
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Residues in contact with ARG 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A GLN* 4.8 13.1 - - - +
173B THR* 3.3 17.9 - - + +
174B LEU* 1.3 108.4 - - + +
176B THR* 1.3 62.5 + - - +
178B ARG* 3.1 18.0 + - - +
179B LEU* 3.2 16.7 + - - +
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Residues in contact with THR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ASP 4.5 4.5 - - - +
135B SER* 5.8 0.2 - - - -
172B ALA* 4.2 7.9 - - + -
173B THR* 2.4 38.3 + - - +
175B ARG* 1.3 72.1 - - - +
177B SER* 1.3 55.6 + - - +
179B LEU* 3.4 15.1 - - + +
180B LEU* 2.8 52.7 + - + +
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Residues in contact with SER 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LEU* 3.3 37.3 - - - +
155B ILE* 4.0 5.7 - - - +
172B ALA* 3.6 5.0 + - - +
173B THR 2.7 23.2 + - - -
174B LEU* 2.7 20.2 + - - -
176B THR* 1.3 70.3 - - - +
178B ARG* 1.3 65.8 + - - +
180B LEU* 4.0 3.5 - - - +
181B LEU* 2.8 29.7 + - - +
218B VAL* 4.2 16.1 - - - +
221B MET* 4.7 0.4 - - - -
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Residues in contact with ARG 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B LEU 2.6 15.1 + - - +
175B ARG* 3.1 14.1 + - - +
177B SER* 1.3 76.9 - - - +
179B LEU* 1.3 64.1 + - + +
181B LEU* 3.2 9.8 + - - +
182B GLU* 3.2 17.6 + - - +
221B MET* 3.2 56.7 + - - +
224B GLU* 4.1 27.0 + - - +
225B VAL* 3.3 24.8 - - - +
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLU* 5.2 5.1 - - - +
175B ARG 3.2 10.5 + - - +
176B THR* 3.4 20.4 - - + +
178B ARG* 1.3 78.8 - - + +
180B LEU* 1.3 64.8 + - + +
182B GLU* 3.6 8.4 + - + +
183B ARG* 3.2 23.9 + - - +
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B PHE* 4.3 5.5 - - + -
134B ASP* 3.3 26.0 - - - +
135B SER* 3.5 5.2 - - - -
136B GLU* 3.4 41.7 - - + +
139B LEU* 3.9 14.3 - - + +
153B LEU* 4.2 13.9 - - + -
172B ALA* 4.2 11.0 - - + -
176B THR* 2.8 49.3 + - + +
177B SER* 3.2 6.0 + - - +
179B LEU* 1.3 73.4 - - + +
181B LEU* 1.3 65.9 + - - +
183B ARG* 4.4 2.0 - - + -
184B ALA* 3.2 24.9 + - - +
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 6.3 0.2 - - - -
153B LEU* 4.1 11.2 - - + -
177B SER* 2.8 25.8 + - - +
178B ARG* 3.5 4.3 - - - +
180B LEU* 1.3 77.6 - - - +
182B GLU* 1.3 62.2 + - - +
184B ALA* 3.5 4.8 + - - +
185B LYS* 3.1 21.9 + - - +
191B VAL* 4.4 11.2 - - + -
218B VAL* 4.1 14.4 - - + +
221B MET* 3.3 41.3 - - + +
222B GLY* 4.1 10.8 - - - -
225B VAL* 4.2 10.3 - - + -
227B PHE* 3.7 18.9 - - + -
229B MET* 4.0 26.0 - - + -
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Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ARG* 3.2 16.1 + - - +
179B LEU* 3.8 12.8 - - + +
180B LEU 3.3 0.2 - - - -
181B LEU* 1.3 76.3 - - - +
183B ARG* 1.4 57.6 + - - +
185B LYS* 3.0 12.0 - - - +
186B GLU* 2.9 30.1 + - + +
225B VAL* 4.9 7.0 - - + +
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Residues in contact with ARG 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B GLU* 3.2 38.7 + - + +
139B LEU* 4.3 14.8 - - + -
140B MET* 4.8 13.3 - - - +
179B LEU 3.2 15.5 + - - +
180B LEU* 3.3 6.3 + - - +
181B LEU 3.3 0.4 - - - -
182B GLU* 1.4 79.4 - - - +
184B ALA* 1.3 57.7 + - - +
186B GLU* 2.4 52.6 + - - +
187B LEU* 2.9 46.4 - - + +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LEU* 3.8 22.2 - - + +
180B LEU 3.2 16.4 + - - +
181B LEU 3.7 4.0 - - - +
183B ARG* 1.3 74.6 - - - +
185B LYS* 1.3 66.6 + - - +
187B LEU* 3.2 15.9 + - - +
189B ILE* 3.0 36.6 + - + +
191B VAL* 3.9 21.8 - - + -
227B PHE* 4.5 1.3 - - + -
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Residues in contact with LYS 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B LEU 3.1 11.1 + - - +
182B GLU* 3.0 17.5 - - - +
184B ALA* 1.3 71.8 - - - +
186B GLU* 1.3 61.6 + - - +
187B LEU 2.7 2.8 + - - -
188B ASN* 3.0 21.1 + - - +
225B VAL* 3.0 42.4 - - + +
226B GLY* 4.0 11.7 + - - -
227B PHE* 3.3 38.7 - - + -
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Residues in contact with GLU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B GLU* 2.9 16.6 + - + +
183B ARG* 2.4 60.4 + - - +
185B LYS* 1.3 70.9 - - - +
187B LEU* 1.3 62.9 + - + +
188B ASN* 3.7 1.4 + - - -
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 3.9 29.2 - - + +
140B MET* 3.8 27.1 - - + -
143B ALA* 4.7 6.5 - - + +
183B ARG* 2.9 47.6 - - + +
184B ALA* 3.5 10.3 - - - +
185B LYS 2.7 6.3 + - - -
186B GLU* 1.3 78.5 - - + +
188B ASN* 1.3 65.8 + - - +
189B ILE* 4.0 24.2 - - + +
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Residues in contact with ASN 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B PRO 4.4 6.2 - - - +
148B LYS* 5.6 4.0 + - - -
184B ALA 3.9 0.9 - - - -
185B LYS* 3.0 17.8 + - - +
186B GLU 3.5 1.3 - - - -
187B LEU* 1.3 80.5 - - - +
189B ILE* 1.3 62.4 + - - +
190B ASP 4.1 1.0 + - - -
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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