Contacts of the helix formed by residues 164 - 182 (chain A) in PDB entry 3DAN
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 PHE 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A TYR* 5.2 0.4 - + - -
148A LEU* 3.8 27.4 - - + -
149A PHE* 5.1 3.4 - + - -
152A LEU* 3.8 23.3 - - + -
162A ALA 3.4 3.7 + - - +
163A ALA* 1.3 74.0 - - - +
165A ASN* 1.3 57.7 + - - +
166A ASP 3.3 1.1 + - - -
167A VAL* 3.4 4.7 - - - +
168A GLY* 2.8 43.3 + - - -
285A PHE* 4.3 8.3 - + + -
286A PRO* 3.9 38.8 - - + -
289A LEU* 3.9 25.4 - - + -
439A PHE* 3.7 32.3 - + - -
463A VAL* 2.9 21.9 + - + +
465A LEU* 5.0 4.7 - - + -
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Residues in contact with ASN 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA* 3.8 2.9 - - + +
164A PHE* 1.3 79.7 - - - +
166A ASP* 1.3 61.8 + - - +
168A GLY* 3.2 0.9 + - - -
169A GLU* 2.8 46.7 + - - +
282A LYS 4.7 2.8 - - - +
286A PRO* 3.7 18.6 - - - +
461A ALA 3.3 15.3 + - - +
462A ALA* 3.5 9.4 - - - +
463A VAL* 3.0 37.6 + - - +
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Residues in contact with ASP 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA* 5.1 13.5 + - + +
164A PHE 3.3 0.8 + - - -
165A ASN* 1.3 78.8 - - - +
167A VAL* 1.3 67.2 + - + +
169A GLU* 3.0 21.5 + - - +
170A GLN* 3.2 23.5 + - - +
195A PRO* 5.4 0.3 - - - +
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU* 3.5 14.4 - - + +
152A LEU* 3.7 20.2 - - + -
155A GLU* 5.1 7.4 - - - +
163A ALA 3.6 15.9 - - - +
164A PHE 3.4 10.3 - - - +
166A ASP* 1.3 79.7 - - + +
168A GLY* 1.3 59.3 + - - +
170A GLN* 3.4 19.8 + - - +
171A ALA* 3.0 27.7 + - - +
174A ARG* 5.4 0.2 + - - -
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Residues in contact with GLY 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A TYR* 4.3 3.1 + - - -
148A LEU* 4.1 19.0 - - - +
164A PHE* 2.8 33.7 + - - -
165A ASN 3.5 1.6 - - - -
167A VAL* 1.3 79.6 - - - +
169A GLU* 1.3 57.4 + - - +
171A ALA* 3.3 3.3 + - - +
172A ALA* 2.9 27.0 + - - +
285A PHE* 6.1 0.3 - - - -
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Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ASN* 2.8 32.4 + - - +
166A ASP* 3.5 10.3 - - - +
168A GLY* 1.3 75.8 - - - +
170A GLN* 1.3 65.4 + - - +
172A ALA* 3.2 3.2 + - - -
173A PHE 3.1 18.2 + - - -
195A PRO* 3.8 17.8 - - + +
199A SER* 4.5 2.3 + - - -
278A PHE* 3.4 29.3 - - + -
282A LYS* 3.0 59.6 + - + +
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Residues in contact with GLN 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 ASP* 3.2 21.7 + - - +
167A VAL* 3.6 22.2 - - - +
169A GLU* 1.3 75.5 - - - +
171A ALA* 1.3 63.6 + - - +
173A PHE* 3.4 3.0 + - - +
174A ARG* 3.0 32.7 + - - +
186A GLU* 4.1 6.1 - - - +
192A THR* 3.7 37.3 + - - +
195A PRO* 3.8 20.9 - - + -
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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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144A THR* 3.2 14.7 - - + +
145A TYR* 4.1 6.5 - - + -
148A LEU* 3.9 26.5 - - + -
167A VAL 3.0 17.6 + - - +
168A GLY 3.5 5.2 - - - +
170A GLN* 1.3 74.3 - - - +
172A ALA* 1.3 61.6 + - - +
174A ARG* 3.2 27.7 + - - +
175A PHE* 2.9 27.2 + - - +
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Residues in contact with ALA 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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145A TYR* 3.4 16.3 + - - +
168A GLY 2.9 14.1 + - - +
169A GLU* 3.2 13.0 + - + +
171A ALA* 1.3 76.5 - - - +
173A PHE* 1.3 58.1 + - - +
175A PHE* 3.3 4.7 + - - +
176A LEU* 3.0 35.8 + - + +
278A PHE* 4.3 12.3 - - + -
281A VAL* 4.0 24.2 - - + -
282A LYS* 5.7 1.1 - - - +
285A PHE* 5.9 0.2 - - + -
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Residues in contact with PHE 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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169A GLU 3.1 11.9 + - - +
170A GLN 4.0 3.4 - - - +
172A ALA* 1.3 75.7 - - - +
174A ARG* 1.3 66.1 + - - +
176A LEU* 3.3 8.8 + - + +
177A GLY* 3.0 20.5 + - - -
185A PRO* 3.6 31.2 - - + +
190A LEU* 3.8 12.3 - - + -
194A ALA* 3.3 31.2 - - + -
195A PRO* 4.8 3.6 - - + -
198A ILE* 3.6 28.7 - - + -
240A LEU* 5.0 2.0 - - + -
243A TYR* 4.3 6.1 - + - -
244A PHE* 4.0 23.6 - + - -
273A VAL* 4.3 9.6 - - + -
274A CYS* 4.2 10.3 - - - -
278A PHE* 4.3 16.9 - + + -
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Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A THR* 3.3 23.7 + - - +
147A GLU* 2.8 35.8 + - - +
148A LEU* 4.2 5.3 - - - +
170A GLN* 3.0 16.4 + - - +
171A ALA* 3.6 23.8 - - - +
173A PHE* 1.3 76.1 - - - +
175A PHE* 1.3 62.1 + - - +
177A GLY 3.5 0.3 + - - -
178A ARG* 3.1 50.1 + - - +
184A ASN* 3.6 20.0 - - - +
185A PRO* 3.8 13.4 - - + +
186A GLU* 2.7 48.1 + - - +
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Residues in contact with PHE 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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137A VAL* 3.5 27.6 - - + -
140A GLN* 3.8 5.4 - - + -
141A PHE* 3.5 44.0 - + - -
144A THR* 3.7 18.1 - - + +
145A TYR* 4.0 8.5 - + + -
171A ALA 2.9 17.7 + - - +
172A ALA* 3.5 4.3 - - - +
174A ARG* 1.3 75.1 - - - +
176A LEU* 1.3 74.3 + - + +
178A ARG* 3.2 3.1 + - - +
179A ALA* 2.8 49.2 + - + +
285A PHE* 6.4 0.2 - + - -
431A PHE* 4.0 14.8 - + - -
435A ILE* 3.8 32.3 - - + -
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Residues in contact with LEU 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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172A ALA* 3.0 26.4 + - + +
173A PHE* 3.3 9.6 + - + +
175A PHE* 1.3 97.7 - - + +
177A GLY* 1.3 57.5 + - - +
179A ALA* 4.5 1.8 - - - +
180A TYR* 2.9 53.8 + - + +
181A PHE* 5.6 0.4 - - - -
273A VAL* 4.0 17.9 - - + +
277A THR* 3.3 38.8 - - + -
278A PHE* 3.9 22.2 - - + +
281A VAL* 5.6 3.8 - - + -
431A PHE* 4.2 7.9 - - + -
435A ILE* 5.4 2.2 - - + -
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Residues in contact with GLY 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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173A PHE* 3.0 16.8 + - - -
174A ARG 4.0 0.7 - - - -
176A LEU* 1.3 75.9 - - - +
178A ARG* 1.3 57.4 + - - +
181A PHE* 3.0 29.2 + - - +
183A SER 2.8 30.2 + - - +
185A PRO* 4.1 2.2 - - - -
243A TYR* 3.7 17.0 - - - -
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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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136A ARG* 3.4 9.4 + - - -
140A GLN* 3.5 32.0 + - + +
143A THR* 3.9 10.6 - - - +
144A THR* 2.9 34.3 + - - +
147A GLU* 2.9 38.4 + - - -
174A ARG* 3.1 29.9 + - - +
175A PHE 3.2 4.0 + - - +
177A GLY* 1.3 77.7 - - - +
179A ALA* 1.3 58.8 + - - +
182A ASN* 2.9 25.4 + - - +
183A SER 3.0 17.1 + - - +
184A ASN* 3.4 31.3 - - + +
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Residues in contact with ALA 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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133A SER* 3.0 19.3 - - - -
136A ARG* 2.8 31.1 + - - +
137A VAL* 4.5 14.6 - - + +
140A GLN* 4.3 2.6 - - + +
175A PHE* 2.8 48.2 + - + +
176A LEU* 4.1 2.2 - - - +
178A ARG* 1.3 72.3 - - - +
180A TYR* 1.3 60.5 + - + +
431A PHE* 4.9 6.5 - - + -
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Residues in contact with TYR 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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129A MET* 3.8 28.2 - - + +
130A LEU* 3.7 21.9 - - + +
132A ASN* 4.4 6.9 + - - -
133A SER* 4.1 14.3 - - - -
136A ARG* 3.1 13.9 + - - -
176A LEU* 2.9 39.5 + - + +
179A ALA* 1.3 75.0 - - + +
181A PHE* 1.3 83.1 + + + +
250A PRO* 5.9 0.9 - - - +
251A VAL* 5.5 0.9 - - - +
273A VAL* 3.8 37.7 - - + -
277A THR* 3.1 22.8 + - - +
431A PHE* 3.5 26.9 - + - -
600A HEM 3.4 19.6 - - - +
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Residues in contact with PHE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A MET* 4.1 15.7 - - - -
136A ARG* 4.3 2.7 - - - +
176A LEU 4.9 0.7 - - - -
177A GLY* 3.0 21.0 + - - +
180A TYR* 1.3 103.0 - + + +
182A ASN* 1.3 73.8 + - - +
183A SER* 3.1 6.2 + - - -
243A TYR* 4.4 2.7 - + - -
244A PHE* 3.7 26.0 - + - -
247A VAL* 3.6 47.5 - - + +
248A ALA* 3.7 19.7 - - + -
250A PRO* 5.7 4.5 - - + -
251A VAL* 4.4 9.4 - - + -
269A ILE* 3.7 23.3 - - + -
273A VAL* 4.2 6.7 - - + -
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Residues in contact with ASN 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG* 3.8 32.6 + - - +
140A GLN* 5.1 9.9 - - - +
178A ARG* 2.9 21.0 + - - +
181A PHE* 1.3 79.6 - - - +
183A SER* 1.3 57.8 + - - +
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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
------------------------------------------------------------
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