Contacts of the helix formed by residues 157 - 173 (chain F) in PDB entry 6D6Q
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 ALA 157 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60F THR* 5.0 3.8 - - + -
62F VAL* 5.8 0.3 - - - +
100F PHE* 5.3 3.6 - - + -
102F ARG* 5.4 5.6 - - - +
122F LEU* 6.1 2.2 - - + -
150F LEU* 3.5 31.9 - - + +
153F ASP* 4.3 11.7 - - - +
155F GLY 2.9 9.8 + - - +
156F SER* 1.3 72.5 - - - +
158F LEU* 1.3 67.3 + - - +
159F ALA 3.2 1.3 - - - -
160F ALA* 3.2 7.0 + - - +
161F ALA* 3.0 22.5 + - - +
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Residues in contact with LEU 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F PHE* 5.4 2.9 - - + -
122F LEU* 3.6 57.8 - - + +
125F ALA* 4.2 14.4 - - + -
126F LEU* 3.9 14.1 - - + -
157F ALA* 1.3 78.1 - - - +
159F ALA* 1.3 58.8 + - - +
161F ALA* 3.2 7.3 + - + +
162F LEU* 2.9 47.9 + - + +
212F THR* 4.0 21.1 - - + +
226F LEU* 5.3 7.0 - - + -
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Residues in contact with ALA 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F SER* 4.6 10.7 - - - +
157F ALA 3.2 1.4 - - - +
158F LEU* 1.3 76.9 - - - +
160F ALA* 1.3 65.7 + - - +
162F LEU* 3.2 9.2 + - - +
163F THR* 2.9 27.7 + - - -
182F GLY* 3.5 8.3 - - - +
183F CYS* 3.2 42.8 - - - +
184F GLY* 4.1 2.9 - - - +
212F THR* 4.3 8.5 - - + +
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Residues in contact with ALA 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F LEU* 3.8 24.6 - - + +
57F ALA* 6.0 3.4 - - + -
60F THR* 4.0 19.5 - - + -
62F VAL* 4.0 11.2 - - + +
156F SER* 3.9 14.5 + - - +
157F ALA 3.2 9.0 + - - +
159F ALA* 1.3 78.2 - - - +
161F ALA* 1.3 57.7 + - - +
163F THR* 3.4 2.8 + - - -
164F ALA* 2.9 31.4 + - - +
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Residues in contact with ALA 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F VAL* 4.4 15.0 - - + +
64F CYS* 5.2 0.9 - - - +
100F PHE* 3.8 28.5 - - + -
126F LEU* 3.9 14.8 - - + +
148F ALA* 4.8 5.9 - - + +
157F ALA 3.0 12.8 + - - +
158F LEU* 3.5 10.5 - - + +
159F ALA 3.1 0.4 - - - -
160F ALA* 1.3 74.1 - - - +
162F LEU* 1.3 65.8 + - - +
164F ALA* 3.8 1.9 - - - +
165F ALA* 2.9 26.3 + - - +
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Residues in contact with LEU 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F ALA 4.3 0.7 - - - +
126F LEU* 3.3 31.4 - - + +
129F ALA* 3.4 27.8 - - + -
130F LEU* 4.5 8.8 - - + +
158F LEU* 2.9 38.4 + - + +
159F ALA* 3.5 11.0 - - - +
161F ALA* 1.3 77.4 - - - +
163F THR* 1.3 64.0 + - - +
165F ALA* 3.3 3.9 + - - +
166F ALA* 2.9 23.6 + - - +
180F VAL* 4.2 13.1 - - + +
182F GLY* 4.8 2.7 - - - -
212F THR* 5.0 1.6 - - + -
213F VAL 4.9 0.9 - - - +
214F ALA* 3.3 31.9 - - + -
224F GLY 4.8 2.2 - - - +
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Residues in contact with THR 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F LEU* 4.2 14.8 - - + -
159F ALA 2.9 17.3 + - - -
160F ALA* 3.7 4.4 - - - -
162F LEU* 1.3 75.7 - - - +
164F ALA* 1.3 58.2 + - - +
166F ALA* 3.3 2.8 + - - +
167F LEU* 2.9 28.4 + - + +
180F VAL 3.8 11.3 + - - +
181F VAL* 4.0 2.1 - - - +
182F GLY* 3.4 21.1 + - - -
251F LEU* 5.0 5.3 - - + +
255F LEU* 3.4 45.8 - - + -
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Residues in contact with ALA 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F ALA* 3.6 9.2 - - + +
55F LEU* 4.6 7.8 - - + +
62F VAL* 4.1 20.9 - - + +
63F LEU 4.8 0.2 - - - -
64F CYS* 3.8 19.5 - - + +
160F ALA 2.9 17.5 + - - +
161F ALA* 3.8 5.2 - - - +
162F LEU 3.2 0.2 - - - -
163F THR* 1.3 76.0 - - - +
165F ALA* 1.3 59.7 + - - +
167F LEU* 3.3 12.4 + - - +
168F ALA* 2.9 29.3 + - - +
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Residues in contact with ALA 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F CYS* 3.4 24.6 - - - -
66F VAL* 4.7 0.2 - - - +
126F LEU* 5.3 6.3 - - + -
130F LEU* 3.9 24.7 - - + -
146F VAL* 4.1 9.0 - - + -
148F ALA* 5.9 0.2 - - + -
161F ALA 2.9 17.4 + - - +
162F LEU* 3.8 4.5 - - - +
164F ALA* 1.3 76.0 - - - +
166F ALA* 1.3 63.8 + - - +
168F ALA* 3.3 1.4 + - - +
169F LEU* 2.9 31.3 + - + +
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Residues in contact with ALA 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F LEU* 4.5 6.1 - - + +
162F LEU 2.9 14.1 + - - +
163F THR 3.5 8.3 - - - +
165F ALA* 1.3 77.5 - - - +
167F LEU* 1.3 64.0 + - + +
169F LEU* 4.6 0.4 - - - -
170F ALA* 2.9 26.6 + - - +
176F MET* 3.5 13.2 - - + +
179F LEU* 4.4 8.9 - - + +
180F VAL* 3.9 39.5 - - + +
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Residues in contact with LEU 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F ALA* 4.2 15.0 - - + -
42F ARG 5.2 2.0 - - - +
43F ALA* 4.9 2.9 - - + -
53F ALA* 3.6 18.8 - - + -
54F TYR 5.1 4.7 - - - +
55F LEU* 5.3 3.6 - - + -
163F THR* 2.9 20.7 + - + +
164F ALA* 3.6 10.8 - - - +
166F ALA* 1.3 76.1 - - + +
168F ALA* 1.3 58.6 + - - +
170F ALA* 3.4 4.9 + - - +
171F ASP* 2.8 31.1 + - - +
179F LEU* 5.3 4.9 - - + -
255F LEU* 3.7 47.1 - - + +
258F SER* 5.2 5.8 - - - +
259F LEU* 4.0 30.9 - - + +
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Residues in contact with ALA 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F GLY* 3.9 2.8 - - - -
52F SER* 4.1 10.5 - - - -
53F ALA* 3.7 6.0 - - + +
64F CYS* 3.7 26.7 - - - +
66F VAL* 3.4 22.0 - - + +
164F ALA 2.9 17.2 + - - +
165F ALA 3.7 2.9 - - - +
166F ALA 3.3 0.2 - - - -
167F LEU* 1.3 75.8 - - - +
169F LEU* 1.3 58.8 + - - +
171F ASP* 3.2 6.2 + - - +
172F ALA* 2.9 29.3 + - - +
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Residues in contact with LEU 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F VAL* 3.5 33.2 - - + -
96F LEU* 4.7 4.0 - - + -
130F LEU* 4.5 22.2 - - + -
134F VAL* 3.9 25.1 - - + -
144F LEU* 4.7 10.8 - - + -
146F VAL* 4.0 15.3 - - + -
165F ALA 2.9 23.7 + - - +
166F ALA* 4.8 0.2 - - - -
168F ALA* 1.3 75.3 - - - +
170F ALA* 1.3 63.4 + - - +
171F ASP 2.9 1.6 + - - -
172F ALA* 3.1 12.6 + - - +
173F GLY 3.1 9.4 + - - -
174F VAL* 3.4 24.9 + - + +
176F MET* 3.3 16.8 - - + -
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Residues in contact with ALA 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F ALA 2.9 18.5 + - - +
167F LEU 3.8 3.1 - - - +
169F LEU* 1.3 76.0 - - - +
171F ASP* 1.3 60.8 + - - +
173F GLY* 3.6 7.3 + - - -
174F VAL 4.6 5.2 - - - -
176F MET* 3.3 13.9 - - + +
179F LEU* 4.1 5.6 - - + -
259F LEU* 4.0 23.6 - - + -
10I PRO* 4.0 18.8 - - + -
37I LEU* 5.4 0.4 - - - +
38I ALA* 3.2 24.9 + - - +
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Residues in contact with ASP 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F ALA* 3.8 18.7 - - + +
44F GLY* 4.0 6.1 + - - -
50F LYS 4.2 2.1 - - - +
51F GLY* 3.3 22.0 - - - -
52F SER 3.5 14.6 + - - +
167F LEU 2.8 17.8 + - - +
168F ALA* 3.4 8.5 - - - +
170F ALA* 1.3 74.7 - - - +
172F ALA* 1.3 56.6 + - - +
173F GLY 2.9 4.8 + - - -
259F LEU* 4.7 5.4 - - + +
262F ALA* 4.3 1.0 - - - +
266F ARG* 2.3 38.8 + - - -
38I ALA* 5.0 2.9 - - - +
57I ARG* 2.9 29.3 + - - -
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Residues in contact with ALA 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LYS* 3.2 56.8 + - + -
51F GLY* 3.8 9.6 - - - +
66F VAL* 4.4 15.7 - - + -
68F GLY* 6.1 0.2 - - - -
168F ALA 2.9 16.8 + - - +
169F LEU 3.1 4.2 + - - +
171F ASP* 1.3 76.6 + - - +
173F GLY* 1.3 59.4 + - - +
174F VAL* 3.5 6.5 - - + +
57I ARG* 3.6 11.2 + - - +
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Residues in contact with GLY 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LYS* 5.6 2.2 + - - -
139F TYR* 3.5 7.5 + - - -
169F LEU 3.1 2.6 + - - -
170F ALA 3.9 7.6 - - - -
171F ASP 2.9 5.6 + - - -
172F ALA* 1.3 80.2 - - - +
174F VAL* 1.3 63.2 + - - +
175F GLU* 4.9 0.2 - - - +
37I LEU* 2.9 26.2 - - - +
38I ALA 5.5 0.7 - - - -
57I ARG* 3.7 19.7 - - - -
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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