Contacts of the helix formed by residues 159 - 170 (chain S) in PDB entry 3A68
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 ASP 159 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40S LYS 3.3 11.9 - - - +
41S TYR* 3.4 14.4 - - - -
42S VAL 4.8 0.3 + - - -
45S SER* 4.2 11.5 + - - +
105S ARG* 2.9 44.9 + - - -
154S ALA* 2.8 19.5 + - - +
155S THR* 5.0 0.6 - - - +
157S ASN* 3.2 4.4 - - + +
158S GLY* 1.3 73.6 - - - +
160S VAL* 1.3 65.1 + - - +
161S GLN* 3.6 2.6 + - - +
162S LEU* 3.0 20.4 + - + -
163S ALA* 3.1 23.3 + - - +
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Residues in contact with VAL 160 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C LEU* 4.0 21.0 - - + +
151C HIS* 3.5 41.7 - - + +
152C SER* 6.2 0.2 - - - +
167C GLU* 3.8 8.3 - - + +
171C LEU* 3.4 23.8 - - + -
158S GLY* 3.2 13.3 + - - +
159S ASP* 1.3 72.4 + - - +
161S GLN* 1.3 59.0 + - - +
163S ALA* 3.4 5.6 + - - +
164S ASP* 3.0 26.5 + - - +
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Residues in contact with GLN 161 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C LEU* 5.1 4.3 - - + +
171C LEU* 3.7 37.7 - - + +
172C GLY* 3.6 16.9 - - - +
175C VAL* 3.7 23.3 - - + +
101S TYR* 2.5 39.1 + - - -
105S ARG* 3.7 9.6 + - - +
159S ASP* 3.4 2.2 + - - +
160S VAL* 1.3 78.6 - - - +
162S LEU* 1.3 61.2 + - - +
164S ASP* 3.3 10.7 + - + +
165S PHE* 2.9 34.9 + - - +
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Residues in contact with LEU 162 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41S TYR* 4.4 3.1 - - + -
45S SER* 3.8 30.3 - - - +
49S VAL* 3.9 17.0 - - + -
101S TYR* 3.2 36.0 + - + +
105S ARG* 3.9 1.1 - - - +
150S LEU* 4.4 15.9 - - + -
153S VAL* 5.7 0.2 - - + -
154S ALA* 3.7 22.0 - - + +
159S ASP* 3.0 23.5 + - - +
161S GLN* 1.3 76.4 - - - +
163S ALA* 1.3 64.7 + - - +
165S PHE* 3.2 3.1 + - + +
166S VAL* 3.0 45.1 + - + +
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Residues in contact with ALA 163 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151S HIS* 3.6 27.0 - - + +
154S ALA* 3.7 16.1 - - + +
155S THR* 4.4 7.0 - - - +
159S ASP 3.1 17.9 + - - +
160S VAL* 3.7 6.1 - - - +
162S LEU* 1.3 76.8 - - - +
164S ASP* 1.3 62.0 + - - +
166S VAL* 3.4 1.7 + - - -
167S GLU* 3.0 31.6 + - - +
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Residues in contact with ASP 164 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C GLU* 3.5 42.5 + - + +
168C THR* 4.4 7.0 + - - -
172C GLY* 5.5 1.9 + - - -
321C CA 2.6 26.5 - - - -
160S VAL 3.0 16.8 + - - +
161S GLN* 3.7 14.1 + - + +
163S ALA* 1.3 75.1 - - - +
165S PHE* 1.3 59.5 + - - +
167S GLU* 3.3 7.6 + - - +
168S THR* 2.8 46.7 + - - -
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Residues in contact with PHE 165 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97S LYS* 4.1 17.3 - - + -
98S LEU* 3.8 21.1 - - + -
101S TYR* 3.6 59.5 - + + -
104S LYS* 6.1 2.9 - - - -
161S GLN* 2.9 26.3 + - - +
162S LEU* 3.2 4.2 + - + +
164S ASP* 1.3 76.6 + - - +
166S VAL* 1.3 69.1 + - + +
168S THR* 4.7 2.5 - - - -
169S GLU* 2.8 58.6 + - + +
170S TYR* 3.7 21.5 - + - -
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Residues in contact with VAL 166 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147S LEU* 4.0 33.4 - - + +
150S LEU* 3.6 30.5 - - + -
151S HIS* 4.4 13.7 - - + +
162S LEU* 3.0 27.3 + - + +
163S ALA* 3.7 5.8 - - - +
165S PHE* 1.3 84.0 - - + +
167S GLU* 1.3 64.2 + - - +
170S TYR* 3.0 25.3 + - + +
171S LEU* 3.1 24.1 + - + -
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Residues in contact with GLU 167 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C CA 2.6 29.6 - - - -
323C CA 4.2 3.8 - - - -
160R VAL* 4.1 8.0 - - + +
164R ASP* 3.6 32.2 - - - +
167R GLU* 5.0 1.5 - - - +
151S HIS* 2.7 34.5 + - + +
163S ALA* 3.0 20.2 + - - +
164S ASP* 3.3 9.8 + - - +
166S VAL* 1.3 77.5 - - - +
168S THR* 1.3 62.8 + - - +
171S LEU* 3.5 32.7 + - + +
172S GLY* 3.9 6.2 + - - -
173S GLU* 4.6 0.2 - - - +
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Residues in contact with THR 168 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164R ASP* 4.7 5.3 + - - -
164S ASP* 2.8 37.2 + - - -
165S PHE* 4.1 3.4 - - - -
167S GLU* 1.3 79.6 - - - +
169S GLU* 1.3 74.1 + - - +
173S GLU* 3.6 1.6 - - - +
215S CA 2.5 28.2 - - - -
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Residues in contact with GLU 169 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97S LYS* 2.7 39.0 + - + -
165S PHE* 2.8 43.6 + - + +
168S THR* 1.3 90.9 - - - +
170S TYR* 1.3 81.7 + - + +
173S GLU* 3.3 23.2 - - - +
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Residues in contact with TYR 170 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56S GLU* 4.3 6.7 - - - -
94S HIS* 2.7 53.2 + + + -
97S LYS* 3.3 22.2 - - + +
98S LEU* 3.2 24.4 - - + +
147S LEU* 3.7 35.1 - - + +
165S PHE* 3.7 32.5 - + - -
166S VAL* 3.0 16.9 + - + +
168S THR 3.6 0.4 - - - -
169S GLU* 1.3 93.2 - - + +
171S LEU* 1.3 61.3 + - - +
172S GLY 3.5 2.2 - - - -
173S GLU* 3.4 6.0 + - + +
174S GLN* 2.8 32.0 + - - +
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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