Contacts of the helix formed by residues 159 - 170 (chain T) in PDB entry 3A9Q
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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40T LYS 3.4 10.4 - - - +
41T TYR* 3.3 16.3 - - - -
42T VAL 5.0 0.3 + - - -
45T SER* 4.2 14.2 + - - +
105T ARG* 2.8 45.5 + - - -
154T ALA* 2.8 17.5 + - - +
155T THR* 5.6 0.4 - - - -
157T ASN* 3.3 3.7 - - + +
158T GLY* 1.3 73.2 - - - +
160T VAL* 1.3 64.4 + - - +
161T GLN* 3.5 3.5 + - - +
162T LEU* 3.0 20.7 + - + -
163T ALA* 3.2 21.8 + - - +
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Residues in contact with VAL 160 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148L LEU* 3.3 31.4 - - + +
151L HIS* 3.4 42.2 - - + +
167L GLU* 4.1 6.2 - - + +
171L LEU* 3.5 18.8 - - + -
158T GLY 3.2 10.3 + - - +
159T ASP* 1.3 72.9 + - - +
161T GLN* 1.3 56.6 + - - +
163T ALA* 3.5 6.4 + - - +
164T ASP* 3.0 26.5 + - - +
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Residues in contact with GLN 161 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148L LEU* 5.2 3.8 - - + +
167L GLU 5.6 0.8 + - - -
171L LEU* 3.7 35.6 - - + +
172L GLY* 3.6 18.9 - - - +
175L VAL* 3.7 21.1 - - + +
101T TYR* 2.6 36.2 + - - -
105T ARG* 4.0 10.5 + - - +
159T ASP* 3.3 2.7 + - - +
160T VAL* 1.3 82.7 - - + +
162T LEU* 1.3 60.2 - - - +
164T ASP* 3.3 9.4 + - + +
165T PHE* 2.9 39.2 + - - +
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Residues in contact with LEU 162 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41T TYR* 4.4 3.6 - - + -
45T SER* 3.8 31.4 - - - +
49T VAL* 3.9 23.1 - - + -
98T LEU* 5.9 0.4 - - + -
101T TYR* 3.3 35.7 + - + +
105T ARG* 4.0 1.3 - - - +
150T LEU* 4.5 9.9 - - + -
153T VAL* 6.0 0.2 - - + -
154T ALA* 3.7 22.4 - - + +
159T ASP* 3.0 23.1 + - - +
161T GLN* 1.3 76.5 - - - +
163T ALA* 1.3 63.6 + - - +
165T PHE* 3.2 4.7 + - + +
166T VAL* 3.0 42.0 + - + +
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Residues in contact with ALA 163 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151T HIS* 3.3 27.6 - - + +
154T ALA* 3.8 11.4 - - + +
155T THR* 3.9 16.4 - - - +
159T ASP 3.2 15.3 + - - +
160T VAL* 3.7 6.7 - - - +
162T LEU* 1.3 80.4 - - - +
164T ASP* 1.3 56.6 + - - +
166T VAL* 3.3 2.9 + - - -
167T GLU* 3.0 34.4 + - - +
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Residues in contact with ASP 164 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167L GLU* 2.9 41.6 - - + +
168L THR* 4.6 2.8 + - - -
171L LEU* 6.5 0.2 - - + -
215L CA 2.6 28.1 - - - -
160T VAL 3.0 18.7 + - - +
161T GLN* 3.7 11.8 + - + +
163T ALA* 1.3 75.0 - - - +
165T PHE* 1.3 59.9 + - - +
167T GLU* 4.2 10.9 + - - +
168T THR* 2.8 49.8 + - - +
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Residues in contact with PHE 165 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97T LYS* 4.1 19.1 - - + -
98T LEU* 3.9 13.2 - - + -
101T TYR* 3.6 61.9 - + + -
104T LYS* 6.1 2.5 - - - -
161T GLN* 2.9 25.2 + - - +
162T LEU* 3.5 7.0 - - + +
164T ASP* 1.3 75.9 + - - +
166T VAL* 1.3 67.1 + - + +
168T THR* 4.0 4.7 - - - -
169T GLU* 2.8 60.9 + - + +
170T TYR* 3.7 29.4 - + - -
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Residues in contact with VAL 166 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98T LEU* 5.7 0.2 - - + -
147T LEU* 3.9 24.9 - - + +
150T LEU* 3.5 33.9 - - + -
151T HIS* 4.3 9.9 - - + +
162T LEU* 3.0 28.8 + - + +
163T ALA* 3.7 7.4 - - - +
164T ASP 3.2 0.2 - - - -
165T PHE* 1.3 82.9 - - + +
167T GLU* 1.3 63.4 + - - +
170T TYR* 3.0 31.0 + - + +
171T LEU* 3.0 27.1 + - + -
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Residues in contact with GLU 167 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167L GLU* 5.2 1.0 - - - +
160M VAL* 4.6 8.7 - - + +
163M ALA* 5.9 1.0 - - - +
164M ASP* 3.6 42.4 + - + +
167M GLU* 4.2 11.1 - - - +
151T HIS* 2.6 34.1 + - + +
163T ALA* 3.0 23.6 + - - +
164T ASP* 3.2 16.5 + - - +
166T VAL* 1.3 78.9 - - - +
168T THR* 1.3 62.9 + - + +
171T LEU* 3.5 30.3 + - + +
172T GLY 3.8 4.0 + - - -
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Residues in contact with THR 168 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168L THR* 5.8 2.5 - - - +
215L CA 4.6 3.1 - - - -
164M ASP* 3.9 17.7 - - - +
168M THR* 5.2 3.8 - - - +
164T ASP* 2.8 46.0 + - - +
165T PHE* 3.6 5.2 + - - -
167T GLU* 1.3 74.5 - - + +
169T GLU* 1.3 84.1 + - - +
170T TYR 5.5 0.2 - - - -
172T GLY* 5.4 2.8 + - - -
173T ALA 5.9 0.3 + - - -
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Residues in contact with GLU 169 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97T LYS* 2.7 45.2 + - - +
165T PHE* 2.8 41.0 + - + +
168T THR* 1.3 103.0 + - - +
170T TYR* 1.3 72.0 + - + +
173T ALA* 4.4 12.6 - - - +
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Residues in contact with TYR 170 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56T GLU* 4.1 7.2 - - - -
94T HIS* 2.6 50.0 + + + -
97T LYS* 3.4 20.7 - - + +
98T LEU* 3.2 28.6 - - + +
147T LEU* 3.9 34.8 - - + +
150T LEU* 6.5 0.2 - - + -
165T PHE* 3.7 33.4 - + - -
166T VAL* 3.0 17.7 + - + +
168T THR 3.6 0.2 - - - -
169T GLU* 1.3 93.0 - - + +
171T LEU* 1.3 62.5 + - - +
172T GLY 3.5 2.0 - - - -
173T ALA* 3.5 5.2 + - - +
174T GLN* 3.0 30.5 + - - +
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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