Contacts of the helix formed by residues 159 - 170 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40H LYS 3.4 12.2 - - - +
41H TYR* 3.4 14.0 - - - -
42H VAL 4.9 0.2 + - - -
45H SER* 4.2 14.7 + - - +
105H ARG* 2.9 44.3 + - - -
154H ALA* 2.8 17.4 + - - +
155H THR* 5.2 0.8 - - - -
157H ASN* 3.2 4.4 - - + +
158H GLY* 1.3 75.2 - - - +
160H VAL* 1.3 61.6 + - - +
161H GLN 3.4 4.0 + - - -
162H LEU* 3.0 20.7 + - + +
163H ALA* 3.2 22.1 + - - +
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Residues in contact with VAL 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158H GLY 3.3 11.5 + - - +
159H ASP* 1.3 73.8 + - - +
161H GLN* 1.3 59.1 + - - +
163H ALA* 3.4 6.2 + - - +
164H ASP* 3.0 25.1 + - - +
148X LEU* 4.1 22.0 - - + +
151X HIS* 3.4 44.6 - - + +
167X GLU* 3.8 10.0 - - + +
171X LEU* 3.5 18.6 - - + -
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Residues in contact with GLN 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H TYR* 2.5 39.4 + - - -
105H ARG* 3.6 9.5 + - - +
159H ASP* 3.4 2.0 + - - +
160H VAL* 1.3 77.2 - - - +
162H LEU* 1.3 60.7 + - - +
164H ASP* 3.3 11.4 + - + +
165H PHE* 2.9 34.3 + - - +
148X LEU* 5.3 3.7 - - + +
171X LEU* 3.7 39.2 - - + +
172X GLY* 3.7 16.5 - - - +
175X VAL* 3.6 24.8 - - + +
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Residues in contact with LEU 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H TYR* 4.5 2.9 - - + -
45H SER* 3.9 29.6 - - - +
49H VAL* 4.0 21.5 - - + -
98H LEU* 6.0 0.2 - - + -
101H TYR* 3.2 36.6 + - + +
105H ARG* 4.0 1.8 - - - +
150H LEU* 4.5 11.2 - - + -
153H VAL* 5.7 0.2 - - + -
154H ALA* 3.6 23.1 - - + +
159H ASP* 3.0 21.6 + - - +
161H GLN* 1.3 77.1 - - - +
163H ALA* 1.3 62.6 + - - +
165H PHE* 3.2 4.3 + - + +
166H VAL* 3.0 37.7 + - + +
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Residues in contact with ALA 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151H HIS* 3.5 23.8 - - - +
154H ALA* 3.7 10.0 - - + +
155H THR* 4.0 19.3 - - + -
159H ASP 3.2 16.1 + - - +
160H VAL* 3.7 6.3 - - - +
162H LEU* 1.3 79.0 - - - +
164H ASP* 1.3 63.7 + - - +
166H VAL* 3.4 1.1 + - - -
167H GLU* 3.0 33.3 + - - +
167X GLU* 6.0 0.4 - - - +
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Residues in contact with ASP 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A CA 3.9 9.2 - - - -
160H VAL 3.0 17.8 + - - +
161H GLN* 3.5 15.3 + - + +
163H ALA* 1.3 77.4 - - - +
165H PHE* 1.3 57.5 + - - +
167H GLU* 3.4 6.3 + - - +
168H THR* 2.9 47.3 + - - -
164X ASP* 5.2 0.2 - - - +
167X GLU* 3.4 52.5 + - + +
168X THR* 4.7 6.9 + - - -
171X LEU* 5.9 0.4 - - + -
172X GLY* 5.3 2.6 + - - -
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Residues in contact with PHE 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H LYS* 4.1 19.3 - - + -
98H LEU* 3.8 14.8 - - + -
101H TYR* 3.6 58.3 - + + -
104H LYS* 6.1 2.9 - - - -
161H GLN* 2.9 23.3 + - - +
162H LEU* 3.5 4.0 - - + +
164H ASP* 1.3 79.1 + - - +
166H VAL* 1.3 66.9 + - + +
168H THR* 4.8 1.8 - - - -
169H GLU* 2.8 62.7 + - + +
170H TYR* 3.7 27.6 - + - -
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Residues in contact with VAL 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H LEU* 3.9 30.5 - - + +
150H LEU* 3.6 32.1 - - + -
151H HIS* 4.3 14.4 - - + +
162H LEU* 3.0 32.6 + - + +
163H ALA* 3.8 4.3 - - - +
165H PHE* 1.3 82.9 - - + +
167H GLU* 1.3 64.0 + - - +
170H TYR* 3.0 25.0 + - + +
171H LEU* 3.2 23.0 + - + -
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Residues in contact with GLU 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A VAL* 3.9 17.1 - - + +
164A ASP* 3.3 31.9 - - - +
167A GLU* 3.6 4.9 - - - +
351A CA 2.6 27.6 - - - -
353A CA 4.3 0.9 - - - -
151H HIS* 2.7 33.1 + - + +
163H ALA* 3.0 25.4 + - - +
164H ASP* 3.7 6.4 + - - +
166H VAL* 1.3 79.2 - - - +
168H THR* 1.3 62.8 + - - +
171H LEU* 3.4 24.3 + - + +
172H GLY 3.9 4.5 + - - -
167X GLU* 5.1 3.5 - - - +
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Residues in contact with THR 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ASP* 4.6 8.4 + - - -
164H ASP* 2.9 35.2 + - - -
165H PHE* 4.1 2.2 - - - -
167H GLU* 1.3 77.7 - - - +
169H GLU* 1.3 78.3 + - - +
173H GLU* 3.6 1.4 - - - +
215H CA 2.4 28.3 - - - -
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Residues in contact with GLU 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94H HIS* 6.2 0.3 - - - -
97H LYS* 2.8 39.2 + - + +
165H PHE* 2.8 46.4 + - + +
168H THR* 1.3 96.1 - - - +
170H TYR* 1.3 81.7 + - + +
173H GLU* 3.3 21.1 - - - +
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Residues in contact with TYR 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H GLU* 4.2 5.8 - - - -
94H HIS* 2.7 53.6 + + + -
97H LYS* 3.3 21.4 - - + +
98H LEU* 3.2 24.9 + - + +
147H LEU* 3.8 33.3 - - + +
165H PHE* 3.7 29.6 - + - -
166H VAL* 3.0 20.7 + - + +
168H THR 3.5 0.4 - - - -
169H GLU* 1.3 93.9 - - + +
171H LEU* 1.3 62.1 + - - +
172H GLY 3.5 1.8 - - - -
173H GLU* 3.4 7.1 + - + +
174H GLN* 2.9 32.3 + - - +
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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