Contacts of the helix formed by residues 159 - 166 (chain H) in PDB entry 2HOD
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 SER 159 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155H GLU* 3.1 25.1 + - - -
158H ASN* 1.3 78.6 - - - +
160H ASN* 1.3 66.0 + - - +
162H PRO* 2.9 30.0 - - - +
163H THR* 4.1 9.5 + - - -
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Residues in contact with ASN 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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191G LYS* 3.2 48.1 + - + +
192G ASP 5.6 0.9 - - - +
155H GLU* 3.6 10.8 + - - -
156H THR* 3.4 35.2 + - - +
159H SER* 1.3 80.5 + - - +
161H ILE* 1.3 65.9 + - - +
162H PRO 3.1 2.2 - - - -
163H THR* 3.6 8.0 + - - +
164H ASN* 3.2 21.4 + - - +
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Residues in contact with ILE 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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129G LYS 4.3 6.1 - - - +
130G VAL* 3.6 30.1 - - + -
133G ILE* 5.0 7.4 - - + -
156H THR* 3.1 25.7 + - - +
157H VAL* 4.6 6.1 - - + -
158H ASN 4.4 4.0 - - - +
160H ASN* 1.3 79.3 - - - +
162H PRO* 1.4 62.3 - - + +
164H ASN* 3.0 17.9 - - + +
165H LEU* 2.8 35.5 + - + +
103I HIS* 3.2 49.8 - - + +
107I ILE* 6.5 0.2 - - + -
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Residues in contact with PRO 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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158H ASN* 3.9 10.1 - - - +
159H SER* 2.9 40.2 - - - +
161H ILE* 1.4 91.1 - - + +
163H THR* 1.3 56.3 + - - +
164H ASN 2.5 15.7 + - - -
165H LEU* 2.7 17.2 + - + -
166H ARG* 2.9 20.2 + - + +
103I HIS* 6.2 0.9 - - + -
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Residues in contact with THR 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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188G VAL* 3.9 27.4 - - + +
159H SER 4.1 9.2 + - - -
160H ASN* 3.6 9.1 + - - -
162H PRO* 1.3 77.2 - - - +
164H ASN* 1.3 61.2 + - - +
166H ARG* 3.8 13.9 + - - +
167H VAL* 3.8 16.6 - - + +
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Residues in contact with ASN 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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130G VAL* 5.6 1.9 - - - +
133G ILE* 4.4 20.1 - - - +
134G GLN* 5.8 0.9 - - - -
137G GLN* 3.2 30.7 + - - +
188G VAL* 3.5 15.7 + - - +
160H ASN 3.2 13.7 + - - +
161H ILE* 3.0 22.0 - - + +
162H PRO 2.5 4.6 + - - -
163H THR* 1.3 70.6 - - - +
165H LEU* 1.3 65.3 + - + +
166H ARG 2.8 10.4 + - - -
167H VAL* 3.1 14.2 + - - +
168H LEU* 3.4 19.7 + - - +
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Residues in contact with LEU 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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133G ILE* 5.7 3.1 - - + -
161H ILE* 2.8 25.8 + - + +
162H PRO* 2.7 9.6 + - + +
164H ASN* 1.3 78.2 - - + +
166H ARG* 1.3 83.4 + - - +
167H VAL 3.3 2.2 - - - -
168H LEU* 4.9 4.3 - - + +
169H ARG* 3.0 38.7 - - + +
103I HIS* 5.2 4.5 - - + +
106I SER* 2.7 49.1 - - - +
107I ILE* 3.7 16.2 - - + -
110I LEU* 3.9 10.5 - - + -
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Residues in contact with ARG 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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162H PRO* 2.9 21.0 + - + +
163H THR* 4.0 10.5 - - + +
164H ASN 2.8 1.4 + - - -
165H LEU* 1.3 113.0 + - + +
167H VAL* 1.3 66.9 + - + +
169H ARG* 3.5 28.2 + - - +
170H SER* 3.7 15.9 + - - -
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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