Contacts of the helix formed by residues 161 - 170 (chain H) in PDB entry 3CII
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 GLU 161 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64G LYS* 3.4 33.9 + - - -
126H TYR* 4.0 13.1 + - - +
159H ASN* 2.9 20.1 + - + +
160H GLU* 1.3 77.8 - - - +
162H GLU* 1.3 65.5 + - - +
163H MET 3.1 1.3 - - - -
164H LYS* 3.8 8.8 + - + +
165H PHE* 3.7 12.1 + - - +
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Residues in contact with GLU 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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126H TYR* 4.5 16.4 + - + -
131H TYR* 2.2 37.4 + - + +
156H SER 3.7 4.1 - - - +
157H ILE* 3.4 6.5 - - - +
158H ASP* 2.6 36.7 + - + +
159H ASN* 3.2 16.4 + - + +
161H GLU* 1.3 78.1 - - - +
163H MET* 1.3 57.5 + - - +
165H PHE* 3.2 13.6 + - + +
166H LEU* 2.9 39.3 + - + +
230H LYS* 2.6 21.8 + - - -
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Residues in contact with MET 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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157H ILE* 3.4 38.1 - - + +
159H ASN 3.3 5.1 + - - +
160H GLU* 3.6 35.4 - - - +
161H GLU 3.1 0.4 - - - -
162H GLU* 1.3 76.2 - - - +
164H LYS* 1.3 66.0 + - - +
166H LEU* 3.5 6.4 + - - +
167H SER* 3.4 20.3 + - - -
196H HIS* 4.0 15.9 - - + -
211H LEU* 4.1 21.0 - - + +
214H ASN* 3.5 37.0 - - - +
215H ARG* 4.6 5.2 - - - -
216H LEU* 4.9 13.9 - - + -
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Residues in contact with LYS 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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65A ARG* 4.7 4.9 - - - +
77G SER* 4.2 22.0 + - - +
171G ARG* 3.1 35.0 - - - +
160H GLU 4.5 5.1 + - - +
161H GLU* 3.8 12.1 + - + +
162H GLU 3.4 0.4 - - - -
163H MET* 1.3 74.2 - - - +
165H PHE* 1.3 66.9 + - - +
167H SER* 2.6 25.8 + - - +
168H ILE* 3.4 23.6 - - + +
214H ASN* 4.0 22.5 + - - +
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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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66G VAL* 4.1 15.7 - - + -
75G ILE* 5.3 5.8 - - + -
124H ILE* 4.1 15.0 - - + -
126H TYR* 3.5 61.7 - + + +
131H TYR* 4.0 9.9 - + - -
161H GLU 3.7 7.1 + - - +
162H GLU* 3.2 16.7 + - + +
164H LYS* 1.3 79.0 - - - +
166H LEU* 1.3 91.3 + - + +
168H ILE* 2.8 28.7 + - - +
169H ILE* 3.2 38.4 + - + +
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Residues in contact with LEU 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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124H ILE* 6.3 0.2 - - + -
131H TYR* 4.3 13.5 - - + -
133H ILE* 5.8 1.1 - - + -
155H LEU* 3.5 40.4 - - + -
157H ILE* 3.7 18.8 - - + -
162H GLU* 2.9 27.9 + - + +
163H MET* 3.9 7.0 - - - +
164H LYS 3.3 0.4 - - - -
165H PHE* 1.3 96.8 - - + +
167H SER* 1.3 57.0 + - - +
168H ILE 3.4 0.2 - - - -
169H ILE* 3.9 10.8 - - + -
170H SER 3.1 29.3 + - - +
211H LEU* 3.9 16.8 - - + +
228H HIS* 4.7 9.9 - - + -
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Residues in contact with SER 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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5C ARG* 4.6 6.9 + - - -
110G SER* 5.6 0.3 + - - -
163H MET 3.4 9.8 + - - -
164H LYS* 2.6 26.9 + - - +
166H LEU* 1.3 77.4 - - - +
168H ILE* 1.3 61.9 + - - +
169H ILE 3.2 5.1 + - - -
170H SER* 4.2 2.1 + - - -
171H PRO* 4.0 26.6 - - - +
211H LEU* 5.0 4.2 - - - +
213H VAL* 4.5 14.0 - - - +
214H ASN* 4.3 21.4 + - - +
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Residues in contact with ILE 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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75G ILE* 3.7 22.7 - - + -
76G SER 4.5 10.1 - - - +
77G SER* 5.5 0.7 - - - -
108G MET* 3.5 19.0 - - - +
111G SER* 4.4 11.1 - - - +
113G GLN* 5.6 3.8 - - + -
115G TYR* 3.4 24.7 - - + +
171G ARG* 4.0 15.9 - - - +
164H LYS* 3.4 41.1 - - + +
165H PHE* 2.8 11.2 + - + +
167H SER* 1.3 80.9 - - - +
169H ILE* 1.3 62.1 + - + +
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Residues in contact with ILE 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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66G VAL* 4.8 0.7 - - + -
75G ILE* 4.0 15.5 - - + -
107G PHE* 3.1 47.0 - - + +
108G MET* 3.7 7.3 - - - -
110G SER* 3.4 10.3 + - - -
124H ILE* 4.4 6.5 - - + -
133H ILE* 3.6 36.6 - - + -
165H PHE* 3.2 48.4 + - + +
166H LEU* 3.9 13.9 - - + +
167H SER 3.2 0.6 - - - -
168H ILE* 1.3 81.3 - - - +
170H SER* 1.3 69.2 + - - +
228H HIS* 5.1 0.7 - - - +
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Residues in contact with SER 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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107G PHE 3.5 11.1 + - - -
109G SER* 5.6 0.9 - - - -
110G SER* 3.6 10.1 + - - -
133H ILE* 4.2 6.8 - - - +
135H LYS* 6.1 0.2 - - - +
166H LEU 3.1 14.2 + - - +
167H SER 4.2 1.1 + - - -
169H ILE* 1.3 89.6 + - - +
171H PRO* 1.3 73.2 - - - +
172H SER 3.5 3.9 + - - +
211H LEU* 4.8 2.9 - - - +
226H ILE* 5.9 1.3 - - - -
228H HIS* 3.2 40.7 + - - -
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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
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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