Contacts of the helix formed by residues 161 - 170 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64I LYS* 4.1 23.5 + - - -
126J TYR* 4.1 13.4 + - - +
159J ASN* 2.9 19.1 - - + +
160J GLU* 1.3 79.5 - - - +
162J GLU* 1.3 65.2 + - - +
163J MET 3.1 0.9 - - - -
164J LYS* 3.8 9.0 + - + +
165J PHE* 3.8 11.3 + - - +
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Residues in contact with GLU 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J TYR* 4.6 15.9 + - + -
131J TYR* 2.2 37.9 + - + +
156J SER 3.7 4.6 - - - +
157J ILE* 3.5 6.5 - - + +
158J ASP* 2.6 38.2 + - + +
159J ASN* 3.2 15.4 + - + +
161J GLU* 1.3 77.6 - - - +
163J MET* 1.3 57.0 + - - +
165J PHE* 3.2 13.0 + - + +
166J LEU* 2.9 37.7 + - + +
230J LYS* 2.7 20.9 + - - -
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Residues in contact with MET 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J ILE* 3.4 36.6 - - + -
159J ASN 3.3 4.8 + - - +
160J GLU* 3.6 35.7 - - - +
161J GLU 3.1 0.6 - - - -
162J GLU* 1.3 80.3 - - - +
164J LYS* 1.3 60.9 + - - +
166J LEU* 3.4 13.4 + - - +
167J SER* 3.4 14.4 + - - -
196J HIS* 4.1 15.0 - - + -
211J LEU* 4.1 23.0 - - + +
214J ASN* 3.6 36.2 - - - +
215J ARG* 4.6 5.2 - - - -
216J LEU* 4.9 13.0 - - + -
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Residues in contact with LYS 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D ARG* 4.4 20.2 - - - +
77I SER* 5.1 12.9 + - - +
171I ARG* 4.4 13.0 - - - +
160J GLU 4.5 5.7 + - - +
161J GLU* 3.8 12.2 + - + +
162J GLU 3.4 0.4 - - - -
163J MET* 1.3 73.8 - - - +
165J PHE* 1.3 65.9 + - - +
167J SER* 2.6 25.5 + - - +
168J ILE* 3.3 30.2 - - + +
214J ASN* 4.0 24.0 + - - +
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Residues in contact with PHE 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66I VAL* 4.3 14.4 - - + -
75I ILE* 5.3 5.2 - - + -
124J ILE* 4.1 14.6 - - + -
126J TYR* 3.5 57.0 - + + +
131J TYR* 4.0 12.1 - + - -
161J GLU 3.8 6.7 + - - +
162J GLU* 3.2 17.2 + - + +
164J LYS* 1.3 80.7 - - - +
166J LEU* 1.3 88.0 + - + +
167J SER 3.1 0.2 - - - -
168J ILE* 2.8 29.2 + - + +
169J ILE* 3.2 39.8 + - + +
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Residues in contact with LEU 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J ILE* 6.3 0.2 - - + -
131J TYR* 4.3 14.4 - - + -
133J ILE* 5.8 1.6 - - + -
155J LEU* 3.5 41.5 - - + -
157J ILE* 3.7 18.8 - - + -
162J GLU* 2.9 27.6 + - + +
163J MET* 3.4 7.4 + - - +
164J LYS 3.3 0.4 - - - -
165J PHE* 1.3 94.6 - - + +
167J SER* 1.3 55.9 + - - +
169J ILE* 4.0 11.0 - - + -
170J SER 3.0 27.5 + - - +
211J LEU* 3.9 17.7 - - + +
228J HIS* 4.6 10.8 - - + -
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Residues in contact with SER 167 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5F ARG* 5.2 2.1 + - - -
110I SER* 4.3 3.8 + - - -
111I SER* 6.1 0.2 - - - -
163J MET 3.4 8.6 + - - -
164J LYS* 2.6 27.5 + - - +
166J LEU* 1.3 77.7 - - - +
168J ILE* 1.3 62.6 + - - +
169J ILE 3.1 5.3 + - - -
170J SER 4.1 1.6 + - - -
171J PRO* 4.0 26.9 - - - +
211J LEU* 5.3 3.4 - - - -
213J VAL* 4.5 14.1 - - - +
214J ASN* 4.4 21.1 + - - +
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Residues in contact with ILE 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I ILE* 4.3 16.6 - - + -
76I SER 5.0 4.9 - - - +
77I SER* 5.9 1.3 - - - -
108I MET* 3.9 16.0 - - + +
110I SER* 5.0 1.6 - - - -
111I SER* 4.3 11.5 - - - +
115I TYR* 3.3 26.2 - - - +
171I ARG* 4.1 17.5 - - - +
164J LYS* 3.3 43.7 - - + +
165J PHE* 2.8 10.6 + - + +
167J SER* 1.3 81.1 - - - +
169J ILE* 1.3 63.6 + - + +
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Residues in contact with ILE 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66I VAL* 4.9 0.7 - - + -
75I ILE* 4.2 12.3 - - + -
107I PHE* 3.0 55.9 - - + +
108I MET* 3.7 8.1 - - + +
110I SER* 3.2 13.4 - - - -
124J ILE* 4.4 3.8 - - + -
133J ILE* 3.6 28.7 - - + -
165J PHE* 3.2 48.9 + - + +
166J LEU* 4.0 13.9 - - + +
167J SER 3.1 0.4 - - - -
168J ILE* 1.3 83.3 - - + +
170J SER* 1.3 68.1 + - - +
228J HIS* 5.2 0.7 - - - +
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Residues in contact with SER 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106I ASP 5.2 0.3 + - - -
107I PHE 3.6 8.0 + - - -
109I SER* 5.1 0.3 + - - -
110I SER* 3.5 11.5 + - - -
133J ILE* 4.2 8.1 - - - +
135J LYS* 6.1 0.3 - - - +
166J LEU 3.0 15.6 + - - +
167J SER 4.2 0.4 - - - -
169J ILE* 1.3 88.4 + - - +
171J PRO* 1.4 73.6 - - - +
172J SER 3.6 3.3 + - - +
211J LEU* 4.7 2.9 - - - +
226J ILE* 5.9 1.1 - - - -
228J HIS* 3.1 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