Contacts of the helix formed by residues 160 - 166 (chain C) in PDB entry 4PEI
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 TYR 160 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C TYR* 5.0 3.3 - - - -
115C VAL* 3.6 25.0 - - + +
116C CYS* 5.3 1.6 - - - -
138C GLU 4.8 0.2 + - - -
142C TYR* 3.6 16.0 - + - -
158C ARG* 3.2 37.9 - - + +
159C ASN* 1.3 74.9 - - - +
161C VAL* 1.3 72.5 + - + +
162C ILE 3.0 0.4 - - - -
163C GLN* 3.0 27.1 + - - +
164C MET* 3.2 30.2 + - + +
286C PHE* 3.6 29.9 - + - -
293C PRO* 3.4 33.7 - - + -
295C LEU* 4.4 26.1 - - + +
299C ILE* 4.4 10.3 - - + +
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Residues in contact with VAL 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C VAL* 3.7 32.3 - - + +
116C CYS* 4.0 17.5 - - + -
129C VAL* 4.1 4.3 - - + -
157C THR* 4.0 10.1 - - + -
158C ARG 3.1 25.6 - - - +
159C ASN 3.1 0.6 + - - -
160C TYR* 1.3 87.9 - - + +
162C ILE* 1.3 67.7 + - - +
164C MET* 4.1 5.8 - - - -
165C LEU* 3.1 28.4 + - + +
213C ILE* 3.7 21.5 - - + -
217C ILE* 4.1 9.6 - - + -
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Residues in contact with ILE 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B SER* 4.7 8.1 - - - +
304B SER* 3.9 27.6 - - - -
159C ASN* 3.0 27.7 + - - +
161C VAL* 1.3 79.2 - - - +
163C GLN* 1.3 62.7 + - - +
165C LEU* 3.8 1.0 - - - +
166C SER* 2.9 36.1 + - - -
213C ILE* 4.0 35.0 - - + +
216C VAL* 3.6 31.9 - - + -
217C ILE* 4.1 14.7 - - + +
220C THR* 5.3 2.5 - - - +
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Residues in contact with GLN 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B SER* 3.6 22.2 + - - -
300B SER* 3.4 31.1 + - - +
301B GLU* 4.7 2.6 + - - +
159C ASN* 3.7 22.3 + - - +
160C TYR* 3.0 11.8 + - - +
162C ILE* 1.3 78.3 - - - +
164C MET* 1.3 63.1 + - - +
165C LEU 3.4 0.3 + - - -
166C SER* 3.6 16.2 + - - -
167C ASN 4.9 1.0 + - - -
295C LEU* 6.1 1.4 - - - +
298C SER* 5.8 1.8 + - - +
299C ILE* 3.4 33.9 - - + +
300C SER* 4.1 21.7 - - - +
303C LEU* 3.2 18.4 - - - +
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Residues in contact with MET 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C CYS* 4.0 9.4 - - - -
160C TYR* 3.2 34.6 + - + +
161C VAL* 3.3 7.4 + - - +
163C GLN* 1.3 75.8 - - - +
165C LEU* 1.3 60.1 + - - +
275C TRP* 3.6 40.5 - - + -
278C ASN* 2.9 33.9 + - + +
279C LEU* 4.7 7.9 - - + -
282C THR* 3.4 29.6 - - + +
286C PHE* 4.2 20.0 - - + -
299C ILE* 3.7 19.7 - - - -
303C LEU* 4.3 3.8 - - - -
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C CYS* 3.8 24.2 - - + -
117C SER 4.3 6.1 - - - +
127C VAL* 4.1 16.8 - - + -
129C VAL* 3.7 29.2 - - + -
161C VAL* 3.1 18.1 + - + +
162C ILE 4.3 1.3 - - - +
164C MET* 1.3 80.8 - - - +
166C SER* 1.3 64.7 + - - +
167C ASN 3.1 3.9 + - - -
168C LEU* 3.2 42.1 + - + +
217C ILE* 3.9 14.4 - - + -
221C LEU* 3.5 15.9 - - + +
275C TRP* 4.0 17.7 - - + -
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Residues in contact with SER 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B THR* 6.2 0.2 - - - +
162C ILE* 2.9 26.2 + - - -
163C GLN* 3.6 11.3 + - - -
164C MET 3.6 1.4 - - - -
165C LEU* 1.3 76.8 - - - +
167C ASN* 1.3 63.1 + - - +
168C LEU 3.3 0.7 + - - -
169C SER* 4.7 2.6 + - - -
170C GLN* 4.8 2.3 + - - +
217C ILE* 6.5 0.2 - - - -
220C THR* 3.4 34.9 - - - +
221C LEU* 3.8 7.7 - - - +
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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