Contacts of the helix formed by residues 163 - 175 (chain C) in PDB entry 3UNF
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 GLY 163 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C THR* 4.7 1.6 - - - -
162C ARG* 1.3 88.2 - - - +
164C ALA* 1.3 60.0 + - - +
165C LYS* 3.5 2.0 - - - -
166C SER* 3.6 14.7 + - - -
167C VAL* 3.0 35.4 + - - +
197C VAL* 3.9 16.2 - - - -
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Residues in contact with ALA 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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30C THR* 5.4 0.2 - - - -
159C ALA* 3.6 31.2 - - - +
160C ILE* 3.8 12.6 - - - +
161C GLY 3.2 19.2 + - - +
162C ARG 3.2 1.8 - - - -
163C GLY* 1.3 76.4 - - - +
165C LYS* 1.3 58.3 + - - +
168C ARG* 2.7 46.7 + - - +
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Residues in contact with LYS 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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163C GLY 3.5 0.4 - - - -
164C ALA* 1.3 78.1 - - - +
166C SER* 1.3 62.1 + - - +
168C ARG* 4.1 16.1 - - - +
169C GLU* 3.3 46.5 + - + +
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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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163C GLY* 3.8 10.0 - - - -
164C ALA 3.1 0.4 - - - -
165C LYS* 1.3 79.4 - - - +
167C VAL* 1.3 62.9 + - - +
169C GLU* 3.6 10.4 + - - +
170C PHE* 3.3 19.4 + - - +
196C GLU* 4.4 6.8 - - - +
197C VAL* 3.7 23.7 - - - +
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Residues in contact with VAL 167 (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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30C THR* 4.4 11.7 - - + -
32C VAL* 4.4 9.4 - - + -
159C ALA* 3.9 17.5 - - + -
163C GLY 3.0 21.7 + - - +
166C SER* 1.3 73.2 - - - +
168C ARG* 1.3 66.1 + - - +
170C PHE* 3.0 8.5 + - - +
171C LEU* 3.0 40.0 + - + +
193C ALA* 3.4 32.3 - - + +
194C LEU* 5.4 1.3 - - + -
196C GLU* 4.6 1.3 - - - +
197C VAL* 3.6 22.2 - - + -
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Residues in contact with ARG 168 (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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145C GLN* 5.1 5.3 - - - +
155C TRP* 4.3 12.8 - - + -
158C ASN* 3.6 23.3 + - - +
159C ALA* 3.5 30.2 + - + +
160C ILE* 5.1 3.0 - - - +
164C ALA* 2.7 33.7 + - - +
165C LYS* 4.1 20.2 - - - +
167C VAL* 1.3 73.1 - - - +
169C GLU* 1.3 60.5 + - - +
171C LEU* 3.1 16.8 + - - +
172C GLU* 2.9 25.5 + - - +
47D THR 5.9 0.2 - - - -
48D SER* 4.6 16.4 - - - +
50D LEU* 3.5 14.5 - - + +
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Residues in contact with GLU 169 (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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165C LYS* 3.3 35.1 + - + +
166C SER* 3.8 9.1 - - - +
167C VAL 3.3 0.4 - - - -
168C ARG* 1.3 79.1 - - + +
170C PHE* 1.3 61.6 + - - +
172C GLU* 3.5 22.7 + - - +
173C LYS* 3.3 29.2 + - - +
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Residues in contact with PHE 170 (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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166C SER 3.3 11.0 + - - +
167C VAL* 3.0 12.9 + - - +
169C GLU* 1.3 78.3 - - - +
171C LEU* 1.3 62.2 + - + +
173C LYS* 3.2 9.4 + - + +
174C ASN* 3.0 60.3 + - + +
189C LEU* 4.2 10.8 - - + -
192C LYS* 3.7 28.5 - - + -
193C ALA* 3.6 34.3 - - + -
196C GLU* 4.2 28.0 - - + +
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Residues in contact with LEU 171 (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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32C VAL* 4.1 13.0 - - + -
34C VAL* 5.1 5.6 - - + -
157C ALA* 3.8 25.1 - - + -
158C ASN* 4.9 3.8 - - - +
159C ALA* 5.4 0.7 - - + -
167C VAL* 3.0 45.0 + - + +
168C ARG* 3.1 10.5 + - - +
170C PHE* 1.3 78.2 - - + +
172C GLU* 1.3 56.5 + - - +
174C ASN* 4.4 1.3 - - - +
175C TYR* 3.0 39.1 + - + +
189C LEU* 4.3 33.9 - - + -
190C VAL* 6.5 0.2 - - - -
193C ALA* 4.0 12.3 - - + -
50D LEU* 3.7 16.4 - - + -
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Residues in contact with GLU 172 (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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168C ARG* 2.9 23.5 + - - +
169C GLU* 3.5 29.4 - - - +
170C PHE 3.2 0.2 - - - -
171C LEU* 1.3 74.5 - - - +
173C LYS* 1.3 63.2 + - + +
175C TYR* 4.3 5.5 + - - +
47D THR 5.1 0.3 - - - +
48D SER* 2.6 29.2 + - - -
49D PRO* 3.3 24.8 - - + +
50D LEU* 3.6 16.6 - - + -
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Residues in contact with LYS 173 (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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169C GLU* 3.3 19.1 - - - +
170C PHE* 3.2 9.5 + - + +
172C GLU* 1.3 78.8 - - + +
174C ASN* 1.3 70.9 + - - +
175C TYR 3.7 0.8 + - - -
176C THR* 5.5 2.8 + - - +
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Residues in contact with ASN 174 (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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170C PHE* 3.0 53.5 + - + +
171C LEU* 3.3 2.9 + - - +
173C LYS* 1.3 94.6 + - - +
175C TYR* 1.3 56.7 + - - +
176C THR* 3.5 9.0 + - - -
179C ALA* 3.8 18.2 - - - +
189C LEU* 3.8 13.4 - - + +
192C LYS* 3.6 14.0 + - - -
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Residues in contact with TYR 175 (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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34C VAL* 3.8 11.0 - - + -
35C ARG* 2.7 24.9 + - - +
156C LYS* 3.1 63.3 + - + +
157C ALA* 3.6 21.1 - - + -
171C LEU* 3.0 18.9 + - + +
172C GLU 4.3 4.5 + - - +
173C LYS 3.7 2.4 + - - -
174C ASN* 1.3 74.3 - - - +
176C THR* 1.3 66.6 + - - +
180C ILE* 3.3 26.9 - - + +
189C LEU* 4.5 13.0 - - + -
50D LEU* 4.0 9.4 - - + -
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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