Contacts of the helix formed by residues 163 - 169 (chain C) in PDB entry 6M17
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 VAL 163 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C PRO* 3.3 37.2 + - + +
155C LEU 3.8 13.9 - - - +
156C ASN* 3.6 9.9 - - - +
162C TYR* 1.3 77.1 - - - +
164C ASP* 1.3 69.3 + - + +
165C GLU* 3.3 7.2 - - + +
166C CYS* 3.2 12.4 + - + +
167C ALA* 3.0 21.5 + - - +
174C TYR* 3.9 24.0 - - + +
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Residues in contact with ASP 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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156C ASN* 4.6 1.6 + - - -
162C TYR 3.7 1.7 + - - -
163C VAL* 1.3 79.1 - - + +
165C GLU* 1.3 59.1 + - - +
167C ALA* 3.7 5.4 + - - +
168C ARG* 2.8 58.7 + - - +
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Residues in contact with GLU 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 VAL* 4.5 4.9 - - + +
164C ASP* 1.3 77.0 - - - +
166C CYS* 1.3 59.7 + - - +
167C ALA 3.4 0.4 - - - -
168C ARG* 4.3 9.2 - - - +
169C SER* 2.9 26.5 + - - -
173C ASP 5.7 0.5 - - - +
174C TYR* 3.6 33.6 - - + -
178C ARG* 3.3 28.4 + - - +
563C TRP* 3.4 26.0 + - - -
565C PRO* 4.1 24.7 - - + +
570C PHE* 4.4 9.6 - - + -
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Residues in contact with CYS 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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152C ASP 5.2 0.2 - - - -
153C CYS* 2.0 60.2 - - + -
154C PRO* 4.4 0.4 - - + -
163C VAL* 3.2 18.1 + - + +
165C GLU* 1.3 79.4 - - - +
167C ALA* 1.3 58.8 + - - +
168C ARG 3.5 0.4 - - - -
169C SER* 3.0 18.3 - - - +
170C SER 4.3 1.6 - - - -
171C PRO* 3.7 12.7 - - - +
174C TYR* 3.6 37.2 - - + -
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Residues in contact with ALA 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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153C CYS* 5.3 0.4 - - - -
162C TYR* 4.8 17.5 - - + +
163C VAL 3.0 15.6 + - - +
164C ASP* 4.0 6.5 - - - +
165C GLU 3.4 0.2 - - - -
166C CYS* 1.3 78.3 - - - +
168C ARG* 1.3 65.6 + - + +
169C SER 3.8 3.1 - - - +
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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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164C ASP* 2.8 40.4 + - - +
165C GLU* 4.3 6.2 - - - +
167C ALA* 1.3 82.9 - - + +
169C SER* 1.3 59.7 + - - +
565C PRO* 3.9 23.8 + - - +
566C GLY* 5.3 3.0 - - - -
567C TYR 4.8 5.1 + - - -
568C GLU* 5.9 1.8 - - - +
570C PHE* 4.1 39.1 - - + +
571C PRO* 4.0 17.7 - - + +
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Residues in contact with SER 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 GLU 2.9 21.8 + - - -
166C CYS 3.0 16.1 - - - +
167C ALA 3.8 3.6 - - - +
168C ARG* 1.3 81.5 - - - +
170C SER* 1.3 70.2 + - - +
171C PRO* 4.3 1.4 - - - +
173C ASP* 3.6 19.7 - - - +
174C TYR 4.5 1.6 + - - -
563C TRP* 4.3 8.5 - - - -
570C PHE* 3.8 18.8 - - - -
571C PRO* 4.7 9.6 - - - -
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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