Contacts of the helix formed by residues 217 - 222 (chain C) in PDB entry 3M4D
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 SER 217 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B SER 5.6 0.2 + - - -
107B ILE* 5.6 0.2 - - - -
108B ASP* 4.4 11.4 + - - -
152C ASP* 3.6 25.9 + - - +
153C PHE* 3.7 21.3 - - - -
171C PHE* 6.0 0.2 - - - -
174C MET* 3.5 13.8 - - - +
213C PRO 4.6 1.9 - - - +
216C ALA* 1.3 75.2 - - - +
218C SER* 1.3 65.2 + - - +
219C LEU* 3.4 16.6 + - - +
220C LEU* 3.1 31.1 + - - +
221C SER* 4.2 1.6 + - - -
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Residues in contact with SER 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASN* 3.3 33.9 + - - +
106B SER 4.3 5.9 + - - -
108B ASP* 4.6 6.7 + - - -
154B LYS* 5.0 6.3 - - - +
156B ILE* 4.3 26.0 - - - -
213C PRO 5.4 0.9 - - - -
216C ALA 3.2 5.2 + - - -
217C SER* 1.3 73.3 + - - +
219C LEU* 1.3 67.9 + - - +
220C LEU 3.2 0.6 + - - -
221C SER* 3.4 6.0 + - - -
222C SER* 3.1 25.5 + - - -
223C GLY 3.2 4.8 + - - -
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Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASN* 4.2 8.1 - - + +
106B SER 3.9 17.7 - - - +
107B ILE* 3.7 26.2 - - + -
63C GLY* 3.4 1.6 - - - -
84C PHE* 3.3 28.0 - - + -
153C PHE* 3.7 34.3 - - + -
169C VAL* 4.4 1.1 - - + -
217C SER* 3.1 14.6 - - - +
218C SER* 1.3 89.8 - - - +
220C LEU* 1.3 61.7 + - - +
223C GLY* 3.3 29.0 - - - +
224C PHE* 3.9 25.4 - - + -
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Residues in contact with LEU 220 (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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63C GLY* 3.2 10.6 - - - -
65C TYR* 3.1 37.2 + - + +
80C TRP* 3.6 33.0 - - + -
81C PRO* 3.3 21.4 - - + +
153C PHE* 4.0 12.1 - - + -
171C PHE* 4.5 3.1 - - + -
174C MET* 3.7 11.9 - - - -
196C PHE* 3.7 28.9 - - + -
213C PRO* 6.4 0.9 - - + -
216C ALA* 3.7 23.3 - - + -
217C SER* 3.1 18.0 + - - +
219C LEU* 1.3 78.8 - - - +
221C SER* 1.3 58.7 + - - +
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Residues in contact with SER 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B SER* 3.8 4.5 + - - -
168B LYS* 5.6 2.9 + - - -
62C ALA* 4.6 0.3 - - - +
63C GLY 2.9 20.4 + - - -
64C GLN* 3.2 7.9 + - - +
65C TYR* 4.0 13.0 - - - +
213C PRO* 3.9 32.4 + - - +
217C SER 4.6 0.5 + - - -
218C SER* 3.4 10.5 + - - -
220C LEU* 1.3 78.7 - - - +
222C SER* 1.3 69.8 + - - +
223C GLY 3.2 0.7 - - - -
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Residues in contact with SER 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASN* 3.5 10.8 - - - -
156B ILE* 3.3 20.0 - - - +
157B LEU 3.3 22.7 + - - +
158B GLU* 4.0 4.9 - - - -
159B SER* 2.5 34.1 + - - -
168B LYS* 3.9 15.9 + - - -
60C THR* 4.4 3.3 + - - -
62C ALA* 3.8 3.6 - - - -
63C GLY 3.9 0.2 - - - -
218C SER 3.1 6.7 + - - -
221C SER* 1.3 82.3 + - - +
223C GLY* 1.3 59.4 + - - +
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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