Contacts of the helix formed by residues 215 - 222 (chain A) in PDB entry 3SN5
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 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A GLN 4.3 3.1 - - - +
212A PHE 3.2 15.3 + - - +
214A LYS* 1.3 81.9 - - + +
216A PHE* 1.3 65.0 + - - +
217A PRO* 3.4 3.8 - - - -
218A ALA* 2.9 18.3 + - - +
219A LEU* 3.1 34.2 + - + +
225A ILE* 4.7 2.5 - - + -
228A PHE* 3.8 37.0 - - + -
231A ALA* 3.6 28.3 - - + -
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Residues in contact with PHE 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LEU* 4.5 7.6 - - + -
108A ALA* 3.6 26.5 - - + -
109A PHE* 3.5 38.1 - + - -
212A PHE* 3.5 22.2 + + - +
213A ASP* 3.3 23.9 + - - +
215A VAL* 1.3 75.7 - - - +
217A PRO* 1.4 66.0 - - + +
219A LEU* 3.0 19.1 + - + +
220A VAL* 3.1 35.6 + - + +
284A TRP* 3.4 41.7 - + - -
483A ARG* 4.2 1.6 - - - +
486A LEU* 3.9 13.7 - - + -
1429A K2B 5.3 3.4 - - + -
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Residues in contact with PRO 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LYS 3.9 9.0 - - - +
215A VAL 3.5 4.3 - - - -
216A PHE* 1.4 92.9 - - + +
218A ALA* 1.4 54.1 + - - +
220A VAL* 3.5 5.4 + - + +
221A ALA* 3.1 27.1 + - - +
482A SER* 3.3 37.0 - - - +
483A ARG* 3.7 18.4 - - + +
486A LEU* 3.8 19.7 - - + -
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A VAL* 2.9 15.8 + - - +
217A PRO* 1.4 71.7 - - - +
219A LEU* 1.3 63.0 + - - +
221A ALA* 3.3 8.8 + - - +
222A GLY 3.2 5.4 + - - -
223A LEU* 3.0 37.2 + - + +
228A PHE* 3.7 30.3 - - + -
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Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LYS* 4.7 16.0 - - - +
108A ALA* 3.7 30.1 - - + +
212A PHE* 3.6 31.9 - - + -
215A VAL* 3.1 28.4 + - + +
216A PHE* 3.0 14.4 + - + +
218A ALA* 1.3 75.4 - - - +
220A VAL* 1.3 61.4 + - - +
222A GLY* 3.2 12.8 + - - -
223A LEU 3.8 15.2 - - - +
225A ILE* 3.8 38.8 - - + +
228A PHE* 4.3 6.7 - - + -
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Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PHE* 5.8 6.7 - - + -
104A LEU* 3.5 43.1 - - + -
107A LYS* 5.4 6.6 - - - +
108A ALA* 5.2 0.2 - - + -
216A PHE* 3.1 35.8 + - + +
217A PRO* 3.7 6.7 - - + +
219A LEU* 1.3 74.6 - - + +
221A ALA* 1.3 63.3 + - - +
222A GLY* 3.2 1.6 + - - -
486A LEU* 3.8 16.8 - - + -
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Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A TYR* 5.5 3.8 + - - -
72A MET* 4.2 38.3 - - + +
217A PRO 3.1 14.2 + - - +
218A ALA* 3.3 12.1 + - - +
220A VAL* 1.3 76.6 - - - +
222A GLY* 1.3 55.7 + - - +
223A LEU* 3.7 15.8 - - + +
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Residues in contact with GLY 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LYS* 5.6 8.1 - - - -
218A ALA 3.2 1.4 + - - -
219A LEU 3.2 7.5 + - - -
220A VAL 3.2 5.3 - - - -
221A ALA* 1.3 79.6 - - - +
223A LEU* 1.3 65.9 + - - +
224A PRO* 3.6 4.5 - - - +
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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