Contacts of the helix formed by residues 215 - 220 (chain A) in PDB entry 4H36
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 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLN* 2.8 26.2 + - - -
93A LYS* 3.8 3.1 - - - -
207A ASP* 3.4 12.3 - - - -
210A LEU* 3.5 23.7 - - - +
211A ALA 3.4 2.4 + - - -
213A THR* 2.9 16.3 - - - -
214A ALA* 1.3 76.0 - - - +
216A THR* 1.3 60.7 + - - -
217A SER 3.5 0.8 + - - -
218A PHE 4.1 0.2 + - - -
219A MET* 3.2 7.4 - - - +
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Residues in contact with THR 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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78A VAL* 4.1 23.8 - - + -
93A LYS* 2.8 24.2 + - - +
111A GLU* 4.7 1.0 + - - -
146A MET* 4.2 22.3 - - + +
206A LEU* 4.4 14.8 - - + +
207A ASP* 3.0 15.7 + - - -
210A LEU* 4.5 1.4 - - - +
215A GLY* 1.3 70.8 - - - -
217A SER* 1.3 66.1 + - - +
219A MET* 3.2 17.6 + - - +
220A MET* 3.4 21.4 - - - +
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Residues in contact with SER 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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191A LYS* 4.3 7.0 - - - -
193A SER* 2.8 38.9 + - - -
194A ASN* 3.8 19.0 - - - +
206A LEU* 5.1 4.2 - - - +
207A ASP* 2.8 21.9 + - - -
216A THR* 1.3 74.7 - - - +
218A PHE* 1.3 62.0 + - - +
219A MET 3.3 0.2 + - - -
220A MET* 3.3 6.3 + - - +
221A THR* 3.1 31.6 + - - +
223A TYR* 5.0 1.5 - - - -
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Residues in contact with PHE 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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72A SER 5.5 1.3 - - - -
73A GLY* 5.2 0.4 - - - -
74A ALA* 3.9 16.4 - - + -
75A GLN* 3.4 30.1 - - - +
191A LYS* 6.1 2.4 - - - +
207A ASP* 4.5 0.6 + - - -
212A ARG* 5.1 4.7 - - + -
213A THR* 3.4 39.2 - - - -
215A GLY 4.1 0.8 + - - -
216A THR 3.4 0.6 - - - -
217A SER* 1.3 79.4 - - - +
219A MET* 1.3 64.2 + - - +
220A MET 3.5 5.5 + - - +
223A TYR* 3.4 40.6 - + + +
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Residues in contact with MET 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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71A GLY* 3.4 0.5 - - - -
72A SER* 2.5 48.9 + - - +
73A GLY* 3.4 2.2 - - - +
75A GLN* 3.4 26.0 - - - +
76A GLY* 3.2 32.5 - - - +
77A ILE* 3.7 1.8 - - - +
78A VAL* 3.5 37.0 - - + +
93A LYS* 3.9 15.7 - - - -
215A GLY 3.2 24.7 - - - +
216A THR 3.2 7.2 - - - +
218A PHE* 1.3 78.3 - - - +
220A MET* 1.3 56.4 + - + +
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Residues in contact with MET 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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70A ILE* 3.5 27.1 - - + +
71A GLY* 3.5 17.0 - - - -
78A VAL* 3.8 31.0 - - + -
148A LEU* 6.2 1.1 - - + -
216A THR* 3.4 28.9 - - + +
217A SER* 3.3 3.7 + - - +
218A PHE 3.3 5.4 - - - +
219A MET* 1.3 85.2 - - + +
221A THR* 1.3 98.0 + - + +
223A TYR* 4.2 4.2 - - - +
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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