Contacts of the helix formed by residues 212 - 223 (chain A) in PDB entry 4II9
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 PRO 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A PHE* 4.0 3.4 - - + -
210A HIS* 4.4 2.2 - - + +
211A ARG* 1.3 91.9 - - + +
213A ILE* 1.3 67.6 + - - +
214A GLU* 3.1 18.4 - - + +
215A TYR* 3.1 25.1 + - + +
216A PHE* 3.6 4.0 - - - -
102B MUB 4.3 13.5 - - - +
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Residues in contact with ILE 213 (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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192A LEU* 4.4 18.8 - - + -
193A ASP* 3.8 23.3 - - - +
196A PHE* 3.5 56.1 - - + -
212A PRO* 1.3 73.3 - - - +
214A GLU* 1.4 78.8 + - - +
216A PHE* 3.0 8.0 + - + -
217A GLN* 2.9 42.6 + - + +
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Residues in contact with GLU 214 (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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212A PRO* 3.1 19.6 - - + +
213A ILE* 1.4 93.0 + - - +
215A TYR* 1.3 61.1 + - - +
217A GLN* 3.5 20.1 - - - +
218A ARG* 2.9 45.5 + - + +
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Residues in contact with TYR 215 (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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32A TRP* 3.7 3.5 - - - -
35A VAL* 3.4 22.3 - - + +
36A LYS* 2.8 28.7 + - + -
211A ARG* 3.4 47.1 - - + -
212A PRO* 3.1 20.1 + - + +
213A ILE 3.1 0.4 + - - -
214A GLU* 1.3 79.9 - - - +
216A PHE* 1.4 67.4 + + + +
218A ARG* 3.3 28.3 + - - +
219A MET* 3.0 48.6 + - + +
256A TYR* 3.6 9.2 - + - -
7B DAL 2.6 22.1 + - - -
101B UDP 4.1 4.3 - - - -
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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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192A LEU* 3.5 23.8 - - + +
195A PHE* 3.7 18.6 - + - -
196A PHE* 4.4 3.1 - + - -
199A TYR* 3.6 42.0 - + - -
211A ARG* 4.0 12.3 - - + -
212A PRO 3.6 17.7 - - - -
213A ILE* 3.0 10.4 + - - +
215A TYR* 1.4 81.0 - + - +
217A GLN* 1.3 60.2 + - - +
219A MET* 3.3 19.1 + - + +
220A GLN* 2.8 28.2 + - - +
228A MET* 4.2 3.7 - - + +
244A ILE* 3.8 15.3 - - + -
256A TYR* 3.8 37.5 - + - -
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Residues in contact with GLN 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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192A LEU* 3.6 20.3 - - + +
193A ASP* 5.9 0.4 + - - -
213A ILE* 2.9 35.3 + - + +
214A GLU* 3.5 31.9 + - - +
216A PHE* 1.3 76.6 - - - +
218A ARG* 1.3 58.9 + - + +
220A GLN* 3.3 7.0 + - - +
221A ALA* 3.0 28.5 + - - +
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Residues in contact with ARG 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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34A LYS* 3.3 24.6 + - + +
35A VAL* 2.9 34.7 + - - -
37A ASN* 3.3 36.8 + - - +
38A ASN* 5.2 2.4 + - - -
214A GLU* 2.9 49.7 + - + +
215A TYR* 3.6 27.4 - - - +
216A PHE 3.2 0.2 - - - -
217A GLN* 1.3 75.1 - - + +
219A MET* 1.3 67.5 + - - +
221A ALA* 3.2 7.7 + - - +
222A ALA* 2.9 24.8 + - - +
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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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32A TRP* 4.5 14.6 - - + -
35A VAL* 3.7 14.9 - - + +
215A TYR* 3.0 44.4 + - + +
216A PHE* 3.4 24.7 - - + +
218A ARG* 1.3 77.4 - - - +
220A GLN* 1.3 63.1 + - - +
222A ALA 3.1 0.9 + - - -
223A PHE* 3.1 46.9 + - + -
228A MET* 3.5 27.0 - - - +
244A ILE* 4.9 3.8 - - - -
246A LEU* 4.3 18.2 - - + -
255A MET* 4.9 3.4 - - - -
256A TYR* 4.4 8.7 - - + -
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Residues in contact with GLN 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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187A ASN* 2.9 48.7 + - - +
188A SER* 3.1 30.3 + - - +
189A ALA* 3.7 9.1 - - - +
192A LEU* 3.9 16.7 - - - +
216A PHE 2.8 19.5 + - - +
217A GLN* 3.3 7.0 + - - +
219A MET* 1.3 72.5 - - - +
221A ALA* 1.3 59.2 + - - +
223A PHE 3.1 18.4 - - - +
228A MET* 3.7 10.6 - - + -
230A ILE* 3.6 11.3 - - - +
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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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34A LYS* 5.4 1.4 + - - -
217A GLN 3.0 16.6 + - - +
218A ARG* 3.7 8.1 - - - +
219A MET 3.2 0.2 - - - -
220A GLN* 1.3 78.5 - - - +
222A ALA* 1.3 61.5 + - - +
223A PHE 3.7 0.9 + - - -
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Residues in contact with ALA 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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29A ASP* 5.6 0.2 - - - +
31A GLY* 3.8 26.6 - - - +
34A LYS* 4.1 28.8 + - + +
35A VAL* 4.7 0.2 - - + -
218A ARG 2.9 16.3 + - - +
219A MET* 3.1 4.7 + - - +
221A ALA* 1.3 81.1 - - - +
223A PHE* 1.3 75.8 + - + +
224A ASP 4.3 0.7 + - - -
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Residues in contact with PHE 223 (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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26A VAL* 3.6 28.0 - - + -
29A ASP* 3.6 24.0 - - - -
31A GLY* 3.8 20.2 - - - -
32A TRP* 3.9 23.3 - + - -
35A VAL* 4.2 3.6 - - + -
187A ASN* 3.3 10.6 - - - +
219A MET* 3.1 37.9 + - + +
220A GLN 3.1 16.7 - - - +
221A ALA 3.4 0.9 - - - -
222A ALA* 1.3 93.2 - - + +
224A ASP* 1.3 63.3 + - - +
227A THR* 3.9 21.5 - - + -
228A MET* 3.9 16.6 - - + -
246A LEU* 4.2 5.2 - - + -
248A TYR* 4.9 2.5 - + - -
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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