Contacts of the strand formed by residues 212 - 217 (chain H) in PDB entry 1A46
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 ILE 212 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H LEU* 4.2 10.3 - - + -
54H THR* 3.7 9.9 - - - +
55H ALA* 3.8 13.9 - - + +
102H ASP 4.1 6.5 - - - +
103H ILE* 3.6 38.4 - - + -
196H GLY* 3.6 32.8 - - - +
197H GLY 3.2 4.0 - - - +
209H GLN* 3.6 19.1 - - - +
211H GLY* 1.3 73.4 - - - -
213H VAL* 1.3 70.6 + - - +
228H TYR* 3.1 10.3 - - - +
229H THR* 3.1 36.8 + - - +
231H VAL* 3.9 8.3 - - + -
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Residues in contact with VAL 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55H ALA* 3.8 8.5 - - - +
138H VAL* 3.6 29.8 - - + -
139H THR 5.3 0.9 - - - +
190H ALA* 3.6 25.8 - - + -
194H ASP* 3.6 21.3 - - + +
195H SER* 3.7 18.3 - - - +
196H GLY* 2.9 25.1 + - - +
197H GLY* 2.7 24.7 + - - +
198H PRO 4.6 1.1 - - - +
212H ILE* 1.3 68.7 - - - +
214H SER* 1.4 63.3 - - - +
215H TRP 5.2 0.4 - - - +
227H PHE 5.4 0.4 - - - +
228H TYR* 3.9 15.0 - - + -
372H 00K 4.9 9.2 - - + -
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Residues in contact with SER 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H HIS* 3.1 23.0 + - - -
99H LEU* 4.0 2.8 + - - +
102H ASP* 2.5 32.0 + - - +
195H SER* 4.0 1.5 + - - -
212H ILE* 3.1 7.8 + - - -
213H VAL* 1.4 78.3 - - - +
215H TRP* 1.3 81.4 + - - +
227H PHE 3.2 14.9 + - - -
228H TYR 4.4 0.9 - - - -
229H THR* 4.0 15.3 - - - -
372H 00K 3.3 10.2 + - - -
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Residues in contact with TRP 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98H ASN 3.7 12.9 + - - -
99H LEU* 3.9 15.4 + - + -
172H THR* 4.4 7.0 - - - -
174H ILE* 3.7 39.9 - - + -
176H ILE* 3.6 22.2 - - + -
180H MET* 3.9 14.4 - - - +
213H VAL* 5.2 1.2 - - - +
214H SER* 1.3 96.2 - - - +
216H GLY* 1.3 74.6 + - - +
217H GLU* 4.4 10.5 - - + -
226H GLY* 3.8 2.1 - - - -
227H PHE* 3.0 76.0 + + + +
372H 00K 3.3 53.2 - + + +
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Residues in contact with GLY 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H ASP* 5.7 0.2 - - - -
192H GLU* 5.0 0.5 - - - +
215H TRP* 1.3 86.9 - - - +
217H GLU* 1.3 60.3 + - - -
219H GLY 3.7 6.9 + - - -
225H TYR 4.2 12.1 - - - -
226H GLY* 4.9 0.7 - - - -
372H 00K 2.7 53.7 + - - +
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Residues in contact with GLU 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H SER* 5.4 0.2 + - - -
172H THR* 3.0 29.7 + - - -
173H ARG* 4.6 2.4 + - - +
174H ILE* 4.0 8.0 - - - +
215H TRP* 4.4 15.5 - - + -
216H GLY* 1.3 73.8 - - - +
219H GLY* 1.3 63.7 + - - +
221H ARG* 3.5 27.3 - - + +
224H LYS* 2.8 53.8 + - + +
225H TYR 4.8 3.6 + - - -
227H PHE* 5.5 2.4 - - - -
372H 00K 4.4 14.1 - - + -
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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