Contacts of the helix formed by residues 215 - 219 (chain B) in PDB entry 1X9H
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 215 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A MET* 3.8 2.0 - - + -
72A LYS 3.8 15.9 - - - +
73A ASP* 3.3 29.4 - - - +
74A TYR* 4.1 5.2 - - + -
94A GLU* 3.4 33.0 - - + +
188B GLU* 4.9 0.7 - - + +
214B LEU* 1.3 85.1 - - + +
216B GLU* 1.3 65.2 + - - +
217B ALA 3.2 2.9 - - - -
218B HIS* 3.0 16.9 + - - +
219B HIS* 3.3 10.9 - - - -
241B HIS* 4.4 7.2 - - + +
244B ARG* 3.8 23.8 - - + +
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Residues in contact with GLU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A MET* 3.5 19.0 - - + +
46A GLY* 2.8 30.5 + - - +
72A LYS* 3.6 44.0 + - + +
195A TYR* 6.5 0.9 - - + -
199A ASN* 3.9 7.7 + - - +
601A GOL 6.1 0.9 - - - -
188B GLU* 6.1 0.9 - - - +
191B ARG* 6.3 0.9 - - - +
212B GLU* 6.0 0.9 - - - +
213B ILE* 3.4 10.9 + - + +
214B LEU 3.4 0.2 - - - -
215B PRO* 1.3 76.7 - - - +
217B ALA* 1.3 58.7 + - - +
219B HIS* 2.9 22.2 + - - +
220B ASN* 2.9 26.0 + - - +
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B ILE* 5.0 0.2 - - + -
212B GLU* 3.6 28.9 - - + +
213B ILE 2.9 17.7 + - - +
214B LEU* 3.9 11.0 - - + -
215B PRO 3.2 0.8 + - - -
216B GLU* 1.3 75.7 - - - +
218B HIS* 1.3 60.4 + - - +
219B HIS 3.1 1.6 - - - -
220B ASN* 3.7 10.1 - - - -
221B TRP* 3.3 23.6 + - + -
222B ILE 3.1 27.0 + - - -
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Residues in contact with HIS 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ILE* 3.5 24.3 - - - +
297A LEU* 3.4 37.9 - - + +
298A LYS* 5.9 0.5 - - - +
301A LEU* 4.0 2.4 - - + +
214B LEU* 3.4 19.1 - - + +
215B PRO 3.0 10.7 + - - +
216B GLU 3.0 0.4 + - - -
217B ALA* 1.3 78.6 - - - +
219B HIS* 1.3 62.4 + - + +
220B ASN 3.5 0.7 - - - -
221B TRP* 4.9 1.3 - + - -
222B ILE* 3.6 18.3 - - + +
244B ARG* 3.0 65.2 + - - +
247B ALA* 4.6 0.2 - - + -
248B THR* 2.7 25.9 + - - -
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Residues in contact with HIS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A MET* 3.6 26.7 - - + +
46A GLY* 3.7 11.4 - - - -
92A THR* 3.9 10.1 - - + -
94A GLU* 2.8 25.9 + - - -
203A GLU* 3.5 3.1 - - - -
294A ILE* 3.5 15.6 - - - +
298A LYS* 3.8 15.8 - - + -
603A GOL 5.2 0.9 - - - -
701A F6R 2.6 64.0 + - - +
215B PRO 3.3 19.2 + - - -
216B GLU 2.9 11.1 + - - +
218B HIS* 1.3 83.5 - - + +
220B ASN* 1.3 63.5 + - - +
244B ARG* 4.5 6.7 + - - -
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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