Contacts of the helix formed by residues 217 - 222 (chain A) in PDB entry 2PFV
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 LEU 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A ASP* 3.6 21.8 - - - +
161A PRO* 4.3 11.9 - - + -
162A GLN* 4.0 15.0 - - + +
165A ILE* 5.4 0.9 - - + -
213A CYS 4.4 3.6 - - - +
214A MET* 2.9 10.7 + - + +
216A PHE* 1.3 95.2 - - + +
218A GLU* 1.3 65.5 + - - +
219A PRO 3.0 3.3 - - - -
220A PHE* 3.2 10.4 + - + +
221A ALA* 3.0 24.6 + - - +
238A GLY 4.8 1.7 - - - +
241A SER* 4.3 8.3 - - - +
242A TYR* 3.7 30.5 - - + +
245A ALA* 3.5 32.1 - - + -
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Residues in contact with GLU 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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214A MET* 3.0 14.3 + - + +
215A ALA* 3.9 10.5 + - - +
217A LEU* 1.3 76.8 - - - +
219A PRO* 1.3 64.2 - - - +
221A ALA* 4.0 2.8 - - - +
222A LYS* 3.4 25.2 + - - +
242A TYR* 4.2 14.3 - - + +
286A LEU* 4.5 14.8 - - + +
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Residues in contact with PRO 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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215A ALA 4.5 7.4 - - - +
216A PHE 5.4 2.7 - - - +
217A LEU 3.0 1.2 - - - -
218A GLU* 1.3 85.4 - - - +
220A PHE* 1.3 66.3 + - + +
221A ALA 3.1 1.5 + - - -
222A LYS* 3.3 16.1 + - + +
223A GLU* 4.1 3.1 + - - -
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Residues in contact with PHE 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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216A PHE 4.5 13.5 - - - -
217A LEU* 3.2 11.0 + - + +
219A PRO* 1.3 77.7 - - + +
221A ALA* 1.3 58.2 + - - +
223A GLU* 3.6 14.3 - - - +
238A GLY* 3.2 26.5 + - - +
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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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217A LEU 3.0 14.6 + - - +
218A GLU 4.2 0.2 - - - +
219A PRO 3.1 0.4 - - - -
220A PHE* 1.3 75.3 - - - +
222A LYS* 1.3 61.5 + - - +
223A GLU* 2.9 7.1 + - - +
237A SER* 4.9 1.0 + - - -
238A GLY* 3.5 25.6 - - - +
239A MET* 4.0 5.4 - - - +
242A TYR* 4.1 5.8 - - + -
286A LEU* 3.2 29.5 - - + +
290A ASN* 3.1 26.9 + - - +
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Residues in contact with LYS 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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218A GLU* 3.4 21.8 + - - +
219A PRO* 3.3 9.7 + - + +
221A ALA* 1.3 76.8 - - - +
223A GLU* 1.3 65.0 + - - +
286A LEU* 3.6 14.4 - - + -
289A ALA* 5.9 3.9 - - + +
290A ASN* 4.4 3.1 - - - +
293A ILE* 3.7 14.4 - - - +
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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