Contacts of the strand formed by residues 219 - 227 (chain v) in PDB entry 6FF7
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 HIS 219 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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681u PRO* 3.7 34.1 - - + +
158v LEU* 5.3 9.0 - - - -
212v GLU 3.9 1.4 - - - +
213v LEU* 3.8 4.9 - - - +
214v ASP* 3.4 25.5 + - + +
217v LEU* 3.5 5.5 - - + +
218v ASN* 1.3 80.2 - - - +
220v VAL* 1.3 65.2 + - - +
221v VAL* 5.7 1.1 - - + -
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Residues in contact with VAL 220 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141v VAL* 5.7 5.2 - - + -
158v LEU* 5.1 9.1 - - + +
159v GLU 3.6 26.1 + - - +
160v ALA* 4.5 14.3 - - + -
211v TYR* 5.4 9.6 - - + -
212v GLU 3.9 7.4 - - - +
213v LEU* 5.0 4.5 - - + +
219v HIS* 1.3 77.7 - - - +
221v VAL* 1.3 61.4 + - - +
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Residues in contact with VAL 221 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211v TYR* 3.7 6.5 - - - -
212v GLU* 3.5 28.8 + - + +
219v HIS* 4.2 2.0 + - + -
220v VAL* 1.3 74.4 - - - +
222v ARG* 1.3 62.5 + - - +
223v LYS* 3.2 8.7 + - + +
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Residues in contact with ARG 222 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209v THR* 6.3 2.9 - - - -
210v PHE 4.0 5.4 - - - +
211v TYR* 5.2 1.6 - - - +
221v VAL* 1.3 71.5 - - - +
223v LYS* 1.3 64.1 + - - +
224v TYR 3.8 4.0 - - - +
225v SER* 6.2 2.7 - - - -
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Residues in contact with LYS 223 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210v PHE* 3.1 18.6 + - + +
212v GLU* 4.3 22.2 - - + -
221v VAL* 3.2 3.8 + - + +
222v ARG* 1.3 75.8 - - - +
224v TYR* 1.3 62.3 + - + +
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Residues in contact with TYR 224 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208v LEU 4.4 1.6 - - - +
209v THR* 3.3 3.1 - - - -
210v PHE* 2.9 41.3 + - + +
222v ARG* 5.1 3.0 - - - +
223v LYS* 1.3 80.3 + - + +
225v SER* 1.3 63.4 + - - +
226v GLU* 5.3 3.1 - - + +
261v PHE* 5.3 13.7 - - + -
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Residues in contact with SER 225 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207v THR* 5.1 9.4 - - - -
208v LEU 3.3 7.2 - - - -
209v THR* 4.6 9.2 - - - -
222v ARG* 6.2 3.8 - - - -
224v TYR* 1.3 77.4 - - - +
226v GLU* 1.3 60.0 + - - +
227v PRO 4.3 0.5 - - - -
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Residues in contact with GLU 226 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207v THR* 4.2 2.2 - - - -
208v LEU* 2.9 37.9 + - + +
224v TYR* 6.0 3.1 - - + -
225v SER* 1.3 74.7 - - - +
227v PRO* 1.3 66.3 - - - +
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Residues in contact with PRO 227 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205v GLN* 5.8 2.9 - - + +
206v GLN 3.4 9.6 - - - +
207v THR* 4.1 5.1 - - - -
225v SER 4.3 0.4 - - - -
226v GLU* 1.3 80.7 - - - +
228v LEU* 1.3 62.6 + - - +
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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