Contacts of the strand formed by residues 219 - 223 (chain B) in PDB entry 4AQD
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 ARG 219 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B SER* 4.7 5.1 + - - -
192B VAL 3.3 2.8 + - - -
193B THR* 3.3 13.2 + - - +
194B LEU 2.8 24.5 + - - -
217B PHE* 3.4 10.3 - - - -
218B THR* 1.3 98.2 - - - +
220B ALA* 1.3 62.7 + - - +
315B THR* 3.4 9.6 - - - +
316B GLN* 2.7 54.2 + - - +
474B PHE* 2.9 37.4 + - + -
475B ALA 2.8 22.4 + - - -
476B LYS 3.4 15.6 + - - -
477B TYR 4.1 2.8 + - - -
478B GLY* 3.5 18.6 - - - +
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Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU 3.3 4.9 - - - -
204B VAL* 3.5 24.0 - - + -
208B LEU* 4.1 23.1 - - + -
217B PHE* 4.3 4.3 - - + -
219B ARG* 1.3 79.8 - - - +
221B ILE* 1.3 62.8 - - - +
222B LEU* 3.9 8.1 - - + -
315B THR* 5.0 0.2 - - - +
316B GLN 3.5 4.8 + - - -
317B ILE* 3.3 11.6 - - + +
318B LEU 3.1 22.3 + - - +
474B PHE* 3.7 2.6 - - - -
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Residues in contact with ILE 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 4.6 4.7 - - + -
193B THR* 4.0 15.0 - - + -
194B LEU 2.7 8.3 + - - +
195B PHE* 3.3 33.3 - - + -
196B GLY 3.3 8.1 + - - +
204B VAL* 4.3 3.6 - - - +
220B ALA* 1.3 79.1 - - - +
222B LEU* 1.3 65.3 + - - +
223B GLN* 3.8 13.0 - - + +
318B LEU* 3.3 18.8 - - + +
419B TYR* 5.7 0.2 - - + -
471B TRP* 3.6 54.5 - - + +
474B PHE* 3.8 26.9 - - + -
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Residues in contact with LEU 222 (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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201B ALA* 3.9 15.3 - - + +
204B VAL* 4.0 6.7 - - + -
205B SER* 3.6 30.5 - - - -
208B LEU* 4.7 2.7 - - + -
220B ALA* 3.9 27.6 - - + +
221B ILE* 1.3 77.7 - - - +
223B GLN* 1.3 61.3 + - - +
224B SER 3.7 0.3 + - - -
225B GLY 3.8 20.5 - - - +
226B SER* 4.5 1.1 - - - -
317B ILE* 4.4 8.3 - - + -
318B LEU 2.7 14.7 + - - +
319B VAL* 3.4 17.9 - - + +
320B GLY 3.1 25.5 + - - +
405B PHE* 3.8 22.4 - - + -
419B TYR* 4.5 0.6 + - - -
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Residues in contact with GLN 223 (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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112B TRP* 4.1 16.6 - - - -
195B PHE* 3.8 16.5 - - - -
196B GLY 2.9 19.0 + - - +
197B GLU* 3.0 8.8 - - + +
198B SER 3.0 19.9 + - - -
201B ALA* 3.5 1.3 - - - +
221B ILE* 3.8 10.7 - - + +
222B LEU* 1.3 71.9 - - - +
224B SER* 1.3 71.2 + - - +
225B GLY 3.4 1.0 + - - -
419B TYR* 3.2 24.0 - - + +
441B GLU* 3.1 24.5 + - - +
442B ILE* 4.4 3.8 - - - +
445B VAL* 3.8 19.2 - - - +
471B TRP* 3.0 27.6 + - + -
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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