Contacts of the strand formed by residues 218 - 226 (chain B) in PDB entry 3HO5
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 CYS 218 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589A LEU* 4.8 0.4 - - - -
217B PHE* 1.3 79.8 - - - +
219B ILE* 1.3 61.9 + - - +
537B LEU* 4.3 1.5 - - - +
538B GLY 4.0 2.5 - - - -
540B SER* 3.9 16.2 - - - -
543B CYS* 2.1 60.1 - - - -
544B ARG 4.0 3.6 - - - -
582B ILE* 3.3 7.4 - - - +
583B VAL* 2.6 46.6 + - + +
585B PRO* 3.9 10.5 - - + -
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Residues in contact with ILE 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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218B CYS* 1.3 76.0 - - - +
220B GLN* 1.3 60.9 + - - +
518B PHE* 5.7 1.1 - - + -
537B LEU* 3.5 30.1 - - + -
543B CYS* 3.7 3.9 - - - -
544B ARG* 3.0 37.3 + - - +
546B TYR 3.1 26.3 - - - +
547B PHE* 3.5 31.6 - - + -
564B ILE* 4.2 15.7 - - + -
580B TYR* 4.4 13.0 - - + -
581B LYS 3.2 13.9 - - - +
582B ILE* 4.0 17.9 - - + -
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Residues in contact with GLN 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLN* 3.5 30.6 - - - +
221A GLU 4.9 4.8 + - - -
542A SER* 3.3 24.0 - - - +
589A LEU* 4.6 5.4 - - - +
219B ILE* 1.3 75.6 + - - +
221B GLU* 1.3 69.4 + - - +
222B VAL* 3.4 2.4 + - - +
542B SER* 2.9 32.3 + - - -
543B CYS* 3.2 28.9 + - - +
580B TYR* 3.4 4.5 - - - -
581B LYS* 2.8 40.9 + - + +
583B VAL* 4.5 10.1 - - + +
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Residues in contact with GLU 221 (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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220A GLN* 4.7 4.0 + - - -
542A SER* 4.0 8.8 + - - +
220B GLN* 1.3 78.0 + - - +
222B VAL* 1.3 62.2 + - - +
223B VAL* 4.2 10.1 + - - +
224B SER* 3.7 22.5 + - - -
578B LYS* 3.4 29.8 + - + -
579B LEU 4.2 1.3 - - - +
580B TYR* 3.5 30.0 + - + -
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Residues in contact with VAL 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A SER* 3.7 16.6 - - - -
544A ARG* 3.7 36.5 + - - +
220B GLN 3.6 13.7 - - - +
221B GLU* 1.3 74.2 - - - +
223B VAL* 1.3 66.1 + - + +
254B LEU* 3.8 24.2 - - + -
258B GLY 5.4 0.2 - - - +
563B TYR* 3.9 12.3 - - + +
579B LEU* 2.8 19.1 + - + +
580B TYR 4.3 0.2 - - - -
581B LYS* 3.7 27.6 - - + +
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Residues in contact with VAL 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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221B GLU* 3.8 5.9 - - - +
222B VAL* 1.3 87.8 - - + +
224B SER* 1.3 77.0 + - - +
226B LEU* 3.8 24.5 - - + -
244B ILE* 6.1 0.7 - - + -
254B LEU* 3.8 33.4 - - + -
258B GLY 4.5 5.8 - - - +
260B ILE* 4.0 20.6 - - + -
578B LYS* 3.3 4.5 - - - +
579B LEU* 2.8 37.3 + - + +
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Residues in contact with SER 224 (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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221B GLU* 3.7 13.9 + - - -
223B VAL* 1.3 88.4 - - - +
225B GLY* 1.3 61.2 + - - +
226B LEU* 3.0 12.1 + - - +
576B ASN* 3.4 15.1 + - - -
577B GLY 3.3 7.2 - - - -
578B LYS* 3.6 17.7 - - - -
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Residues in contact with GLY 225 (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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224B SER* 1.3 79.8 + - - +
226B LEU* 1.3 63.5 + - - +
227B ARG* 3.9 1.4 + - - +
252B LYS* 4.4 8.2 + - - -
575B HIS* 3.4 23.5 - - - +
576B ASN* 3.2 10.1 + - - -
577B GLY 3.4 0.8 + - - -
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Residues in contact with LEU 226 (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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223B VAL* 3.8 20.4 - - + -
224B SER 3.0 9.1 + - - +
225B GLY* 1.3 79.1 - - - +
227B ARG* 1.3 59.9 + - - +
229B PRO* 4.4 7.0 - - + -
244B ILE* 3.1 46.2 - - + -
246B GLU* 3.6 13.7 - - - +
252B LYS* 4.5 13.5 - - + +
260B ILE* 4.6 4.5 - - + -
571B MET 4.7 0.2 - - - +
576B ASN 3.1 10.4 + - - -
577B GLY* 2.5 46.1 + - - +
578B LYS 3.9 4.7 - - - +
579B LEU* 3.8 24.0 - - + +
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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