Contacts of the strand formed by residues 218 - 226 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A PHE* 1.3 80.1 - - - +
219A ILE* 1.3 63.0 + - - +
537A LEU* 4.4 1.6 - - - +
538A GLY 4.2 2.7 - - - -
540A SER* 3.8 15.9 - - - -
543A CYS* 2.0 59.0 - - - -
544A ARG 4.0 4.0 - - - -
582A ILE* 3.4 2.6 - - - +
583A VAL* 2.5 48.5 + - + +
585A PRO* 3.8 14.1 - - + -
589B LEU* 4.9 0.7 - - - -
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Residues in contact with ILE 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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218A CYS* 1.3 78.4 - - - +
220A GLN* 1.3 61.9 + - - +
518A PHE* 5.8 1.8 - - + -
537A LEU* 3.8 26.7 - - + -
542A SER 4.7 0.5 - - - +
543A CYS* 3.7 2.5 - - - -
544A ARG* 2.9 53.4 + - - +
545A GLY 3.7 4.5 - - - -
546A TYR* 3.2 41.5 - - - +
547A PHE* 4.0 12.8 - - + -
564A ILE* 4.9 12.1 - - + -
580A TYR* 4.7 11.4 - - + -
581A LYS 3.4 4.7 - - - +
582A ILE* 3.9 25.8 - - + -
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Residues in contact with GLN 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ILE* 1.3 74.6 - - - +
221A GLU* 1.3 69.3 + - - +
222A VAL* 3.3 2.1 + - - +
542A SER* 3.1 36.9 + - - -
543A CYS* 3.1 23.0 + - - +
580A TYR* 3.2 5.3 - - - -
581A LYS* 2.7 42.6 + - + +
583A VAL* 4.3 14.1 - - + +
589A LEU* 6.2 0.5 - - - +
220B GLN* 3.5 31.6 - - - +
221B GLU 4.7 4.6 + - - -
542B SER* 3.7 22.4 - - - +
589B LEU* 4.7 5.0 - - - +
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Residues in contact with GLU 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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220A GLN* 1.3 83.7 + - - +
222A VAL* 1.3 61.6 + - - +
223A VAL 4.4 6.2 - - - +
224A SER* 3.7 21.1 + - - -
578A LYS* 3.6 32.3 - - + +
579A LEU 4.2 4.3 - - - +
580A TYR* 3.5 28.8 + - + -
220B GLN* 4.9 4.5 + - - -
542B SER* 4.8 2.3 + - - +
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Residues in contact with VAL 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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220A GLN 3.9 0.7 - - - +
221A GLU* 1.3 78.2 - - - +
223A VAL* 1.3 62.0 + - + +
254A LEU* 3.8 28.7 - - + -
258A GLY 5.7 0.9 - - - +
563A TYR* 3.8 14.4 - - + -
579A LEU* 2.7 21.1 + - + +
581A LYS* 3.7 35.4 - - + +
542B SER* 3.9 15.0 - - - -
544B ARG* 3.8 26.8 + - - +
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Residues in contact with VAL 223 (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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221A GLU* 4.4 5.3 - - - +
222A VAL* 1.3 85.1 - - + +
224A SER* 1.3 76.1 + - - +
226A LEU* 3.9 19.7 - - + -
244A ILE* 6.3 0.4 - - + -
254A LEU* 3.8 39.0 - - + -
258A GLY 5.1 2.9 - - - +
260A ILE* 4.0 25.1 - - + -
578A LYS* 3.3 4.0 - - - +
579A LEU* 2.6 42.2 + - + +
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Residues in contact with SER 224 (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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221A GLU* 3.7 18.8 + - - -
223A VAL* 1.3 86.8 - - - +
225A GLY* 1.3 66.1 + - - +
226A LEU* 3.2 4.9 + - - +
576A ASN* 3.6 12.1 - - - -
577A GLY 3.4 7.2 - - - -
578A LYS* 3.8 10.5 - - - +
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Residues in contact with GLY 225 (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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224A SER* 1.3 77.8 + - - +
226A LEU* 1.3 60.3 + - - +
227A ARG* 4.2 1.2 + - - +
252A LYS* 4.5 7.6 + - - -
575A HIS* 3.2 24.5 - - - +
576A ASN* 3.2 11.4 + - - -
577A GLY 3.2 3.8 + - - -
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Residues in contact with LEU 226 (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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223A VAL* 3.9 26.5 - - + -
224A SER 4.8 0.4 - - - +
225A GLY* 1.3 79.4 - - - +
227A ARG* 1.3 63.0 + - - +
228A GLN 3.9 0.2 + - - -
229A PRO* 4.7 5.8 - - + -
244A ILE* 3.2 43.3 - - + -
246A GLU* 3.7 13.5 - - - +
252A LYS* 4.1 17.3 - - + +
260A ILE* 4.8 5.2 - - + -
575A HIS* 3.2 12.2 - - - -
577A GLY* 2.7 43.8 + - - +
578A LYS 3.9 4.0 - - - +
579A LEU* 3.9 23.1 - - + +
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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