Contacts of the strand formed by residues 219 - 223 (chain A) in PDB entry 2XOA
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 VAL 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A GLY 4.4 2.5 - - - +
218A HIS* 1.3 73.4 - - - +
220A LEU* 1.3 64.7 + - - +
259A LEU* 4.1 22.0 - - + -
260A TRP 3.2 9.4 - - - +
261A ARG* 4.1 24.9 - - + +
285A VAL* 4.2 14.4 - - + -
392A ARG* 3.9 7.8 + - - +
393A CYS* 3.0 35.9 + - + +
398A SER* 3.4 29.4 - - - +
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Residues in contact with LEU 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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214A VAL* 4.3 0.9 - - + -
218A HIS* 4.4 2.7 - - + +
219A VAL* 1.3 78.2 - - - +
221A ARG* 1.3 69.2 + - - +
222A LEU* 3.9 26.2 - - + -
259A LEU* 3.8 6.1 - - - -
260A TRP* 2.8 41.2 + - + +
262A LEU* 3.6 38.1 - - + -
341A TYR* 4.1 18.6 - - + +
390A LEU* 4.1 21.5 - - + -
391A THR 3.2 19.1 - - - +
392A ARG* 4.1 3.4 - - - -
393A CYS* 3.9 3.8 - - - +
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Residues in contact with ARG 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 LEU* 1.3 79.4 - - - +
222A LEU* 1.3 63.3 + - - +
223A PHE* 3.7 29.5 + - + -
230A CYS* 4.6 4.7 - - + -
253A CYS* 3.1 25.1 + - - +
254A THR* 3.4 8.5 - - - +
255A HIS 2.8 23.6 + - - -
258A SER* 2.8 37.3 + - - +
259A LEU* 3.6 15.7 - - + +
389A PHE 3.8 0.3 - - - +
390A LEU* 3.5 5.0 - - - -
391A THR* 2.8 34.2 + - - +
393A CYS* 4.7 6.0 - - + +
397A GLU* 2.5 42.8 + - - -
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Residues in contact with LEU 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 LEU* 3.9 14.1 - - + -
221A ARG* 1.3 74.4 - - - +
223A PHE* 1.3 61.3 + - - +
224A HIS 4.2 0.2 + - - -
230A CYS* 3.1 3.8 - - - +
231A LEU* 2.9 51.6 + - + +
247A TYR* 5.8 0.3 - - - -
258A SER 5.0 0.4 + - - -
260A TRP* 3.6 33.1 - - + -
262A LEU* 5.7 0.7 - - + -
282A ILE* 5.2 11.4 - - + -
316A PHE* 4.1 20.4 - - + -
348A VAL* 4.4 3.8 - - + -
357A LEU* 5.5 0.2 - - + -
388A LEU* 3.9 30.6 - - + +
389A PHE 3.6 5.8 - - - +
390A LEU* 3.8 22.0 - - + -
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Residues in contact with PHE 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 ARG* 3.7 37.2 - - + -
222A LEU* 1.3 74.4 - - - +
224A HIS* 1.3 59.8 + - - +
225A GLY 3.9 4.2 + - - +
229A GLU 3.2 22.4 - - - -
230A CYS* 3.8 5.4 - - + -
253A CYS* 3.8 31.0 - - + -
388A LEU* 3.2 8.4 - - - -
389A PHE* 2.9 64.6 + + + +
391A THR* 3.6 32.5 - - + -
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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