Contacts of the strand formed by residues 268 - 274 (chain A) in PDB entry 1W21
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 LYS 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ILE* 3.9 18.4 - - + -
220A THR* 3.9 3.8 - - - +
264A PHE* 3.4 3.8 - - - -
265A LYS 2.9 31.7 + - - +
266A GLU* 4.0 10.1 - - + +
267A GLY* 1.3 80.0 - - - +
269A ILE* 1.3 67.0 + - - +
270A GLN* 3.1 13.1 + - - +
2422C ASN* 5.2 10.4 + - - -
2424C GLU* 5.3 6.3 + - - -
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Residues in contact with ILE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A THR* 3.9 23.8 + - + +
222A ILE* 4.1 21.3 - - + -
262A ILE* 4.1 4.7 - - + -
263A TYR 3.8 3.8 - - - -
264A PHE* 3.8 20.9 - - + -
267A GLY 4.1 0.2 + - - -
268A LYS* 1.3 73.3 - - - +
270A GLN* 1.3 63.2 + - - +
271A LYS* 3.6 16.2 - - - +
272A ILE* 3.7 35.4 - - + -
2459C LYS* 4.9 8.1 - - - +
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Residues in contact with GLN 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A VAL* 5.1 4.5 - - + -
263A TYR 2.8 16.4 + - - +
264A PHE 4.2 1.6 - - - -
265A LYS* 3.7 39.0 - - + +
268A LYS* 3.1 27.9 - - - +
269A ILE* 1.3 74.8 - - - +
271A LYS* 1.3 63.0 + - - +
317A MET* 4.0 26.5 - - + +
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Residues in contact with LYS 271 (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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262A ILE* 3.5 2.6 - - - +
263A TYR* 2.9 38.7 + - + -
269A ILE* 3.5 3.5 - - - +
270A GLN* 1.3 82.2 - - - +
272A ILE* 1.3 79.1 + - - +
273A GLU* 3.8 19.3 + - - -
316A MET 3.6 9.1 + - - -
317A MET* 2.5 52.8 + - + +
318A THR* 3.8 9.1 - - - +
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Residues in contact with ILE 272 (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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222A ILE* 5.9 4.3 - - + -
225A TRP* 6.3 0.4 - - + -
260A LYS* 3.7 30.1 - - + -
261A ILE 3.5 3.4 - - - +
262A ILE* 4.1 24.5 - - + -
269A ILE* 3.7 28.0 - - + -
271A LYS* 1.3 86.7 - - - +
273A GLU* 1.3 70.5 + - - +
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Residues in contact with GLU 273 (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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260A LYS* 3.2 7.5 - - - -
261A ILE* 2.8 41.0 + - + +
263A TYR* 2.7 31.0 + - + -
271A LYS* 3.8 21.3 + - - -
272A ILE* 1.3 81.2 - - - +
274A GLU* 1.3 67.5 + - - +
317A MET 3.5 17.0 - - - +
318A THR* 3.5 12.8 - - - +
319A HIS* 2.9 26.2 + - + -
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Residues in contact with GLU 274 (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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259A THR 3.8 5.4 - - - +
260A LYS* 3.9 24.4 + - - +
273A GLU* 1.3 77.9 - - - +
275A LEU* 1.3 69.9 + - - +
276A ALA* 3.5 3.1 + - - +
319A HIS* 3.2 13.1 - - - -
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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