Contacts of the strand formed by residues 293 - 299 (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 VAL 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LEU* 4.8 0.4 - - - +
288A TYR* 3.8 1.2 - - - +
289A GLY* 3.3 2.5 - - - -
290A ALA 3.0 32.1 + - - +
291A GLY 3.8 9.2 - - - +
292A GLY* 1.3 84.5 - - - +
294A ILE* 1.3 69.8 - - - +
295A LYS* 4.1 17.4 + - + +
311A THR* 3.6 31.2 - - + -
312A ILE 3.8 6.7 - - - +
313A ASP* 5.6 5.8 - - + +
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Residues in contact with ILE 294 (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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93A LEU* 3.5 30.1 - - + -
238A VAL* 3.9 20.2 - - + +
240A HIS* 5.3 0.7 - - + -
245A PRO* 3.7 35.2 - - + -
287A CYS* 4.2 9.0 - - + -
288A TYR 3.4 9.9 - - - +
289A GLY* 4.4 0.2 - - - -
293A VAL* 1.3 74.6 - - - +
295A LYS* 1.4 67.7 + - - +
296A CYS* 4.2 17.0 - - - -
310A ILE 3.8 0.9 - - - +
311A THR* 3.6 2.1 - - - -
312A ILE* 2.8 48.5 + - + +
314A PRO* 4.1 12.3 - - + -
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Residues in contact with LYS 295 (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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286A SER 3.8 1.4 - - - +
287A CYS* 3.2 2.6 - - - -
288A TYR* 3.0 64.0 + - + +
293A VAL* 4.1 19.7 + - + +
294A ILE* 1.4 74.9 - - - +
296A CYS* 1.3 62.7 + - - +
297A ILE* 4.1 8.5 - - + -
309A VAL* 4.8 3.6 - - + -
310A ILE 3.5 4.9 - - - +
311A THR* 4.6 10.8 - - - +
362A LEU* 2.9 25.2 + - + +
363A ASP* 4.9 1.8 - - - +
390A GLU* 2.8 38.3 + - - +
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Residues in contact with CYS 296 (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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233A GLN* 5.0 0.2 - - - -
247A VAL* 4.1 8.1 - - - -
285A CYS* 3.9 12.3 - - + -
286A SER 3.5 3.4 - - - -
287A CYS* 2.1 44.2 - - - -
294A ILE* 4.2 4.5 - - - -
295A LYS* 1.3 77.3 - - - +
297A ILE* 1.3 63.5 + - - +
298A CYS* 3.6 7.4 - - - -
309A VAL* 3.3 5.0 - - - -
310A ILE* 2.8 46.1 + - + +
312A ILE* 4.0 24.7 - - - -
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Residues in contact with ILE 297 (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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286A SER 2.8 32.7 + - - +
288A TYR* 4.5 2.0 - - + -
295A LYS* 4.2 12.3 - - + +
296A CYS* 1.3 83.1 - - - +
298A CYS* 1.3 61.2 + - - +
307A ARG* 3.6 34.3 - - + -
308A PRO 3.6 2.9 - - - +
309A VAL* 4.1 16.6 - - + -
324A LEU* 5.2 2.7 - - + -
358A GLY 3.6 7.4 - - - +
359A PHE* 3.7 18.6 - - - +
360A ALA* 3.5 39.0 - - + +
362A LEU* 3.8 20.2 - - + -
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Residues in contact with CYS 298 (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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282A ILE* 4.2 17.3 - - + -
283A GLU 3.3 8.5 - - - +
284A GLU 4.4 2.2 - - - -
285A CYS* 2.1 50.0 - - - +
296A CYS 3.6 13.5 - - - -
297A ILE* 1.3 77.3 - - - +
299A ARG* 1.3 62.3 + - - +
307A ARG* 2.9 35.1 + - - +
308A PRO* 2.9 17.6 + - + +
310A ILE* 3.9 13.7 - - - -
358A GLY 5.4 1.3 - - - -
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Residues in contact with ARG 299 (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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282A ILE 3.5 1.6 - - - -
283A GLU* 2.7 52.8 + - + +
284A GLU* 2.8 35.7 + - - +
298A CYS* 1.3 78.8 - - - +
300A ASP* 1.3 65.5 + - - +
301A ASN* 2.9 29.2 + - - +
307A ARG* 3.7 4.0 - - - +
308A PRO* 4.2 2.7 - - - -
331A ASP* 4.2 6.1 - - - +
354A PRO* 4.7 4.2 - - - +
355A GLY* 3.3 20.6 + - - +
356A VAL* 3.6 28.5 - - - +
357A LYS* 4.5 4.7 - - - -
378A ARG* 4.1 0.2 - - - +
412A TYR* 3.0 24.0 + - - -
1477A SIA 3.2 40.5 + - - -
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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