Contacts of the strand formed by residues 290 - 295 (chain A) in PDB entry 3R2W
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 290 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A GLN* 4.1 3.1 - - - +
287A TYR 3.1 29.8 + - - +
288A GLU 3.5 4.9 + - - -
289A GLY* 1.3 76.5 - - - +
291A LEU* 1.3 64.5 + - - +
292A ARG* 4.0 2.8 + - + +
365A ILE 4.4 1.6 - - - +
366A LYS* 4.5 17.5 - - + +
368A PHE 3.9 7.2 - - - +
369A GLU* 3.5 25.5 + - - +
370A ASN* 3.5 24.5 - - - +
371A SER* 3.8 18.8 - - - +
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PRO* 3.7 21.3 - - + -
74A SER* 3.3 26.9 - - - +
75A ILE* 4.8 11.7 - - + -
284A LEU* 4.9 8.7 - - + +
285A THR 3.7 5.4 - - - +
286A GLN* 3.5 33.9 - - + +
290A LYS* 1.3 74.7 - - - +
292A ARG* 1.3 61.1 + - - +
365A ILE* 3.5 17.5 - - + +
366A LYS* 3.5 20.4 + - - -
371A SER* 2.9 29.9 + - - +
372A LEU* 3.9 6.5 - - + -
373A GLY 4.7 3.4 - - - +
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Residues in contact with ARG 292 (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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283A THR 3.7 0.3 - - - +
284A LEU* 3.2 27.8 - - - +
285A THR 2.9 15.7 + - - +
287A TYR* 3.5 54.1 + - + +
290A LYS* 4.3 3.5 - - - +
291A LEU* 1.3 77.7 - - - +
293A LEU* 1.3 68.4 + - - +
294A VAL* 3.8 10.8 + - + +
340A GLU* 5.1 2.6 + - - -
365A ILE* 5.4 4.0 - - - -
366A LYS* 3.6 50.2 + - + +
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Residues in contact with LEU 293 (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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269A MET* 3.6 31.2 - - + -
281A GLY 6.0 2.0 - - - +
282A GLY* 5.1 4.3 - - - +
283A THR 4.1 10.8 - - - +
284A LEU* 4.9 1.8 - - + +
292A ARG* 1.3 77.8 - - - +
294A VAL* 1.3 70.0 + - - +
295A GLU* 5.4 6.5 - - + +
298A GLN* 4.0 11.3 + - - +
317A ASN* 4.2 21.8 - - + +
340A GLU* 4.7 8.8 - - - +
342A ILE* 6.3 1.6 - - + -
360A ALA* 4.9 9.0 - - + -
362A GLY* 3.6 20.7 + - - +
363A ALA* 4.2 24.0 - - + +
365A ILE* 5.3 3.4 - - + +
366A LYS* 5.5 3.0 - - - +
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Residues in contact with VAL 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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68A GLN* 6.1 2.2 - - + +
282A GLY* 3.1 25.3 - - - -
283A THR* 3.2 16.9 + - - +
285A THR* 3.2 25.6 - - - +
287A TYR* 5.8 6.1 - - + -
292A ARG* 4.1 15.7 - - + +
293A LEU* 1.3 82.2 - - - +
295A GLU* 1.3 69.0 + - - +
298A GLN* 4.0 5.8 - - + +
299A VAL* 4.3 15.3 - - + -
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Residues in contact with GLU 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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281A GLY 4.4 8.7 - - - +
282A GLY* 4.8 0.7 - - - -
293A LEU* 4.2 7.5 - - + -
294A VAL* 1.3 76.0 - - - +
296A ILE* 1.3 63.8 + - + +
297A ALA* 4.0 13.0 - - + +
298A GLN* 3.4 38.9 + - - +
299A VAL* 3.4 23.0 - - - +
342A ILE* 5.9 5.8 - - + -
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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