Contacts of the strand formed by residues 297 - 302 (chain A) in PDB entry 4E70
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 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A ASP 4.9 1.4 + - - -
197A ALA* 2.8 27.6 + - - +
199A GLU 5.2 3.6 + - - -
201A LEU* 4.5 14.3 - - + +
262A ASP 2.9 11.3 + - - +
263A ALA* 3.2 8.3 - - + +
264A VAL 3.1 23.6 + - - -
289A LEU* 3.6 12.7 - - - +
296A GLY* 1.3 76.8 - - - +
298A LEU* 1.3 62.2 + - - +
299A MET* 4.1 19.5 - - + -
365A GLU* 2.7 32.9 + - + +
366A VAL 3.5 12.8 - - - +
367A TYR* 3.9 27.4 - - + -
368A PRO* 4.3 0.4 - - - -
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Residues in contact with LEU 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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264A VAL* 3.5 22.0 - - + +
266A PHE* 3.6 32.1 - - + -
282A LEU* 3.9 26.0 - - + -
285A CYS* 4.9 4.9 - - + -
289A LEU* 3.8 5.3 - - + +
297A LYS* 1.3 73.9 - - - +
299A MET* 1.3 63.4 + - - +
300A ILE* 3.9 20.6 - - + -
344A PHE* 4.8 0.7 - - + -
349A PHE* 3.9 28.5 - - + -
364A ILE 3.6 0.2 - - - +
365A GLU* 3.4 4.9 - - - -
366A VAL* 2.8 53.4 + - + +
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Residues in contact with MET 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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190A LEU* 5.5 0.7 - - + -
197A ALA* 4.1 22.4 - - + +
198A PHE* 3.7 32.1 - - + -
201A LEU* 4.4 4.9 - - - -
204A LEU* 4.2 11.9 - - + -
263A ALA* 3.8 25.1 - - + -
264A VAL 2.7 13.7 + - - +
265A LEU* 3.2 15.2 - - + +
266A PHE* 2.8 26.2 + - - -
297A LYS* 4.1 22.9 - - + -
298A LEU* 1.3 79.4 - - - +
300A ILE* 1.3 64.1 + - - +
301A ALA 4.0 0.2 - - - -
363A LEU* 3.9 21.3 - - + -
364A ILE 3.4 3.1 - - - -
365A GLU* 4.7 2.9 - - + -
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Residues in contact with ILE 300 (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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266A PHE* 3.5 8.3 - - + +
270A LEU* 3.7 28.3 - - + -
282A LEU* 5.0 0.9 - - + -
298A LEU* 3.9 24.7 - - + -
299A MET* 1.3 77.0 - - - +
301A ALA* 1.3 59.4 + - - +
302A ASP* 3.7 22.7 + - + +
340A TRP* 3.9 18.4 - - + -
344A PHE* 3.6 35.2 - - + -
362A VAL 3.5 1.7 - - - +
363A LEU* 3.5 3.3 - - - +
364A ILE* 2.7 52.2 + - + +
366A VAL* 4.3 2.2 - - + -
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Residues in contact with ALA 301 (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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186A PHE* 3.6 33.4 - - + -
190A LEU* 5.2 3.6 - - + -
265A LEU* 4.3 11.0 - - + -
266A PHE 2.9 8.9 + - - +
267A LYS* 3.4 17.3 - - + +
268A TRP* 2.9 26.3 + - - +
299A MET 4.0 1.0 - - - -
300A ILE* 1.3 70.5 - - - +
302A ASP* 1.3 59.0 + - - +
361A ARG* 5.1 2.2 + - - -
362A VAL 3.3 7.9 - - - +
363A LEU* 4.5 7.4 - - + +
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Residues in contact with ASP 302 (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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266A PHE 5.1 0.7 - - - +
268A TRP* 3.7 10.7 + - - -
269A VAL 3.8 0.5 + - - -
270A LEU* 3.8 8.1 + - - +
271A CYS* 3.3 48.5 + - - +
300A ILE* 3.7 20.9 + - + +
301A ALA* 1.3 74.8 - - - +
303A HIS* 1.3 85.6 + - - +
304A VAL* 5.5 0.2 - - - -
334A LEU* 5.9 0.3 - - - -
340A TRP* 4.2 12.2 - - + -
361A ARG* 3.6 15.8 - - - +
362A VAL* 2.9 34.7 + - - +
364A ILE* 5.8 2.0 - - + +
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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