Contacts of the strand formed by residues 288 - 293 (chain A) in PDB entry 2G4C
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 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A SER* 3.2 6.6 - - - -
276A SER* 3.0 32.6 + - - +
277A ASP 5.6 0.2 - - - +
278A CYS* 3.5 26.0 - - + +
287A ASN* 1.3 82.4 - - - +
289A LEU* 1.3 65.2 + - - +
290A TYR* 2.9 38.9 - - + +
299A LEU* 3.8 24.0 - - + -
301A GLU 3.5 5.8 - - - -
302A THR* 4.5 9.6 - - + -
304A TRP* 3.8 18.4 - - - +
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Residues in contact with LEU 289 (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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256A LEU* 3.6 11.0 - - + -
259A ARG* 4.8 2.9 - - + -
260A LEU* 3.3 45.3 - - + +
263A TRP* 4.6 7.4 - - + +
273A PHE* 6.3 0.2 - - + -
274A SER 3.4 7.2 - - - +
275A SER* 3.9 9.2 - - - -
288A LYS* 1.3 73.0 - - - +
290A TYR* 1.3 61.3 + - - +
299A LEU* 3.0 6.6 - - - +
300A ILE* 3.0 36.4 + - + -
301A GLU* 2.6 39.3 + - + +
303A LEU* 3.2 35.0 - - + -
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Residues in contact with TYR 290 (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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272A ASN 4.2 0.4 - - - -
273A PHE* 3.2 9.7 - - - -
274A SER* 2.7 49.9 + - - +
275A SER 4.9 0.4 - - - -
276A SER* 3.2 29.2 + - - -
288A LYS* 2.9 42.6 - - + +
289A LEU* 1.3 77.3 - - - +
291A TYR* 1.3 60.4 + - - +
297A LYS* 4.2 27.8 - - + -
298A GLU* 3.5 6.3 - - - +
299A LEU* 3.8 29.9 - - + +
300A ILE* 4.4 2.9 - - - -
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Residues in contact with TYR 291 (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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272A ASN* 3.1 35.9 + - + -
273A PHE* 3.5 37.2 - + + -
290A TYR* 1.3 75.6 - - - +
292A ASN* 1.3 75.8 + - - +
293A PHE* 3.1 34.9 + + + -
294A PRO* 5.2 1.4 - - - +
297A LYS* 4.2 1.6 - - - -
298A GLU 2.9 28.2 + - - +
300A ILE* 4.1 16.6 - - + +
348A ALA* 3.3 38.6 - - + -
351A TYR* 4.2 6.1 - - + +
352A ASP* 3.6 29.1 + - + +
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Residues in contact with ASN 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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272A ASN* 2.8 44.9 + - + +
291A TYR* 1.3 86.2 + - - +
293A PHE* 1.3 74.9 + - - +
294A PRO* 3.6 3.5 - - - +
296A GLY* 4.0 8.7 + - - -
297A LYS* 3.8 35.6 - - + +
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Residues in contact with PHE 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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92A LEU* 4.3 7.0 - - + -
291A TYR* 3.1 41.0 + + + -
292A ASN* 1.3 79.3 - - - +
294A PRO* 1.3 57.8 - - - +
295A TRP* 2.3 62.2 + + + -
296A GLY 2.5 21.0 + - - +
298A GLU* 3.3 38.8 - - + -
300A ILE* 5.2 0.2 - - + -
344A ARG* 4.1 24.5 - - + -
347A LEU* 4.1 8.3 - - + -
348A ALA* 4.0 17.0 - - + -
351A TYR* 3.7 28.5 - + - -
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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