Contacts of the strand formed by residues 290 - 295 (chain A) in PDB entry 4A4C
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 SER 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A LEU* 4.0 7.1 - - - +
284A PHE* 3.8 17.5 - - - +
287A LYS* 2.9 31.3 + - - +
288A PRO 3.4 2.0 + - - -
289A GLY* 1.3 75.5 - - - +
291A TYR* 1.3 58.1 + - - +
307A TYR* 3.5 2.8 - - - -
308A VAL* 3.1 31.2 + - - +
339A PHE* 3.2 15.2 - - - +
342A GLY* 3.6 21.8 - - - -
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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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265A HIS* 3.5 16.8 + + - -
267A GLY* 4.5 0.9 - - - -
281A LEU* 4.6 3.1 - - - -
289A GLY 3.7 1.3 - - - +
290A SER* 1.3 74.1 - - - +
292A ILE* 1.3 61.4 + - - +
293A PHE* 4.1 20.9 - + - -
305A ILE* 4.5 5.4 - - + -
306A GLY 3.2 15.0 - - - +
307A TYR* 4.1 9.9 - - + -
328A LEU* 3.7 31.1 - - + +
337A TYR* 3.6 40.8 + + + -
338A LEU 3.6 9.0 - - - -
339A PHE 3.2 3.8 + - - -
340A PRO* 3.4 24.5 - - + +
341A ASP 2.8 28.3 + - - +
346A ASN* 2.4 30.4 + - - -
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Residues in contact with ILE 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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267A GLY 3.3 15.0 - - - +
269A MET* 3.7 19.3 - - + -
272A LEU* 4.7 0.2 - - + -
277A VAL* 4.1 31.1 - - + +
280A ARG* 4.0 27.6 - - + -
281A LEU* 4.0 26.0 - - + -
291A TYR* 1.3 82.2 - - - +
293A PHE* 1.3 64.4 + - - +
305A ILE* 3.6 2.4 - - - +
306A GLY 2.9 27.8 + - - +
341A ASP* 3.6 30.5 - - + +
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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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261A LEU 3.3 27.1 - - - -
265A HIS* 3.5 37.5 - + - -
267A GLY* 2.9 15.5 + - - -
268A TYR* 3.6 15.2 - + + -
269A MET* 3.0 26.0 + - - -
291A TYR* 4.1 14.4 - + - -
292A ILE* 1.3 78.3 - - - +
294A ARG* 1.3 63.4 + - - +
303A TRP* 3.8 15.0 - + + -
304A ALA 3.5 10.1 - - - +
305A ILE* 4.1 16.8 - - + -
324A LEU* 3.6 26.2 - - + -
328A LEU* 3.8 21.8 - - + -
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Residues in contact with ARG 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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268A TYR* 4.7 0.7 - - - -
269A MET* 3.5 21.5 - - + +
272A LEU* 3.2 27.6 + - + +
273A THR* 3.8 2.3 + - - +
274A TYR* 3.3 25.9 - - - +
277A VAL* 3.5 23.8 - - + +
293A PHE* 1.3 75.3 - - - +
295A LEU* 1.3 81.5 + - - +
296A SER* 4.0 2.0 - - - +
297A CYS* 4.3 0.8 - - - +
303A TRP* 3.2 17.9 - - - -
304A ALA* 2.9 34.5 + - - +
316A GLN* 2.4 30.7 + - - -
7B PTR 2.6 47.7 + - - -
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Residues in contact with LEU 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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156A LEU* 6.1 0.5 - - - +
160A HIS* 4.9 7.2 - - + +
227A THR* 5.5 3.1 - - + +
230A LEU* 3.8 38.4 - - + -
247A LEU* 3.6 36.1 - - + -
248A PHE* 5.6 2.2 - - + -
268A TYR* 4.1 17.9 - - - +
269A MET 4.7 1.4 + - - +
271A PHE 6.2 0.4 - - - +
272A LEU 4.4 3.1 - - - +
294A ARG* 1.3 95.7 + - - +
296A SER* 1.3 66.6 + - - +
297A CYS* 3.6 1.4 + - - +
300A LEU* 4.2 10.1 - - + -
301A GLY 5.5 0.4 - - - +
302A GLN 3.8 3.8 - - - +
303A TRP* 4.0 18.2 - - + -
304A ALA 4.5 0.2 - - - -
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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