Contacts of the strand formed by residues 346 - 350 (chain E) in PDB entry 4CDC
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 MET 346 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242E MET* 3.7 5.4 - - - -
246E ARG* 4.0 8.3 - - - +
324E VAL* 4.3 2.7 - - - -
336E MET* 3.4 14.4 - - - +
339E GLU* 3.5 19.1 - - + -
340E LEU* 3.1 52.3 - - + +
344E GLY 3.5 3.6 + - - +
345E PRO* 1.3 74.3 - - - +
347E ALA* 1.3 68.9 + - - +
348E VAL* 4.0 7.2 - - + -
384F LEU* 3.5 6.7 - - - +
385F LEU* 2.9 43.6 + - + +
430F ALA* 4.0 18.8 - - + -
431F VAL 3.5 14.4 - - - +
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Residues in contact with ALA 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E ALA* 4.3 15.3 - - + +
242E MET* 3.7 18.8 - - + -
279E PRO* 3.8 33.9 - - + -
346E MET* 1.3 74.1 - - - +
348E VAL* 1.3 64.5 + - - +
383F VAL 3.4 9.0 - - - +
384F LEU* 4.0 3.7 - - - +
429F ILE 4.1 0.8 - - - +
430F ALA* 3.3 0.2 - - - -
431F VAL* 2.9 33.8 + - + +
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Residues in contact with VAL 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E PRO* 5.8 2.0 - - - -
336E MET* 3.8 17.9 - - + -
346E MET* 4.0 10.3 - - + -
347E ALA* 1.3 81.4 - - - +
349E ALA* 1.3 62.0 + - - +
382F ALA* 3.4 5.3 - - - +
383F VAL* 2.8 56.7 + - + +
385F LEU* 4.1 18.8 - - + +
401F VAL* 4.9 1.3 - - + -
426F ILE* 4.1 24.9 - - + +
429F ILE 4.2 6.5 - - - -
430F ALA* 3.7 21.3 - - + +
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Residues in contact with ALA 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278E PHE* 6.3 2.7 - - + -
279E PRO* 6.0 3.8 - - + -
348E VAL* 1.3 76.4 - - - +
350E PHE* 1.3 64.5 + - - +
379F THR* 3.8 18.8 - - - +
381F HIS 3.2 15.0 - - - +
382F ALA* 4.5 5.4 - - + -
425F ALA 3.1 19.4 - - - +
426F ILE* 3.5 8.0 - - - -
429F ILE* 3.4 29.4 - - + +
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Residues in contact with PHE 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349E ALA* 1.3 74.6 - - - +
351E GLU* 1.3 69.3 + - - +
352E VAL* 3.7 23.5 + - + -
356E PHE* 3.8 29.8 - + - -
364E TYR* 5.3 1.3 - + - -
379F THR* 3.8 8.7 - - - -
380F ASN* 3.0 19.8 + - - +
381F HIS* 3.0 40.6 + + + +
383F VAL* 3.8 14.6 - - + -
415F PHE* 3.6 29.6 - + - -
417F ILE* 4.5 8.5 - - + -
424F CYS* 3.2 24.2 - - + +
426F ILE* 3.7 28.9 - - + +
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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