Contacts of the strand formed by residues 346 - 351 (chain E) in PDB entry 5MQF
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 GLN 346 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340E PHE* 3.7 2.1 - - - +
341E ASN* 2.8 44.5 + - + +
343E ALA* 5.9 0.4 - - - +
344E GLY 3.8 8.2 - - - +
345E THR* 1.3 77.2 - - - +
347E PHE* 1.3 59.8 + - - +
359E TRP 3.7 3.6 - - - -
360E ASP* 4.9 1.8 - - - +
361E THR* 6.1 0.2 - - - -
367E ILE* 6.2 2.5 - - + -
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Residues in contact with PHE 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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339E CYS 3.3 14.4 - - - +
340E PHE* 3.7 9.6 - - + +
341E ASN 4.2 0.7 - - - +
344E GLY 5.7 0.7 - - - +
346E GLN* 1.3 77.2 - - - +
348E LEU* 1.3 63.0 + - - +
358E LEU* 3.2 10.7 - - - +
359E TRP* 2.9 44.4 + - + +
361E THR* 5.6 6.5 - - - -
367E ILE* 5.0 0.7 - - - +
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Residues in contact with LEU 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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338E ILE* 3.8 1.7 - - - +
339E CYS* 2.9 50.5 + - + +
340E PHE* 4.2 1.1 - - - +
347E PHE* 1.3 76.8 - - - +
349E SER* 1.3 63.6 + - - +
357E LYS 3.8 0.7 - - - -
358E LEU* 4.0 8.5 - - + +
359E TRP* 5.0 0.9 - - - -
379E VAL* 5.5 3.8 - - + -
391E PHE* 5.5 11.4 - - + -
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Residues in contact with SER 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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335E VAL* 5.6 6.1 - - - -
337E ASP 4.0 5.2 - - - -
338E ILE* 4.9 0.9 - - - +
348E LEU* 1.3 76.5 - - - +
350E ALA* 1.3 61.2 + - - +
351E ALA* 5.4 2.2 - - - -
355E TYR 5.6 0.2 - - - -
356E LEU* 3.0 10.6 - - - +
357E LYS* 2.6 50.7 + - - -
359E TRP* 5.4 5.6 - - - -
379E VAL* 5.1 2.7 - - - -
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Residues in contact with ALA 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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335E VAL* 3.2 5.6 - - - -
336E ARG* 2.4 33.1 + - - -
337E ASP* 2.9 41.6 + - + +
349E SER* 1.3 72.7 - - - +
351E ALA* 1.3 53.8 + - - +
355E TYR 4.2 0.4 - - - -
356E LEU* 4.4 2.2 - - + +
376E PRO* 3.7 28.0 - - + +
378E CYS 5.0 0.2 - - - +
379E VAL* 3.8 14.3 - - + +
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Residues in contact with ALA 351 (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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331E HIS* 5.3 5.4 - - + -
332E SER 5.1 4.7 - - - +
333E LYS 4.2 21.1 - - - +
334E ALA 3.7 4.3 - - - -
335E VAL* 4.0 3.1 - - + +
336E ARG* 4.2 2.0 - - - -
349E SER* 5.6 2.7 - - - -
350E ALA* 1.3 72.4 - - - +
352E TYR* 1.3 53.3 + - - +
353E ASP* 3.0 6.5 - - + +
354E ARG* 2.7 28.4 + - - -
355E TYR* 2.9 36.9 + - + +
357E LYS* 6.1 1.6 - - + -
376E PRO* 3.7 5.2 - - - +
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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