Contacts of the strand formed by residues 352 - 356 (chain E) in PDB entry 6M04
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 PHE 352 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54E CYS* 3.9 25.4 - - + -
55E LEU 3.2 20.0 - - - +
56E PRO* 3.5 16.2 - - + -
57E VAL* 4.0 2.2 - - - -
149E ILE* 3.5 37.7 - - + -
153E CYS* 5.2 1.3 - - + -
338E VAL* 3.4 5.1 - - - +
339E CYS* 2.8 31.9 + - + -
341E PRO* 3.5 37.2 - - + -
349E TYR* 4.1 26.0 - - + -
350E GLU 4.1 1.1 - - - -
351E VAL* 1.3 85.8 - - - +
353E GLU* 1.3 75.7 + - - +
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Residues in contact with GLU 353 (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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148D PHE* 5.1 5.3 - - + -
345D HIS* 4.8 2.8 + - - -
346D LEU* 3.3 43.6 - - + +
53E VAL 4.1 0.3 - - - +
54E CYS* 3.1 7.1 - - - -
55E LEU* 2.9 33.0 + - - +
57E VAL* 3.6 17.4 - - - +
336E GLU* 5.6 11.0 - - + +
337E HIS 3.3 15.7 - - - +
338E VAL* 3.9 16.9 - - + +
339E CYS 4.4 0.7 - - - +
352E PHE* 1.3 93.5 - - - +
354E CYS* 1.3 63.0 + - - +
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Residues in contact with CYS 354 (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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148D PHE* 4.8 3.4 - - - -
52E VAL* 3.9 18.8 - - + -
53E VAL 3.0 7.4 - - - +
54E CYS* 2.0 54.1 - - - -
150E ASN* 4.1 1.6 - - - -
153E CYS* 3.5 22.7 - - - -
158E LEU* 6.4 1.1 - - + -
336E GLU* 3.6 4.6 - - - +
337E HIS* 2.9 36.1 + - + +
353E GLU* 1.3 76.5 - - - +
355E THR* 1.3 67.6 + - - +
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Residues in contact with THR 355 (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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148D PHE* 3.7 24.6 - - + -
151D GLN* 3.7 20.0 - - + -
152D MET* 4.7 8.1 - - + +
52E VAL* 3.3 7.5 - - - +
53E VAL* 2.9 47.2 + - + +
335E PHE* 3.0 43.4 + - + -
336E GLU* 4.8 2.9 - - - -
337E HIS* 5.4 0.4 - - - -
354E CYS* 1.3 76.9 - - - +
356E HIS* 1.3 66.6 + - - +
357E ASN 4.3 0.3 + - - -
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Residues in contact with HIS 356 (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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151D GLN* 4.9 1.3 - - - -
50E ASP* 4.4 9.2 - - - -
52E VAL* 3.3 25.0 - - + +
154E TYR* 4.7 8.1 - + - -
158E LEU* 3.6 33.4 - - + +
162E SER* 4.9 9.4 + - - -
163E LYS* 5.4 6.1 - - + +
333E ILE* 6.3 1.1 - - + -
334E SER 5.1 3.1 - - - +
335E PHE* 3.3 30.9 + - - +
337E HIS* 4.4 16.2 - + + +
355E THR* 1.3 80.8 + - - +
357E ASN* 1.3 62.7 + - - +
358E MET* 3.2 43.5 + - + +
359E ALA* 3.7 14.8 + - + +
362E LEU* 5.7 1.4 - - - +
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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