Contacts of the strand formed by residues 331 - 336 (chain E) in PDB entry 4LQL
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 GLU 331 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306E GLU* 2.5 23.1 - - - +
329E LEU* 4.4 1.0 - - - +
330E MET* 1.3 68.2 - - - +
332E ASP* 1.3 74.8 + - - +
333E TYR* 3.3 16.2 + - + -
346E GLY* 4.4 1.3 - - - -
347E SER 2.7 27.1 + - - +
348E HIS* 2.2 52.2 + - + +
446E HIS* 3.2 41.0 + - + +
447E HIS* 2.7 15.9 + - + +
83F PHE* 3.8 6.4 - - - -
128F HIS* 3.7 10.2 + - - +
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Residues in contact with ASP 332 (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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330E MET* 3.2 5.2 + - - +
331E GLU* 1.3 73.5 - - - +
333E TYR* 1.3 59.6 + - - +
334E THR 3.8 0.2 - - - -
344E ILE* 3.9 17.4 - - + +
346E GLY* 3.6 10.3 - - - +
426E TRP* 3.5 27.2 + - + -
446E HIS* 2.7 38.6 - - - +
448E THR* 4.1 7.3 - - - +
127F ALA* 3.7 26.9 - - + +
128F HIS* 3.2 23.7 + - - +
131F ARG* 4.9 12.0 + - - -
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Residues in contact with TYR 333 (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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306E GLU* 5.0 0.7 + - - -
331E GLU* 3.7 23.7 + - + -
332E ASP* 1.3 77.5 - - - +
334E THR* 1.3 69.7 + - + +
345E MET 2.9 8.4 + - - +
346E GLY* 3.2 2.9 - - - -
347E SER* 3.6 28.7 - - - +
348E HIS* 3.6 27.8 + - - -
349E MET* 4.1 22.9 + - - +
419E LEU* 6.4 0.7 - - + -
83F PHE* 6.2 0.2 - + - -
118F MET* 5.7 3.6 - - + -
121F MET* 3.5 55.4 - - + +
124F HIS 5.2 0.2 - - - +
125F GLN* 4.6 8.7 - - - +
127F ALA* 4.4 2.7 - - - -
128F HIS* 3.2 34.3 - + - -
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Residues in contact with THR 334 (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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333E TYR* 1.3 83.2 - - + +
335E LEU* 1.3 68.7 + - - +
336E ASP* 4.3 0.5 + - - +
344E ILE 3.8 0.2 - - - -
345E MET* 3.0 43.5 + - + +
106F GLN* 3.2 31.5 + - - +
111F ILE* 4.0 25.8 - - + +
116F ILE* 4.5 16.6 - - + -
121F MET* 5.4 0.7 - - + -
124F HIS 5.3 1.8 - - - -
125F GLN* 5.6 0.2 - - - -
126F SER 5.5 0.9 - - - +
127F ALA* 3.6 13.4 - - - +
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Residues in contact with LEU 335 (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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334E THR* 1.3 78.7 + - - +
336E ASP* 1.3 62.5 + - - +
337E LEU* 4.0 12.1 + - + +
343E ALA 3.6 8.7 - - - +
344E ILE* 4.2 14.6 - - + -
432E LEU* 5.2 10.5 - - + -
106F GLN* 3.2 26.6 + - + +
108F LEU 5.2 0.9 - - - +
110F ASN* 5.2 0.2 - - - -
111F ILE* 4.4 4.9 + - - +
126F SER* 6.3 0.7 - - - -
127F ALA* 3.7 26.9 - - + +
131F ARG* 4.6 10.3 - - - +
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Residues in contact with ASP 336 (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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334E THR 4.3 0.6 + - - +
335E LEU* 1.3 72.3 - - - +
337E LEU* 1.3 63.1 + - - +
338E ARG* 3.7 4.0 + - - -
341E HIS 4.3 4.6 - - - +
342E GLU* 3.5 5.8 - - - +
343E ALA* 2.9 44.4 + - + +
344E ILE 6.2 0.2 - - - -
345E MET* 6.6 0.4 - - + -
425E MET* 5.6 4.5 - - + -
432E LEU* 5.6 0.7 - - - -
110F ASN* 4.3 23.8 - - - +
111F ILE* 4.4 15.7 - - + -
113F PHE* 6.2 2.9 - - - -
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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