Contacts of the strand formed by residues 334 - 339 (chain E) in PDB entry 3TMP
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 HIS 334 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217E GLN* 3.4 6.7 + - - -
218E MET 3.2 21.5 + - - -
219E LYS 3.5 14.1 - - - -
220E GLU* 3.4 32.6 - - + +
224E CYS* 3.7 1.3 - - + -
328E SER 3.5 0.7 - - - +
329E TYR* 3.4 5.5 - - - -
330E HIS* 2.8 37.0 + + - +
331E ARG* 3.8 22.2 - - - +
333E ILE* 1.3 80.8 - - + +
335E TYR* 1.3 76.6 + - - +
336E ASN* 3.0 35.4 + - - -
76F GLZ 2.7 23.5 + - - +
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Residues in contact with TYR 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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218E MET* 3.6 9.2 - - - +
224E CYS* 3.5 13.1 - - - +
225E LEU* 3.8 42.6 - - + -
228E ALA* 4.6 2.9 - - + -
280E GLY 4.6 2.0 - - - -
285E MET* 3.7 26.1 - - + +
298E VAL* 4.5 2.2 - - + -
327E VAL* 3.7 18.4 - - + -
328E SER 3.1 12.8 - - - -
329E TYR* 3.4 30.1 - + + -
334E HIS* 1.3 95.0 + - - +
336E ASN* 1.3 65.1 + - - +
73F LEU* 2.5 46.5 + - - +
75F GLY* 3.7 24.2 - - - -
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Residues in contact with ASN 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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215E ILE* 3.8 12.4 - - + +
216E LYS 3.5 7.2 - - - +
217E GLN* 3.5 16.9 + - - -
218E MET* 2.8 30.9 + - - -
228E ALA* 3.8 6.1 - - - +
327E VAL* 3.3 9.7 - - - +
328E SER* 2.8 42.5 + - - +
330E HIS* 3.2 25.9 + - - -
334E HIS* 3.0 22.1 + - - -
335E TYR* 1.3 72.1 - - - +
337E SER* 1.3 60.1 + - - +
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Residues in contact with SER 337 (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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214E ILE 3.6 0.2 - - - +
215E ILE* 3.6 2.8 - - - -
216E LYS* 2.7 37.9 + - - +
218E MET* 3.6 20.0 - - - +
228E ALA* 4.1 15.5 - - - -
231E ASP* 2.8 23.6 + - - -
232E GLN* 2.7 29.7 + - - +
326E ARG 3.9 3.4 - - - -
328E SER* 5.1 0.2 - - - -
336E ASN* 1.3 73.2 - - - +
338E VAL* 1.3 60.1 + - - +
339E VAL* 3.8 2.0 - - - +
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Residues in contact with VAL 338 (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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207E LEU* 5.0 5.4 - - + -
213E PHE* 3.6 41.3 - - + -
214E ILE 3.5 4.9 - - - +
215E ILE* 4.8 5.6 - - + +
232E GLN* 3.0 15.2 + - - +
299E TYR* 4.1 13.7 - - + -
326E ARG* 2.9 38.1 + - + +
327E VAL 3.5 29.2 - - - +
328E SER* 3.5 18.4 - - - +
337E SER* 1.3 70.7 + - - +
339E VAL* 1.3 58.0 + - - +
340E ASN 4.2 0.5 + - - -
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Residues in contact with VAL 339 (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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212E GLY 4.3 0.2 - - - +
213E PHE* 3.4 6.5 - - - -
214E ILE* 2.7 52.9 + - + +
216E LYS* 3.9 24.0 - - + +
231E ASP* 3.9 11.9 - - - +
232E GLN* 4.2 4.9 - - - +
337E SER* 3.8 18.4 - - - +
338E VAL* 1.3 72.5 - - - +
340E ASN* 1.3 73.0 + - - +
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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