Contacts of the strand formed by residues 334 - 339 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217G GLN* 5.0 1.8 + - - -
218G MET 3.1 22.5 + - - -
220G GLU* 3.4 31.2 + - + +
224G CYS* 3.6 10.5 - - + +
328G SER 3.5 0.3 - - - +
329G TYR* 3.4 6.4 - - - -
330G HIS* 2.9 31.5 + + - +
331G ARG* 3.8 27.6 - - - +
333G ILE* 1.3 78.9 - - - +
335G TYR* 1.3 75.7 + - - +
336G ASN* 2.9 37.7 + - - -
76H GLZ 2.8 24.1 + - - +
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Residues in contact with TYR 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218G MET* 3.7 5.7 - - - +
224G CYS* 3.4 15.7 - - - +
225G LEU* 4.0 40.4 - - + -
228G ALA* 4.6 3.1 - - + -
280G GLY 4.7 2.5 - - - -
285G MET* 3.3 33.6 - - + +
298G VAL* 4.2 4.1 - - + +
327G VAL* 3.8 19.5 - - + -
328G SER 3.2 13.7 - - - -
329G TYR* 3.5 28.3 - + + -
334G HIS* 1.3 92.1 + - - +
336G ASN* 1.3 65.8 + - - +
73H LEU* 2.7 38.7 + - - +
75H GLY* 3.7 25.1 - - - -
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Residues in contact with ASN 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215G ILE* 3.7 7.2 - - + -
216G LYS 3.5 6.5 - - - +
217G GLN* 3.3 28.0 + - - +
218G MET* 2.7 31.9 + - - +
228G ALA* 3.5 7.1 - - - +
327G VAL* 3.3 10.6 - - - +
328G SER* 2.9 41.7 + - - +
330G HIS* 3.4 23.6 + - - +
331G ARG* 5.8 0.4 - - - +
334G HIS* 2.9 22.4 + - - -
335G TYR* 1.3 72.8 - - - +
337G SER* 1.3 61.7 + - - +
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Residues in contact with SER 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214G ILE 3.7 0.2 - - - +
215G ILE* 3.6 3.0 - - - -
216G LYS* 2.7 38.4 + - - +
218G MET* 3.7 18.5 - - - +
228G ALA* 4.1 9.9 - - - -
231G ASP* 2.8 33.1 + - - -
232G GLN* 2.9 24.9 + - - +
326G ARG 4.0 3.8 - - - -
336G ASN* 1.3 75.2 - - - +
338G VAL* 1.3 60.1 + - - +
339G VAL* 3.8 2.5 - - - +
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Residues in contact with VAL 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207G LEU* 4.7 6.7 - - + -
213G PHE* 3.6 39.9 - - + -
214G ILE 3.6 5.2 - - - +
215G ILE* 3.7 9.2 - - + -
232G GLN* 2.9 16.7 + - - +
299G TYR* 4.2 12.3 - - + -
326G ARG* 2.9 36.1 + - + +
327G VAL 3.5 15.9 - - - +
328G SER* 3.5 31.6 - - - -
337G SER* 1.3 70.0 + - - +
339G VAL* 1.3 59.8 + - - +
340G ASN 3.9 1.2 + - - -
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Residues in contact with VAL 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213G PHE* 3.3 7.2 - - - -
214G ILE* 2.8 44.0 + - + +
216G LYS* 3.9 32.8 - - + +
231G ASP* 4.0 15.7 - - - +
232G GLN* 4.3 3.4 - - - +
337G SER* 4.1 2.2 - - - +
338G VAL* 1.3 73.4 - - - +
340G ASN* 1.3 72.7 + - - +
341G PRO* 3.4 10.7 - - + +
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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