Contacts of the strand formed by residues 334 - 338 (chain G) in PDB entry 1I43
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 VAL 334 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328G LEU* 3.1 42.6 - - + +
329G GLU* 4.5 5.9 - - - +
331G HIS* 3.2 23.0 + - + +
332G PRO 4.7 2.6 - - - +
333G LYS* 1.3 77.1 - - - +
335G ARG* 1.3 65.5 + - - +
336G HIS 3.9 6.3 - - - +
337G VAL* 3.4 26.5 - - + -
364G PHE* 4.2 12.1 - - + -
365G GLU 3.7 10.5 - - - +
366G VAL* 4.6 0.7 - - - +
367G ASP* 5.1 0.2 - - - -
442G LEU* 3.7 22.4 - - + -
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Residues in contact with ARG 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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333G LYS 3.8 3.2 + - - -
334G VAL* 1.3 74.6 - - - +
336G HIS* 1.3 62.7 + - + +
365G GLU* 2.8 26.9 + - + +
366G VAL 4.1 5.1 + - - +
367G ASP* 2.7 35.1 + - + +
368G GLY* 3.4 23.0 + - - +
420G ASN* 3.7 18.9 + - - -
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Residues in contact with HIS 336 (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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329G GLU* 6.1 0.4 - - - -
334G VAL 3.6 0.2 - - - -
335G ARG* 1.3 83.4 - - + +
337G VAL* 1.3 94.9 + - - +
338G TYR* 3.6 32.4 + + - -
344G SER* 5.3 13.4 + - - -
346G PRO* 6.0 3.6 - - + -
364G PHE* 3.1 4.5 - - - +
365G GLU* 2.6 53.7 + - + +
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Residues in contact with VAL 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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325G ALA* 3.9 10.3 - - + +
328G LEU* 3.8 5.6 - - + -
329G GLU* 3.7 31.1 + - + +
334G VAL* 3.4 28.9 - - + -
336G HIS* 1.3 91.6 + - - +
338G TYR* 1.3 68.9 + - - +
339G TYR 4.0 1.6 + - - -
342G LEU* 3.6 32.8 - - + +
344G SER* 4.7 4.0 + - - -
345G HIS* 5.9 1.2 - - - -
362G VAL* 4.2 13.9 - - + -
363G SER 3.6 7.0 - - - +
364G PHE* 3.5 9.9 - - + -
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Residues in contact with TYR 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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212G PRO 4.7 0.2 - - - +
213G PHE* 3.6 58.2 - + + +
214G LEU* 3.5 7.4 - - - +
215G ARG* 6.4 0.2 - - - -
336G HIS* 3.6 34.0 + + - -
337G VAL* 1.3 72.2 - - - +
339G TYR* 1.3 65.3 + - - +
345G HIS* 4.7 6.3 - + + -
346G PRO* 6.0 3.8 - - + -
362G VAL* 4.0 2.6 - - - +
363G SER* 2.5 53.6 + - - +
364G PHE* 4.2 0.4 - - - -
365G GLU* 3.0 45.8 + - + -
421G LEU* 4.2 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