Contacts of the strand formed by residues 335 - 340 (chain C) in PDB entry 1JIQ
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 THR 335 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328C ILE* 5.9 0.9 - - - +
333C CYS* 4.3 4.2 - - - +
334C GLU* 1.3 85.0 - - + +
336C HIS* 1.3 63.0 + - - +
377C PRO* 4.1 4.0 - - - +
378C ILE* 3.1 19.7 - - + +
380C TRP* 3.1 22.2 + - + +
401C MET 5.2 0.7 + - - +
402C ILE* 3.8 11.3 - - - +
403C PRO* 3.4 24.1 - - - +
334D GLU* 3.9 5.8 + - - +
335D THR* 3.6 31.0 - - + -
378D ILE* 3.7 23.1 - - + +
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Residues in contact with HIS 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C GLY* 5.9 5.4 - - - -
335C THR* 1.3 75.5 - - - +
337C ALA* 1.3 59.6 + - - +
338C MET* 3.8 22.3 - - + +
356C ASP* 5.3 0.7 - - - -
377C PRO* 4.1 20.0 - - + -
378C ILE 2.9 7.6 + - - +
379C VAL* 3.3 13.8 - - + +
380C TRP* 3.2 23.9 + - - +
403C PRO* 3.7 26.2 + - + +
405C ASP* 2.9 42.7 + - - -
475C ASN* 5.1 3.6 - - - -
497C LYS* 3.2 27.4 + - - -
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Residues in contact with ALA 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C THR 4.3 0.2 - - - -
336C HIS* 1.3 72.7 + - - +
338C MET* 1.3 63.0 + - - +
339C LEU* 4.0 13.7 - - + -
380C TRP* 3.2 33.5 - - + +
395C ILE* 5.4 0.2 - - + -
402C ILE* 4.0 4.2 - - + +
403C PRO 3.0 8.3 + - - +
404C CYS* 3.4 25.1 - - - -
405C ASP* 2.8 28.8 + - - +
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Residues in contact with MET 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C HIS* 3.8 22.0 + - + +
337C ALA* 1.3 74.6 - - - +
339C LEU* 1.3 67.6 + - - +
340C PRO* 3.4 11.6 - - + +
348C PHE* 3.5 32.3 - - + +
349C ALA* 3.7 19.9 - - + +
352C PHE* 3.8 25.8 - - + -
356C ASP* 5.7 2.0 - - - +
379C VAL* 3.7 24.9 - - + -
380C TRP 2.8 9.4 + - - +
381C GLY* 3.6 13.2 - - - -
405C ASP* 3.8 8.3 - - + +
407C LEU* 5.1 3.4 - - + -
494C TYR* 3.6 29.2 - - + +
497C LYS* 5.9 0.2 - - - -
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Residues in contact with LEU 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C ALA* 4.3 6.3 - - + -
338C MET* 1.3 86.5 - - - +
340C PRO* 1.3 66.0 - - - +
341C TYR* 3.5 12.8 - - + -
381C GLY* 4.0 7.2 - - - -
382C GLU 3.5 17.9 - - - +
384C GLY 4.9 0.4 - - - +
391C PHE* 4.0 23.1 - - + -
392C TYR* 3.6 30.5 - - + +
395C ILE* 4.6 3.4 - - + -
404C CYS* 3.9 21.3 - - + -
405C ASP 2.8 15.8 + - - +
406C PHE* 3.5 26.2 - - + -
407C LEU* 3.2 19.0 + - - +
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Residues in contact with PRO 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C MET* 3.4 10.8 - - + +
339C LEU* 1.3 86.6 - - - +
341C TYR* 1.3 59.6 + - - +
342C ASP* 2.9 9.2 + - + +
345C LEU* 3.7 52.7 - - + +
348C PHE* 4.3 13.9 - - + -
349C ALA* 5.2 3.8 - - + +
382C GLU 4.2 0.4 - - - +
383C PRO* 3.0 22.9 - - + +
384C GLY 2.9 16.1 + - - -
407C LEU* 3.4 19.2 - - + +
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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