Contacts of the strand formed by residues 335 - 340 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334C GLU* 3.8 6.7 + - - +
335C THR* 3.6 23.6 - - + -
378C ILE* 3.6 30.1 - - + +
328D ILE* 6.0 0.3 - - - +
333D CYS* 3.4 4.1 - - - +
334D GLU* 1.3 84.1 - - - +
336D HIS* 1.3 61.7 + - - +
377D PRO* 4.1 3.9 - - - +
378D ILE* 3.2 17.0 - - + +
380D TRP* 3.1 21.9 + - + +
401D MET 5.1 0.2 + - - -
402D ILE* 3.8 12.3 - - - +
403D PRO* 3.4 24.6 - - - +
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Residues in contact with HIS 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D GLY* 6.0 4.3 - - - -
335D THR* 1.3 75.7 - - - +
337D ALA* 1.3 63.0 + - - +
338D MET* 3.7 25.6 + - + +
356D ASP* 5.3 1.3 - - - -
377D PRO* 4.1 20.9 - - + -
378D ILE 2.9 8.8 + - - +
379D VAL* 3.3 12.0 - - + +
380D TRP* 3.2 24.1 + - - +
403D PRO* 3.8 23.2 + - + +
405D ASP* 2.8 41.7 + - - -
475D ASN* 5.1 1.3 - - - -
494D TYR* 4.7 0.2 - - - -
497D LYS* 3.3 27.0 + - - -
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Residues in contact with ALA 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335D THR 4.3 0.2 - - - -
336D HIS* 1.3 74.7 - - - +
338D MET* 1.3 62.3 + - - +
339D LEU* 4.0 14.8 - - + -
380D TRP* 3.2 31.7 - - + +
402D ILE* 4.1 4.0 - - + +
403D PRO 3.1 8.2 + - - +
404D CYS* 3.4 25.2 - - - -
405D ASP* 2.9 27.4 + - - +
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Residues in contact with MET 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D HIS* 3.7 22.7 - - + +
337D ALA* 1.3 76.0 - - - +
339D LEU* 1.3 67.5 + - - +
340D PRO* 3.4 12.4 - - + +
348D PHE* 3.6 32.1 - - + +
349D ALA* 3.7 19.4 - - + +
352D PHE* 3.8 26.5 - - + -
356D ASP* 5.7 1.8 - - - +
379D VAL* 3.8 24.9 - - + -
380D TRP 2.9 6.7 + - - -
381D GLY* 3.6 13.0 - - - -
405D ASP* 3.8 7.4 - - + +
407D LEU* 5.1 3.1 - - + -
494D TYR* 3.7 28.9 - - + +
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Residues in contact with LEU 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D ALA* 4.3 9.9 - - + -
338D MET* 1.3 80.0 - - - +
340D PRO* 1.3 66.1 - - - +
341D TYR* 3.5 10.8 + - + -
381D GLY* 4.0 4.5 - - - -
382D GLU 3.5 22.2 - - - +
384D GLY 4.8 0.2 - - - -
391D PHE* 3.9 24.5 - - + -
392D TYR* 3.6 31.0 - - + +
395D ILE* 4.7 3.8 - - + -
404D CYS* 3.9 21.1 - - + -
405D ASP 2.8 15.9 + - - +
406D PHE* 3.5 28.3 - - + -
407D LEU* 3.2 17.8 + - - +
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Residues in contact with PRO 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D MET* 3.4 9.4 - - + +
339D LEU* 1.3 87.5 - - - +
341D TYR* 1.3 56.4 + - - +
342D ASP* 2.9 8.7 + - + +
345D LEU* 3.6 52.7 - - + +
348D PHE* 4.3 13.5 - - + -
349D ALA* 5.3 4.0 - - + +
382D GLU 4.4 0.7 - - - +
383D PRO* 3.0 20.4 - - + +
384D GLY 2.8 18.9 + - - -
407D LEU* 3.5 22.8 - - + +
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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