Contacts of the helix formed by residues 356 - 361 (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 ASP 356 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336D HIS* 5.3 1.6 - - - -
338D MET* 5.7 1.6 - - - +
352D PHE* 2.7 26.4 + - + +
355D GLY* 1.3 71.5 - - - +
357D MET* 1.3 59.6 + - - +
359D SER* 3.1 5.0 + - - -
360D ASN* 2.9 36.2 + - - +
376D GLY* 4.9 0.2 - - - -
377D PRO* 3.8 24.2 - - - +
379D VAL* 3.6 24.5 - - + +
494D TYR* 6.2 0.3 - - - -
497D LYS* 4.7 12.8 + - - +
498D ILE* 3.5 27.5 - - + +
501D GLN* 4.7 5.5 + - - -
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Residues in contact with MET 357 (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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380C TRP* 3.7 28.9 - - + -
390C ALA 5.1 0.2 - - - -
391C PHE* 3.8 19.3 - - + +
393C GLN* 4.3 0.2 - - - +
394C LEU* 3.7 32.2 + - + +
353D GLN* 3.0 31.7 + - - +
356D ASP* 1.3 76.6 - - - +
358D GLU* 1.3 56.5 + - - +
360D ASN 5.2 0.2 - - - -
361D GLY* 2.8 30.2 + - - +
376D GLY* 6.1 0.2 - - - -
377D PRO 3.6 14.6 - - - +
378D ILE* 3.7 23.3 - - + -
379D VAL* 3.4 31.9 - - + +
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Residues in contact with GLU 358 (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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388C GLN 5.5 0.2 - - - +
389C HIS* 4.1 8.8 - - - +
390C ALA 3.4 18.2 + - - +
391C PHE* 5.4 0.2 - - - +
393C GLN* 3.5 22.4 + - + +
273D ARG* 2.9 30.3 + - - +
353D GLN 3.9 0.8 + - - -
354D GLN* 2.9 48.9 + - + +
357D MET* 1.3 74.2 - - - +
359D SER* 1.3 62.5 + - - +
362D LYS* 3.4 19.8 + - - -
511D ASP 3.8 0.3 - - - +
512D GLN* 4.0 12.7 - - + +
515D VAL* 3.8 20.1 - - - +
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Residues in contact with SER 359 (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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273D ARG* 2.9 15.1 + - - +
274D TYR* 2.7 17.4 + - - -
354D GLN 3.8 1.2 + - - -
355D GLY 2.6 25.2 + - - -
356D ASP 3.1 3.2 + - - -
358D GLU* 1.3 80.6 - - - +
360D ASN* 1.3 63.4 + - - +
361D GLY 3.6 0.2 - - - -
362D LYS* 2.9 27.0 + - - +
498D ILE* 3.7 16.6 - - - -
509D SER* 3.2 25.1 + - - -
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Residues in contact with ASN 360 (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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356D ASP* 2.9 15.5 + - - +
357D MET 4.8 0.2 - - - -
359D SER* 1.3 76.5 - - - +
361D GLY* 1.3 61.1 + - - +
362D LYS* 2.8 11.1 + - - +
375D THR* 3.3 5.2 + - - -
376D GLY* 3.0 25.0 + - - -
498D ILE* 3.0 39.4 + - - +
501D GLN* 4.1 5.7 - - - +
502D GLY* 3.9 2.5 - - - +
505D TRP* 3.7 28.3 - - + -
507D ILE* 3.3 13.8 - - - +
509D SER* 2.7 26.8 + - - -
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Residues in contact with GLY 361 (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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393C GLN* 3.0 33.1 + - - +
394C LEU* 3.6 28.2 - - - +
397C GLN 3.6 7.7 - - - +
398C GLY* 3.8 5.6 - - - -
357D MET 2.8 20.9 + - - -
358D GLU 4.5 0.2 - - - -
359D SER 3.6 1.2 - - - -
360D ASN* 1.3 73.1 - - - +
362D LYS* 1.3 59.8 + - - +
375D THR* 4.6 0.7 - - - -
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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