Contacts of the helix formed by residues 394 - 402 (chain B) in PDB entry 5J2N
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 GLN 394 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A ARG* 3.9 19.3 - - - +
370A GLU* 3.7 33.0 + - - +
373A GLN* 2.8 32.3 + - - +
407A GLN* 4.3 10.1 + - - +
408A ALA 4.8 0.8 + - - -
393B ILE* 1.3 80.3 - - - +
395B LYS* 1.3 68.8 + - - +
396B GLU* 3.6 19.3 - - + +
397B THR* 3.2 12.0 + - - +
398B TRP* 3.1 20.3 + - - +
812P T 4.8 3.8 - - - +
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Residues in contact with LYS 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B ILE 3.6 2.0 + - - -
394B GLN* 1.3 75.0 - - - +
396B GLU* 1.3 74.3 + - - +
398B TRP* 3.4 2.1 + - - +
399B GLU* 2.8 66.3 + - - +
416B PHE* 3.5 41.9 - - + +
812P T 4.1 33.7 + - - +
813P T 3.2 31.8 + - - +
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ARG* 4.4 7.3 + - - -
358A ARG* 3.0 36.5 + - - +
370A GLU* 6.3 0.2 - - + -
373A GLN* 3.3 19.7 - - + +
394B GLN* 3.3 18.6 - - + +
395B LYS* 1.3 85.5 + - - +
397B THR* 1.3 57.2 + - - +
399B GLU* 3.7 11.7 + - - +
400B THR* 2.5 35.4 + - - +
812P T 6.0 0.9 - - - +
813P T 5.2 5.9 + - - -
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Residues in contact with THR 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A THR* 4.9 0.9 - - - +
373A GLN* 2.3 38.1 + - - +
408A ALA 4.6 5.4 - - - +
409A THR* 4.8 2.8 - - - +
410A TRP 4.6 9.6 - - - +
365B VAL* 4.0 10.0 - - + +
393B ILE* 3.8 22.3 - - + +
394B GLN* 3.2 22.7 + - - +
396B GLU* 1.3 80.9 - - - +
398B TRP* 1.3 62.6 + - - +
400B THR 3.5 2.4 + - - -
401B TRP* 3.3 36.2 + - + +
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Residues in contact with TRP 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B VAL* 4.8 4.7 - - + -
368B LEU* 3.7 25.6 - - + -
369B THR* 3.5 36.1 - - + -
372B VAL* 4.1 15.3 - - + -
391B LEU* 3.8 20.4 - - + -
393B ILE* 3.9 26.0 - - + +
394B GLN 3.1 10.3 + - - +
395B LYS 3.9 0.9 - - - +
397B THR* 1.3 77.9 - - - +
399B GLU* 1.3 63.1 + - + +
400B THR 3.1 0.7 + - - -
401B TRP 3.3 0.7 + - - -
402B TRP* 3.0 61.9 + + + +
414B TRP* 3.2 41.7 - + - -
416B PHE* 3.5 36.3 - + + -
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Residues in contact with GLU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B TRP* 5.5 11.4 - - + +
395B LYS* 2.8 61.7 + - + +
396B GLU* 4.2 10.7 - - - +
398B TRP* 1.3 82.9 - - + +
400B THR* 1.3 60.4 + - - +
402B TRP* 3.5 20.3 + - + +
403B THR* 5.2 4.3 + - - +
414B TRP* 5.8 2.0 + - - +
416B PHE* 4.6 4.2 - - + -
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Residues in contact with THR 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A GLN* 4.4 9.1 - - - +
376A THR* 3.9 27.4 - - + -
377A THR* 3.6 26.2 + - - +
380A ILE* 4.8 12.0 - - + +
396B GLU* 2.5 24.4 + - - +
397B THR 3.8 5.8 - - - -
398B TRP 3.1 1.2 + - - -
399B GLU* 1.3 78.9 - - - +
401B TRP* 1.3 80.9 + - + +
403B THR* 5.2 3.8 + - - -
404B GLU* 5.1 4.3 - - - +
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Residues in contact with TRP 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A VAL* 4.5 3.6 - - + -
373A GLN* 3.6 37.2 - - + -
376A THR* 3.9 28.6 - - + +
380A ILE* 6.5 0.2 - - + -
386A THR* 4.9 6.4 + - - +
410A TRP* 3.7 49.1 - + - -
412A PRO* 3.6 27.5 - - + +
365B VAL* 4.0 18.2 - - + -
397B THR* 3.3 31.7 + - + +
398B TRP 3.3 2.0 + - - -
400B THR* 1.3 93.9 - - + +
402B TRP* 1.3 63.8 + - - +
403B THR* 3.3 3.4 - - - -
404B GLU* 3.2 24.0 + - + +
405B TYR* 3.3 25.1 - - + -
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Residues in contact with TRP 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TRP* 4.4 22.4 - + - -
61B PHE* 4.1 7.6 - + - -
76B ASP* 4.8 0.4 - - - -
78B ARG* 4.7 2.9 - - - -
365B VAL* 4.6 1.7 - - + +
369B THR* 4.0 17.3 - - + +
398B TRP* 3.0 57.8 + + + +
399B GLU* 3.5 22.5 + - - +
400B THR 3.9 0.2 - - - -
401B TRP* 1.3 78.3 - - - +
403B THR* 1.3 81.2 + - + +
404B GLU 3.4 0.5 + - - -
405B TYR* 3.4 9.5 + - - -
406B TRP* 3.5 51.7 + + + +
411B ILE* 3.9 23.1 - - + -
414B TRP* 3.5 36.6 - + - -
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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