Contacts of the helix formed by residues 420 - 427 (chain B) in PDB entry 5J2M
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 PRO 420 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500A GLN* 4.2 16.6 - - + +
417B VAL* 5.8 2.2 - - + -
418B ASN 3.6 7.4 - - - +
419B THR* 1.3 98.0 + - - +
421B PRO* 1.3 68.2 - - + +
422B LEU* 2.9 25.6 + - + +
423B VAL* 3.7 17.8 + - + +
424B LYS* 3.9 4.7 + - - +
720T G 5.8 0.4 - - - +
721T G 4.7 15.0 - - - +
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Residues in contact with PRO 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A TRP* 4.2 20.2 - - + -
500A GLN 5.6 0.7 - - - +
503A LEU* 4.4 6.3 - - + -
504A GLY* 4.6 16.2 - - - -
507A GLN* 3.5 39.9 - - - +
419B THR 3.7 4.4 - - - +
420B PRO* 1.3 83.8 - - + +
422B LEU* 1.3 69.8 + - + +
424B LYS* 4.0 20.1 - - + +
425B LEU* 3.5 25.5 + - - +
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Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A GLN* 3.6 41.1 - - + +
503A LEU* 4.1 15.7 - - + -
535A TRP* 3.6 34.3 - - + -
420B PRO* 2.9 15.4 + - + -
421B PRO* 1.3 83.2 - - + +
423B VAL* 1.3 62.8 + - + +
424B LYS 3.1 1.1 - - - -
425B LEU* 2.9 23.9 + - + +
426B TRP* 3.1 53.1 + - + +
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Residues in contact with VAL 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B TRP* 4.9 8.7 - - + +
328B GLU* 4.7 9.4 - - - +
330B GLN* 3.8 21.8 - - + +
340B GLN* 4.8 0.4 - - - +
419B THR* 5.0 4.3 - - - +
420B PRO* 3.7 16.9 + - + +
422B LEU* 1.3 78.6 - - + +
424B LYS* 1.3 62.1 + - - +
426B TRP* 3.3 23.3 + - + +
427B TYR* 3.4 39.1 + - + +
721T G 6.2 0.2 - - - +
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Residues in contact with LYS 424 (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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403A THR 5.4 1.8 + - - -
404A GLU* 3.7 23.2 + - - +
405A TYR 4.5 1.4 + - - -
406A TRP* 3.8 30.3 - - + +
330B GLN* 4.3 20.6 - - + +
331B LYS* 3.3 23.3 + - - +
332B GLN* 3.1 41.7 + - - +
419B THR* 5.2 3.3 + - + +
420B PRO 3.9 5.0 + - - +
421B PRO* 4.0 20.6 - - + +
422B LEU 3.1 0.4 - - - -
423B VAL* 1.3 78.7 - - - +
425B LEU* 1.3 63.0 + - + +
428B GLN* 3.2 21.5 + - - +
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Residues in contact with LEU 425 (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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259B LYS* 5.0 22.4 - - + +
263B LYS* 4.5 6.9 + - - +
421B PRO 3.5 14.6 + - - +
422B LEU* 2.9 15.5 + - + +
424B LYS* 1.3 79.2 - - + +
426B TRP* 1.3 85.4 + - + +
428B GLN* 3.2 32.6 + - + +
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Residues in contact with TRP 426 (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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535A TRP* 4.1 16.2 - + - -
244B ILE* 4.0 10.7 - - - +
259B LYS* 4.3 6.5 - - + -
262B GLY* 3.8 20.9 - - - -
263B LYS* 3.2 61.5 + - + +
266B TRP* 3.3 65.3 - + + +
422B LEU* 3.1 54.6 + - + +
423B VAL* 3.3 17.6 + - + +
425B LEU* 1.3 95.5 - - + +
427B TYR* 1.3 60.9 + - - +
428B GLN 3.3 0.8 - - - +
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Residues in contact with TYR 427 (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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242B GLN* 5.4 8.1 - - + +
243B PRO 6.3 0.2 - - - -
244B ILE* 4.4 17.9 - - + +
266B TRP* 3.5 36.2 - + - -
270B ILE* 4.0 2.4 - - - +
330B GLN* 4.1 2.5 - - - -
332B GLN* 3.4 20.1 + - - +
338B THR* 3.5 14.2 - - + +
340B GLN* 3.5 42.8 - - + +
348B ASN* 3.5 21.8 + - - -
351B THR* 4.6 12.3 - - + -
423B VAL* 3.4 34.9 + - + +
424B LYS 3.8 0.4 + - - -
425B LEU 3.3 0.4 - - - -
426B TRP* 1.3 77.2 - - - +
428B GLN* 1.3 65.8 + - - +
429B LEU* 3.4 14.9 - - - +
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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