Contacts of the helix formed by residues 390 - 397 (chain A) in PDB entry 1JLH
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 PHE 390 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A LEU* 3.9 19.7 - - + -
379A TRP* 3.6 26.7 - + - -
381A GLU* 3.7 17.0 - - + -
386A GLY* 3.0 25.1 + - - -
389A ALA* 1.3 82.9 - - + +
391A TYR* 1.3 88.2 + + - +
392A GLN* 3.1 5.1 + - - +
393A LEU* 3.2 14.8 + - - +
394A ILE* 3.7 19.6 + - + +
352B GLN* 3.5 37.9 - - + +
356B MET* 3.7 27.7 - - + +
357B GLU* 4.9 1.6 - - - +
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Residues in contact with TYR 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 3.5 28.7 - - + +
340A TYR* 2.9 37.9 + - - -
381A GLU 5.4 0.3 + - - -
383A GLY* 5.2 1.6 - - - -
386A GLY* 3.1 19.9 + - - -
387A GLN* 3.2 40.3 + - + +
389A ALA 3.9 0.6 - - - -
390A PHE* 1.3 94.0 - + - +
392A GLN* 1.3 65.5 + - - +
394A ILE* 3.1 12.4 + - + +
395A HIS* 3.0 36.7 + + + +
405A PHE* 3.6 10.2 - + - -
431A GLN* 3.1 33.7 - - + +
435A LEU* 5.7 1.8 - - + -
513B GLY 5.3 0.7 - - - +
514B VAL* 5.8 2.9 - - + -
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Residues in contact with GLN 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ALA 5.5 0.2 - - - -
390A PHE* 3.1 0.4 - - - +
391A TYR* 1.3 77.6 - - - +
393A LEU* 1.3 58.6 - - - +
395A HIS* 3.9 1.0 - - - +
396A GLN* 2.9 47.5 + - - +
356B MET 4.3 0.2 - - - +
357B GLU* 3.4 47.0 + - + +
360B GLY 3.0 24.5 + - - +
361B LYS* 3.4 19.5 - - - +
511B GLN* 3.3 14.3 - - - +
512B TRP 4.9 0.2 - - - +
513B GLY* 2.7 35.7 + - - +
514B VAL* 4.7 9.3 - - + +
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Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A PHE 3.2 10.1 + - - +
391A TYR 3.1 0.6 - - - -
392A GLN* 1.3 79.8 - - - +
394A ILE* 1.3 61.1 + - + +
397A GLY* 2.8 26.8 + - - -
399A GLU* 3.4 23.0 - - + +
401A ILE* 3.7 24.2 - - + -
471A ARG* 5.2 0.2 + - - -
356B MET* 3.7 37.2 + - + +
360B GLY* 3.7 25.8 - - - -
375B GLY 3.5 24.7 - - - +
376B PRO 3.7 17.5 - - - +
377B ILE* 4.4 2.2 - - + -
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Residues in contact with ILE 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 4.6 4.0 - - + -
379A TRP* 4.2 11.9 - - + -
390A PHE* 3.9 35.4 - - + +
391A TYR* 3.1 22.8 + - + +
393A LEU* 1.3 80.2 - - + +
395A HIS* 1.3 53.0 + - - +
399A GLU 5.0 3.3 - - - +
401A ILE* 4.1 26.5 - - + +
403A CYS* 4.2 30.3 - - - -
405A PHE* 6.3 0.2 - - + -
435A LEU* 3.9 23.3 - - + -
471A ARG* 2.7 33.9 + - + +
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Residues in contact with HIS 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A TYR* 3.0 33.8 + + + +
392A GLN 4.0 1.6 - - - +
394A ILE* 1.3 78.9 - - - +
396A GLN* 1.3 61.6 + - + +
431A GLN* 2.8 33.3 + - - -
434A ALA* 3.8 19.9 - - + +
435A LEU* 3.1 36.5 + - + +
467A PHE* 4.0 28.6 - + + -
468A GLU 5.0 5.9 + - - -
469A GLY 5.2 1.2 + - - -
471A ARG* 3.2 25.2 + - - +
513B GLY 3.8 22.6 + - - +
514B VAL* 5.7 0.6 - - - -
516B LEU* 5.4 0.2 - - + -
517B GLY* 5.1 3.7 + - - -
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Residues in contact with GLN 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A GLN* 2.9 22.7 + - - +
395A HIS* 1.3 82.8 - - + +
397A GLY* 1.3 65.5 + - - +
464A HIS 3.2 24.6 + - - +
466A VAL 3.2 20.3 + - - +
467A PHE* 4.0 19.9 - - + -
471A ARG* 4.3 1.3 - - - +
360B GLY 3.6 3.4 - - - -
361B LYS* 3.2 14.9 - - - +
362B TYR* 3.1 36.8 - - + -
512B TRP* 3.6 3.0 + - - +
513B GLY* 2.9 36.5 + - - +
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Residues in contact with GLY 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A LEU* 2.8 31.0 + - - -
395A HIS 3.8 0.8 - - - -
396A GLN* 1.3 77.7 - - - +
398A THR* 1.3 66.8 + - - +
399A GLU 3.7 1.8 - - - -
471A ARG* 3.4 17.0 + - - +
360B GLY* 3.8 20.2 - - - -
361B LYS 4.2 1.6 - - - -
362B TYR* 4.2 5.4 - - - +
369B ARG* 5.2 2.9 + - - -
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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