Contacts of the helix formed by residues 391 - 398 (chain B) in PDB entry 2CXO
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 391 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A GLN* 3.6 32.3 - - + +
357A MET* 3.7 34.7 - - + +
358A GLU 4.9 0.7 - - - +
339B LEU* 3.8 14.1 - - + -
380B TRP* 3.5 25.8 - + - -
382B GLU* 3.8 36.1 - - + -
387B GLY* 3.2 19.2 + - - -
390B ALA* 1.3 81.6 - - + +
392B TYR* 1.3 90.9 + + - +
393B GLN 3.0 2.7 - - - +
394B LEU* 3.0 16.9 + - - +
395B ILE* 3.2 16.2 + - + +
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Residues in contact with TYR 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A GLY 5.6 0.9 - - - +
339B LEU* 3.4 27.0 - - + +
341B TYR* 2.9 40.4 + - - -
382B GLU 5.6 0.4 - - - -
384B GLY* 4.6 3.3 + - - -
387B GLY* 3.0 37.5 + - - +
388B GLN* 3.5 27.1 - - + +
391B PHE* 1.3 98.1 - + - +
393B GLN* 1.3 66.8 + - - +
395B ILE* 3.6 13.5 - - + -
396B HIS* 2.8 38.9 + + + -
406B PHE* 3.5 11.2 - + - -
432B GLN* 3.3 26.9 - - + +
436B LEU* 5.5 3.1 - - + -
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Residues in contact with GLN 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A MET 4.0 0.7 - - - +
358A GLU* 3.4 46.9 - - + +
361A GLY 2.9 22.1 - - - +
362A LYS* 3.4 12.5 - - - -
512A GLN* 3.2 19.2 - - - +
514A GLY* 2.8 38.5 - - - +
515A VAL* 3.4 12.3 - - + +
391B PHE 4.5 1.3 - - - +
392B TYR* 1.3 78.2 - - - +
394B LEU* 1.3 57.8 + - - +
396B HIS* 3.8 0.9 - - - +
397B GLN* 2.8 46.4 + - - +
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Residues in contact with LEU 394 (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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357A MET* 3.7 36.1 + - + +
361A GLY* 3.6 27.6 - - - +
376A GLY 3.5 24.9 - - - +
377A PRO 3.6 16.8 - - - +
378A ILE* 4.2 6.1 - - + -
391B PHE 3.0 10.3 + - - +
393B GLN* 1.3 78.3 - - - +
395B ILE* 1.3 61.6 + - - +
398B GLY* 2.8 31.0 + - - -
399B THR 5.3 0.2 - - - +
400B LYS* 4.4 15.5 - - + +
402B ILE* 3.7 26.5 - - + +
472B ARG* 4.9 0.2 + - - -
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Residues in contact with ILE 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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337B ALA* 5.4 0.4 - - + -
339B LEU* 4.6 2.9 - - + -
380B TRP* 4.3 9.6 - - + -
391B PHE* 3.2 36.9 + - + +
392B TYR* 3.2 24.6 + - + +
394B LEU* 1.3 77.6 - - + +
396B HIS* 1.3 51.5 + - - +
400B LYS 4.9 3.9 - - - +
402B ILE* 4.1 30.1 - - + +
404B CYS* 4.1 30.7 - - - -
436B LEU* 3.6 24.5 - - + -
472B ARG* 2.6 36.9 + - + +
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Residues in contact with HIS 396 (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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363A TYR* 4.3 3.6 + - - -
514A GLY* 4.4 15.9 + - - -
517A LEU* 4.0 17.6 - - + +
518A GLY* 5.8 0.2 - - - -
521A LEU* 5.0 1.0 - - + +
392B TYR* 2.8 36.2 + + + +
393B GLN 3.9 2.2 - - - +
395B ILE* 1.3 76.1 - - + +
397B GLN* 1.3 58.3 + - - +
432B GLN* 2.9 29.7 + - - -
435B ALA* 4.1 14.1 + - + -
436B LEU* 3.5 42.2 - - + +
468B PHE* 3.9 28.8 - - + +
469B GLU* 5.0 1.0 + - - +
470B GLY 5.3 0.5 + - - -
472B ARG* 3.2 23.5 + - - +
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Residues in contact with GLN 397 (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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361A GLY 3.6 4.3 - - - +
362A LYS* 3.1 30.2 - - - +
363A TYR* 3.1 35.4 + - + +
364A ILE* 5.3 3.0 - - + +
513A TRP* 3.9 10.7 - - - +
514A GLY 3.6 9.3 - - - +
393B GLN* 2.8 34.7 + - - +
396B HIS* 1.3 73.4 - - - +
398B GLY* 1.3 61.6 + - - +
464B PRO 4.6 0.9 - - - +
465B HIS* 2.9 24.8 + - - +
467B VAL 3.3 16.6 - - - +
468B PHE* 3.3 25.1 - - + -
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Residues in contact with GLY 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A GLY* 3.9 16.4 - - - -
362A LYS 4.0 3.1 - - - -
363A TYR* 3.4 9.9 - - - -
370A ARG* 4.6 2.1 + - - -
375A THR* 4.7 0.7 - - - -
394B LEU* 2.8 28.9 + - - -
396B HIS 3.8 0.4 - - - -
397B GLN* 1.3 75.8 - - - +
399B THR* 1.3 66.1 + - - -
400B LYS 3.5 2.5 - - - -
472B ARG* 3.3 18.8 + - - +
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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