Contacts of the helix formed by residues 345 - 362 (chain F) in PDB entry 2JG7
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 THR 345 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F THR* 4.4 17.0 - - + -
343F LEU* 4.3 0.2 - - - +
344F HIS* 1.3 100.7 - - + +
346F LYS* 1.3 64.0 + - - +
347F GLN* 3.5 19.7 + - - +
348F ALA* 3.3 34.3 + - - +
349F VAL* 3.5 10.9 + - - +
378F ASN* 3.7 13.0 - - - +
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Residues in contact with LYS 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ASN* 3.7 30.6 - - - +
345F THR* 1.3 72.2 - - - +
347F GLN* 1.3 71.8 + - - +
348F ALA 3.1 0.2 - - - -
349F VAL* 2.9 22.9 + - + +
350F ASP* 3.1 17.4 + - - +
378F ASN* 3.5 13.4 + - - +
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Residues in contact with GLN 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345F THR* 3.5 16.2 - - - +
346F LYS* 1.3 86.9 + - - +
348F ALA* 1.3 62.8 + - - +
350F ASP* 3.0 25.2 + - - +
351F GLN* 3.0 27.3 + - - +
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Residues in contact with ALA 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F PHE* 6.3 1.6 - - + -
299F GLN* 4.8 4.5 - - - +
343F LEU* 3.8 17.7 - - + -
344F HIS* 4.5 3.4 - - + +
345F THR* 3.3 30.6 + - - +
346F LYS 3.1 0.2 - - - -
347F GLN* 1.3 77.8 - - - +
349F VAL* 1.3 60.7 + - - +
351F GLN* 3.3 16.6 + - - +
352F TYR* 3.1 17.7 + - - +
400F PHE 5.2 3.1 - - - +
401F VAL* 3.5 12.9 - - + +
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Residues in contact with VAL 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343F LEU* 3.9 9.4 - - + -
345F THR 3.6 14.4 - - - +
346F LYS* 2.9 15.5 + - + +
348F ALA* 1.3 75.2 - - - +
350F ASP* 1.3 57.5 + - - +
352F TYR* 3.2 5.1 - - - +
353F LEU* 3.0 31.6 + - + +
372F VAL* 3.9 33.4 - - + -
378F ASN* 3.8 31.9 - - + +
380F VAL* 3.9 13.0 - - + -
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Residues in contact with ASP 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346F LYS* 3.1 14.3 + - - +
347F GLN* 3.0 17.2 + - - +
349F VAL* 1.3 76.7 - - - +
351F GLN* 1.3 60.0 + - - +
353F LEU* 3.3 14.7 + - - +
354F ALA* 2.9 30.9 + - - +
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Residues in contact with GLN 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347F GLN* 3.0 27.0 + - - +
348F ALA* 3.4 15.0 - - - +
350F ASP* 1.3 73.0 - - - +
352F TYR* 1.3 54.4 + - - +
354F ALA* 3.3 5.8 + - - +
355F ALA* 2.8 37.4 + - - +
399F THR* 3.9 21.5 - - + +
400F PHE 5.8 0.9 - - - +
401F VAL* 4.2 4.0 - - + -
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Residues in contact with TYR 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343F LEU* 4.2 2.0 - - + -
348F ALA 3.1 10.3 + - - +
349F VAL* 3.2 13.0 - - - +
351F GLN* 1.3 79.5 - - - +
353F LEU* 1.3 66.0 + - + +
355F ALA* 3.7 1.7 - - - +
356F ILE* 3.0 35.8 + - + +
370F GLY* 3.0 32.7 + - - -
371F LYS 3.5 8.0 + - - -
372F VAL* 4.6 1.8 - - + -
380F VAL* 3.6 36.6 - - + -
381F GLU 2.5 32.3 + - - -
383F THR* 3.0 17.2 + - - -
401F VAL* 3.8 24.8 - - + +
402F PRO* 4.2 5.6 - - + -
403F ILE* 3.8 23.7 - - + +
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Residues in contact with LEU 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349F VAL* 3.0 20.8 + - + +
350F ASP* 3.3 16.6 + - - +
352F TYR* 1.3 81.4 - - + +
354F ALA* 1.3 58.3 + - - +
356F ILE* 3.4 7.7 - - + +
357F GLU* 3.1 32.8 + - - +
370F GLY 4.2 19.1 - - - +
371F LYS* 5.3 0.4 - - - -
372F VAL* 3.8 32.1 - - + +
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Residues in contact with ALA 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350F ASP 2.9 18.2 + - - +
351F GLN* 3.6 6.7 - - - +
353F LEU* 1.3 74.1 - - - +
355F ALA* 1.3 59.1 + - - +
357F GLU* 3.3 6.9 + - - +
358F GLN* 3.0 47.4 + - - +
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Residues in contact with ALA 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351F GLN 2.8 20.0 + - - +
352F TYR 3.7 4.0 - - - +
354F ALA* 1.3 70.2 - - - +
356F ILE* 1.3 61.2 + - - +
358F GLN* 3.4 3.4 + - - +
359F ALA* 2.9 31.1 + - - +
394F ILE* 3.9 28.1 - - + +
399F THR* 4.0 15.7 - - + -
403F ILE* 3.8 17.9 - - + -
405F TYR* 4.1 4.4 + - - +
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Residues in contact with ILE 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352F TYR* 3.0 32.0 + - + +
353F LEU* 3.4 12.1 - - + +
355F ALA* 1.3 76.7 - - - +
357F GLU* 1.3 66.8 + - - +
359F ALA* 3.2 7.9 + - - +
360F LYS* 3.1 50.1 + - - +
366F LEU* 4.4 9.9 - - + +
370F GLY* 3.8 26.5 - - - +
383F THR* 3.7 32.1 - - + +
385F ILE* 4.4 5.6 - - + -
403F ILE* 3.8 15.5 - - + -
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Residues in contact with GLU 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353F LEU* 3.1 15.3 + - - +
354F ALA* 3.3 10.3 + - - +
356F ILE* 1.3 85.1 - - - +
358F GLN* 1.3 62.7 + - + +
360F LYS* 3.1 27.6 + - - +
361F GLN* 3.0 39.8 + - + +
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Residues in contact with GLN 358 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354F ALA* 3.0 38.6 + - - +
355F ALA* 3.9 4.0 - - - +
357F GLU* 1.3 74.9 - - + +
359F ALA* 1.3 58.0 + - - +
361F GLN* 3.3 18.7 + - - +
362F GLN* 2.9 51.4 + - - +
394F ILE* 3.5 23.6 - - + +
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Residues in contact with ALA 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355F ALA 2.9 18.6 + - - +
356F ILE 3.3 6.1 - - - +
357F GLU 3.2 0.2 - - - -
358F GLN* 1.3 76.3 - - - +
360F LYS* 1.3 59.6 + - + +
362F GLN 3.2 6.6 + - - -
363F GLY 3.3 0.5 + - - -
364F GLY* 2.8 25.1 + - - -
366F LEU* 5.4 0.7 - - + -
385F ILE* 3.6 30.1 - - + -
388F LEU* 3.5 16.9 - - + +
394F ILE* 4.2 14.7 - - + +
405F TYR* 4.6 2.5 - - + -
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Residues in contact with LYS 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356F ILE* 3.1 37.4 + - + +
357F GLU* 3.1 30.3 + - + +
359F ALA* 1.3 75.3 - - - +
361F GLN* 1.3 58.3 + - + +
363F GLY* 2.9 21.5 + - - -
364F GLY 3.7 16.9 + - - +
366F LEU* 4.0 24.7 - - + +
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Residues in contact with GLN 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357F GLU* 3.0 31.2 + - + +
358F GLN* 3.3 24.1 + - - +
360F LYS* 1.3 75.8 - - + +
362F GLN* 1.3 62.3 + - + +
363F GLY 3.3 1.3 + - - -
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Residues in contact with GLN 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358F GLN* 2.9 40.9 + - - +
359F ALA 3.6 0.2 - - - -
360F LYS 3.1 0.6 - - - -
361F GLN* 1.3 81.5 - - + +
363F GLY* 1.3 57.5 + - - +
364F GLY 3.6 2.2 - - - -
388F LEU* 3.4 24.7 - - + +
389F ALA 5.1 1.7 + - - -
392F ALA* 3.5 8.1 - - + +
393F PRO* 3.2 27.5 - - + +
394F ILE* 3.0 36.3 + - - +
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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