Contacts of the helix formed by residues 350 - 361 (chain C) in PDB entry 2JLF
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 ALA 350 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C GLY 3.5 3.0 + - - -
349C TYR* 1.3 71.7 - - - +
351C PRO* 1.3 75.4 - - + +
352C TRP* 3.2 32.5 - - + +
353C TRP* 2.8 18.5 + - + +
354C VAL* 3.2 8.0 + - - +
660C SER 3.5 18.8 - - - +
661C VAL* 2.9 13.6 + - - +
662C MET 5.6 0.2 - - - +
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Residues in contact with PRO 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ASN* 5.7 0.4 - - - +
182C LEU* 3.8 21.9 - - + +
345C LEU* 3.6 26.0 - - + -
348C GLY 5.4 0.2 - - - +
349C TYR 3.2 7.4 - - - +
350C ALA* 1.3 83.2 - - + +
352C TRP* 1.3 66.6 + - + +
354C VAL* 2.9 14.4 + - - +
355C LYS* 2.9 13.2 + - - +
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Residues in contact with TRP 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ALA* 3.5 16.8 - - + -
175C GLU* 3.2 66.2 + - + +
178C GLY* 3.6 4.9 - - - -
179C ASN* 3.5 37.7 - - - +
182C LEU* 3.8 9.1 - - - +
350C ALA* 3.0 21.7 + - + +
351C PRO* 1.3 80.1 - - + +
353C TRP* 1.3 87.2 + + + +
355C LYS* 3.1 12.7 + - - +
356C LEU* 3.1 21.5 + - + +
657C PHE* 3.8 20.6 - + - -
660C SER* 3.3 34.8 + - - -
661C VAL* 3.8 10.5 - - + -
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Residues in contact with TRP 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PHE* 4.8 8.3 - + - -
282C PRO* 2.8 32.4 + - + +
283C ILE* 4.0 17.4 - - + +
286C VAL* 3.3 34.3 - - + +
344C LEU* 4.1 15.9 - - + -
349C TYR* 3.9 27.4 - + - -
350C ALA 2.8 13.9 + - - +
352C TRP* 1.3 97.5 - + + +
354C VAL* 1.3 62.3 + - + +
356C LEU* 3.5 7.6 + - + +
357C PHE* 3.1 50.4 + + + -
657C PHE* 3.8 8.7 - + - -
661C VAL* 3.8 32.1 - - + -
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Residues in contact with VAL 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C CYS* 3.5 44.6 - - + +
344C LEU* 4.2 12.3 - - + -
345C LEU* 4.1 20.6 - - + -
349C TYR* 4.0 22.9 - - + -
350C ALA 3.6 12.3 - - - +
351C PRO 2.9 7.6 + - - +
353C TRP* 1.3 83.5 - - + +
355C LYS* 1.3 57.3 + - - +
357C PHE* 3.1 2.1 + - - -
358C GLU* 2.5 36.1 + - + +
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Residues in contact with LYS 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C GLY 4.1 3.4 - - - +
181C MET* 3.6 38.8 - - + -
182C LEU* 3.3 39.0 - - + +
186C PHE* 4.2 14.8 - - - -
351C PRO 2.9 6.2 + - - +
352C TRP 3.1 8.7 + - - +
354C VAL* 1.3 77.0 - - - +
356C LEU* 1.3 52.3 + - - +
358C GLU* 2.7 30.2 + - - +
359C THR* 2.7 43.5 + - - +
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Residues in contact with LEU 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ALA* 3.6 20.6 - - + +
178C GLY* 3.7 23.1 - - - +
181C MET* 3.8 23.3 - - + -
195C MET* 4.2 9.6 - - - -
279C LEU* 3.9 20.9 - - + +
282C PRO* 4.0 27.8 - - + -
283C ILE* 4.3 9.4 - - + -
352C TRP* 3.1 26.9 + - + +
353C TRP* 3.6 9.9 - - + +
355C LYS* 1.3 76.9 - - - +
357C PHE* 1.3 56.6 + - - +
359C THR* 3.9 1.0 - - - -
360C SER* 2.9 30.8 + - - -
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Residues in contact with PHE 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PHE* 5.3 5.2 - + - -
283C ILE* 3.9 12.5 - - + +
337C ARG* 5.4 0.7 - - - -
340C ILE* 4.3 17.5 - - + -
341C CYS* 3.7 19.1 - - - -
344C LEU* 4.7 6.1 - - + -
353C TRP* 3.1 44.1 + + + +
354C VAL* 3.4 8.1 - - - +
356C LEU* 1.3 74.7 - - - +
358C GLU* 1.3 66.3 + - - +
360C SER* 2.6 20.3 + - - -
361C LEU* 3.5 21.9 + - + +
395C GLN* 3.4 24.7 - - - -
397C ALA* 3.8 16.8 - - + -
401C MET* 3.6 33.7 - - + -
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Residues in contact with GLU 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C ARG* 3.8 12.6 - - - +
338C ASP* 4.1 9.5 - - - +
341C CYS* 3.8 22.0 - - + +
354C VAL* 2.5 22.1 + - + +
355C LYS* 2.7 44.1 + - - +
357C PHE* 1.3 73.1 - - - +
359C THR* 1.3 65.9 + - - +
361C LEU* 3.0 14.7 + - - +
362C LYS* 3.5 41.1 + - - +
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Residues in contact with THR 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C MET* 3.4 20.5 - - + -
186C PHE* 3.3 35.1 - - + -
196C GLY* 5.3 1.1 - - - -
279C LEU* 5.2 2.2 - - + -
355C LYS* 2.7 32.3 + - - +
356C LEU 3.9 2.5 - - - -
358C GLU* 1.3 69.5 + - - +
360C SER* 1.3 57.4 + - - +
361C LEU 2.9 4.9 - - - -
362C LYS* 2.8 25.6 + - - +
363C LEU* 3.4 30.6 + - + +
385C PRO* 4.1 9.9 - - + -
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Residues in contact with SER 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C TYR* 2.5 35.6 + - - -
279C LEU* 3.8 22.2 - - - -
280C ASN* 5.4 1.8 - - - -
283C ILE* 3.2 19.1 - - - +
356C LEU 2.9 14.7 + - - -
357C PHE 2.6 20.3 + - - -
359C THR* 1.3 75.0 - - - +
361C LEU* 1.3 56.3 + - - +
362C LYS 3.4 0.7 - - - -
363C LEU* 4.8 1.6 - - - -
392C SER* 4.7 0.9 + - - -
395C GLN* 3.0 27.2 + - - +
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Residues in contact with LEU 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C TYR* 5.9 0.2 - - - -
332C TRP* 4.5 12.8 - - + -
337C ARG* 3.1 48.7 + - + +
357C PHE* 3.6 39.5 - - + +
358C GLU 3.0 7.1 + - - +
359C THR 2.9 1.2 - - - -
360C SER* 1.3 78.1 - - - +
362C LYS* 1.3 59.9 + - - +
363C LEU 3.7 1.6 - - - -
387C LEU 4.2 2.4 - - - +
388C GLU* 5.6 0.3 - - - -
389C VAL 5.6 1.7 + - - -
390C GLY 4.7 13.0 - - - +
391C LEU* 4.0 23.3 - - + -
392C SER* 5.2 8.1 - - - +
395C GLN* 3.6 31.2 - - + +
401C MET* 4.6 1.8 - - + -
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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