Contacts of the helix formed by residues 348 - 361 (chain L) in PDB entry 1F9E
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 TRP 348 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340L TYR* 3.0 55.6 + + + +
342L ASN* 5.3 1.6 - - + -
346L GLY 4.9 4.7 - - - -
347L THR* 1.3 73.1 - - - +
349L TYR* 1.3 64.0 + - - +
351L GLN* 4.2 2.0 - - - +
352L SER* 3.1 26.7 + - - -
377L VAL* 4.0 9.5 - - + +
381L LYS* 3.4 94.8 - - + +
383L GLY 4.6 0.4 - - - -
385L GLN* 3.6 41.3 - - + +
4601V ASP* 2.7 37.6 + - + -
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Residues in contact with TYR 349 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281K PHE* 3.8 9.9 - + + -
282K ILE 4.3 4.0 - - - -
283K GLN* 3.2 15.0 - - + +
330L GLY* 3.4 37.7 + - - -
331L MET 3.6 12.4 + - - -
332L ALA* 3.3 29.8 - - + -
347L THR* 3.1 0.6 - - - -
348L TRP* 1.3 80.2 - - - +
350L ILE* 1.3 74.1 + - + +
352L SER* 3.5 2.4 - - - -
353L LEU* 2.7 45.5 + - + +
370L LEU* 3.6 20.5 - - + +
373L VAL* 3.7 25.6 - - + -
377L VAL* 4.6 3.6 - - - -
385L GLN* 3.7 9.2 - - - +
387L PRO* 4.1 15.7 - - + -
389L PRO* 5.7 1.4 - - + +
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Residues in contact with ILE 350 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185K ASP* 3.3 34.5 - - + +
189K LEU* 3.8 28.7 - - + -
233K CYS* 5.9 0.2 - - + -
235K LEU* 4.1 12.3 - - + -
281K PHE* 4.9 8.5 - - + -
283K GLN* 3.7 26.7 - - + +
347L THR* 3.1 19.7 + - - +
349L TYR* 1.3 85.2 - - + +
351L GLN* 1.3 67.0 + - - +
353L LEU* 2.9 18.0 + - + +
354L CYS* 2.8 26.8 + - - -
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Residues in contact with GLN 351 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184K LEU* 3.7 22.6 + - - +
185K ASP* 3.2 22.4 + - - +
188K ALA* 3.9 14.3 - - - +
345L GLU* 2.9 31.7 + - + +
346L GLY* 4.0 2.0 - - - -
347L THR 3.1 19.5 + - - +
348L TRP* 4.2 2.5 - - - +
350L ILE* 1.3 78.8 - - - +
352L SER* 1.3 58.3 + - - +
354L CYS* 3.2 4.5 + - - +
355L GLN* 2.8 47.0 + - - +
358L ARG* 5.5 3.3 + - - -
381L LYS* 6.4 0.9 - - - -
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Residues in contact with SER 352 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348L TRP 3.1 18.3 + - - -
349L TYR 3.5 2.7 - - - -
351L GLN* 1.3 78.5 - - - +
353L LEU* 1.3 64.3 + - - +
355L GLN* 3.2 16.6 + - - +
356L SER* 2.8 27.8 + - - -
373L VAL* 3.5 21.7 - - - +
376L GLU* 3.8 24.1 - - - +
377L VAL* 4.0 6.5 - - - +
381L LYS* 5.3 5.2 - - - -
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Residues in contact with LEU 353 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189K LEU* 4.9 7.6 - - + -
281K PHE* 3.4 53.6 - - + -
349L TYR* 2.7 25.0 + - + +
350L ILE* 2.9 22.4 + - + +
352L SER* 1.3 74.4 - - - +
354L CYS* 1.3 54.4 + - - +
356L SER* 3.7 1.9 - - - -
357L LEU* 2.8 64.1 + - + +
366L ILE* 5.3 0.9 - - + -
369L ILE* 4.9 3.8 - - + -
370L LEU* 4.4 15.5 - - + -
373L VAL* 4.2 15.4 - - + +
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Residues in contact with CYS 354 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188K ALA* 3.6 31.6 - - + -
189K LEU* 3.7 25.6 - - - -
192K THR* 3.3 26.9 - - - +
350L ILE* 2.8 19.0 + - - +
351L GLN* 3.7 6.5 - - - +
353L LEU* 1.3 72.0 - - - +
355L GLN* 1.3 67.5 + - - +
357L LEU* 3.0 8.8 + - - +
358L ARG* 2.8 37.3 + - - +
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Residues in contact with GLN 355 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351L GLN* 2.8 40.7 + - + +
352L SER* 3.5 16.3 - - - +
354L CYS* 1.3 74.7 - - - +
356L SER* 1.3 65.0 + - - +
358L ARG* 3.2 21.8 + - - +
359L GLU* 3.3 21.2 + - - +
381L LYS* 5.6 8.3 - - - +
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Residues in contact with SER 356 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352L SER* 2.8 21.8 + - - -
353L LEU 3.7 2.9 - - - -
355L GLN* 1.3 75.2 - - - +
357L LEU* 1.3 64.8 + - - +
359L GLU* 3.3 5.0 + - - +
360L ARG* 2.9 32.0 + - - +
369L ILE* 3.2 27.0 + - - +
372L GLU* 2.9 28.8 + - - -
373L VAL* 4.2 10.3 - - - -
376L GLU* 6.5 0.7 - - - -
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Residues in contact with LEU 357 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192K THR* 3.8 17.7 - - + -
193K PHE* 3.7 28.7 - - + -
196K LEU* 4.7 2.9 - - + +
281K PHE* 5.2 0.9 - - + -
353L LEU* 2.8 53.6 + - + +
354L CYS* 3.0 6.3 + - - +
356L SER* 1.3 72.5 - - - +
358L ARG* 1.3 64.1 + - - +
360L ARG* 4.7 0.2 - - - -
361L CYS* 3.0 58.3 + - - +
366L ILE* 5.1 4.9 - - + -
369L ILE* 3.9 19.7 - - + +
400L PHE* 4.5 14.1 - - + -
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Residues in contact with ARG 358 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188K ALA* 4.8 10.8 - - - +
191K THR* 4.3 17.5 - - - +
192K THR* 3.7 28.7 + - + +
195K GLU* 3.8 30.3 + - - +
351L GLN* 5.5 3.4 + - - -
354L CYS* 2.8 32.2 + - - +
355L GLN* 3.8 14.6 - - - +
357L LEU* 1.3 74.4 - - - +
359L GLU* 1.3 58.0 + - - +
362L PRO* 2.9 24.7 - - - +
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Residues in contact with GLU 359 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355L GLN* 3.3 20.8 + - - +
356L SER* 3.5 9.4 - - - +
358L ARG* 1.3 76.7 - - - +
360L ARG* 1.3 62.3 + - + +
362L PRO* 3.0 42.6 + - - +
372L GLU* 3.7 18.2 - - - +
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Residues in contact with ARG 360 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149I LEU 4.9 2.6 + - - -
150I ASP* 2.6 43.0 + - - +
356L SER* 2.9 24.3 + - - +
359L GLU* 1.3 79.8 + - + +
361L CYS* 1.3 57.3 + - - +
362L ARG* 2.8 54.8 + - - +
363L GLY 3.2 4.2 + - - -
364L ASP* 2.8 44.5 + - - +
368L THR* 3.7 13.5 - - - +
369L ILE* 3.7 21.3 - - + +
372L GLU* 2.5 45.1 + - - +
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Residues in contact with CYS 361 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196K LEU* 4.0 15.3 - - + -
357L LEU* 3.0 43.5 + - - +
360L ARG* 1.3 76.0 - - - +
362L PRO* 1.3 67.3 - - + +
363L GLY* 2.8 22.3 + - - +
364L ASP 4.4 8.5 - - - +
369L ILE* 3.8 10.1 - - - +
400L PHE* 3.4 45.7 - - - +
401L PRO* 4.7 4.2 - - - +
402L SER* 4.8 1.2 + - - -
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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