Contacts of the helix formed by residues 348 - 361 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340J TYR* 3.0 56.4 + + + +
342J ASN* 5.3 1.6 - - + -
346J GLY 4.9 4.3 - - - -
347J THR* 1.3 72.5 - - - +
349J TYR* 1.3 63.6 + - - +
351J GLN* 4.2 2.0 - - - +
352J SER* 3.1 27.2 + - - -
377J VAL* 4.0 10.1 - - + +
381J LYS* 3.4 96.8 - - + +
383J GLY 4.6 0.4 - - - -
385J GLN* 3.6 39.5 - - + +
4501U ASP* 3.1 33.1 + - - -
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Residues in contact with TYR 349 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281I PHE* 3.8 15.1 - + + -
282I ILE 4.4 3.6 - - - -
283I GLN* 3.2 16.8 - - + +
330J GLY* 3.4 37.6 + - - -
331J MET 3.7 11.5 + - - -
332J ALA* 3.3 29.8 - - + -
347J THR* 3.1 1.0 + - - -
348J TRP* 1.3 83.3 - - - +
350J ILE* 1.3 75.0 + - + +
352J SER* 3.5 1.9 - - - -
353J LEU* 2.8 33.8 + - + +
370J LEU* 3.6 20.2 - - + +
373J VAL* 3.8 24.5 - - + -
377J VAL* 4.5 3.6 - - - -
385J GLN* 3.7 10.0 - - - +
387J PRO* 4.1 15.9 - - + -
389J PRO* 5.8 1.4 - - - +
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Residues in contact with ILE 350 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185I ASP* 3.3 33.0 - - + +
189I LEU* 3.8 28.5 - - + -
235I LEU* 4.1 12.8 - - + -
281I PHE* 4.9 9.2 - - + -
283I GLN* 3.8 26.2 - - + +
347J THR* 3.1 19.6 + - - +
349J TYR* 1.3 88.2 - - + +
351J GLN* 1.3 66.8 + - - +
353J LEU* 3.0 18.4 + - + +
354J CYS* 2.9 26.5 + - - -
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Residues in contact with GLN 351 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I LEU* 3.7 23.0 + - - +
185I ASP* 3.2 22.6 + - - +
188I ALA* 3.9 13.8 - - - +
345J GLU* 2.9 31.0 + - + +
346J GLY* 4.0 1.1 - - - -
347J THR 3.1 19.8 + - - +
348J TRP* 4.2 2.9 - - - +
350J ILE* 1.3 77.6 - - - +
352J SER* 1.3 58.8 + - - +
354J CYS* 3.2 4.2 + - - +
355J GLN* 2.8 47.3 + - - +
358J ARG* 5.5 3.1 + - - -
381J LYS* 6.4 0.9 - - - -
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Residues in contact with SER 352 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348J TRP 3.1 18.2 + - - -
349J TYR 3.2 3.9 + - - -
351J GLN* 1.3 78.3 - - - +
353J LEU* 1.3 63.5 + - - +
355J GLN* 3.3 15.3 + - - +
356J SER* 2.8 29.6 + - - -
373J VAL* 3.5 21.3 - - - +
376J GLU* 3.7 23.7 - - - +
377J VAL* 4.0 6.2 - - - +
381J LYS* 5.3 6.0 - - - +
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Residues in contact with LEU 353 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189I LEU* 4.9 6.7 - - + -
281I PHE* 3.4 54.1 - - + -
349J TYR* 2.8 23.9 + - + +
350J ILE* 3.2 22.9 - - + +
352J SER* 1.3 72.9 - - - +
354J CYS* 1.3 55.5 + - - +
356J SER* 3.7 1.6 - - - -
357J LEU* 2.8 64.0 + - + +
366J ILE* 5.4 1.3 - - + -
369J ILE* 4.9 3.1 - - + -
370J LEU* 4.5 14.8 - - + -
373J VAL* 4.1 16.0 - - + +
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Residues in contact with CYS 354 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188I ALA* 3.6 33.9 - - + -
189I LEU* 3.7 21.8 - - - -
192I THR* 3.4 25.6 - - - +
350J ILE* 2.9 16.8 + - - +
351J GLN* 3.6 7.0 - - - +
353J LEU* 1.3 76.5 - - - +
355J GLN* 1.3 68.1 + - - +
357J LEU* 3.0 9.0 + - - +
358J ARG* 2.8 36.1 + - - +
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Residues in contact with GLN 355 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351J GLN* 2.8 46.7 + - + +
352J SER* 3.5 11.8 - - - +
354J CYS* 1.3 73.6 - - - +
356J SER* 1.3 65.2 + - - +
358J ARG* 3.2 21.7 + - - +
359J GLU* 3.3 21.9 + - - +
381J LYS* 5.7 7.3 - - - +
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Residues in contact with SER 356 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352J SER* 2.8 21.7 + - - -
353J LEU 3.7 3.1 - - - -
355J GLN* 1.3 74.4 - - - +
357J LEU* 1.3 64.5 + - - +
359J GLU* 3.4 5.0 + - - +
360J ARG* 2.9 31.0 + - - +
369J ILE* 3.2 27.1 + - - +
372J GLU* 2.8 30.7 + - - +
373J VAL* 4.2 11.0 - - - -
376J GLU* 6.5 0.7 - - - -
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Residues in contact with LEU 357 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192I THR* 3.8 18.2 - - + -
193I PHE* 3.7 29.4 - - + -
196I LEU* 4.6 2.2 - - + +
281I PHE* 5.2 1.3 - - + -
353J LEU* 2.8 53.1 + - + +
354J CYS* 3.0 5.6 + - - +
356J SER* 1.3 73.0 - - - +
358J ARG* 1.3 62.8 + - - +
360J ARG* 4.7 0.2 - - - -
361J CYS* 3.0 58.3 + - - +
366J ILE* 5.1 4.7 - - + -
369J ILE* 3.9 19.7 - - + -
400J PHE* 4.4 14.1 - - + -
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Residues in contact with ARG 358 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188I ALA* 4.8 11.2 - - - +
191I THR* 4.3 17.8 - - - +
192I THR* 3.8 28.2 + - + +
195I GLU* 3.8 29.7 + - - +
351J GLN* 5.5 3.0 + - - -
354J CYS* 2.8 32.6 + - - +
355J GLN* 3.2 15.2 + - - +
357J LEU* 1.3 74.6 - - - +
359J GLU* 1.3 55.7 + - - +
362J PRO* 2.9 25.4 - - - +
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Residues in contact with GLU 359 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355J GLN* 3.3 20.7 + - - +
356J SER* 3.6 7.7 - - - +
358J ARG* 1.3 75.0 - - - +
360J ARG* 1.3 64.7 + - + +
362J PRO* 3.0 42.0 + - - +
372J GLU* 3.7 18.0 - - - +
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Residues in contact with ARG 360 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356J SER* 2.9 24.0 + - - +
359J GLU* 1.3 79.8 - - + +
361J CYS* 1.3 58.0 + - - +
362J ARG* 2.8 52.0 + - - +
363J GLY 3.2 6.8 + - - -
364J ASP* 2.8 45.3 + - + +
368J THR* 3.7 15.0 - - - +
369J ILE* 3.7 22.0 - - + +
372J GLU* 2.4 44.2 + - - +
149K LEU 5.0 2.2 + - - -
150K ASP* 2.7 39.4 + - - +
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Residues in contact with CYS 361 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196I LEU* 4.0 15.7 - - + -
357J LEU* 3.0 43.7 + - - +
360J ARG* 1.3 75.8 - - - +
362J PRO* 1.3 66.3 - - + +
363J GLY* 2.8 21.6 + - - +
364J ASP 4.5 8.3 - - - -
369J ILE* 3.8 10.5 - - - -
399J VAL* 5.2 0.3 - - - +
400J PHE* 3.3 44.0 - - - +
401J PRO* 4.7 5.5 - - - +
402J SER* 4.8 1.5 + - - -
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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