Contacts of the helix formed by residues 348 - 361 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340D TYR* 3.0 58.5 + + + +
341D ARG 5.0 0.2 - - - -
342D ASN* 5.3 3.8 - - + -
346D GLY 4.9 4.5 - - - -
347D THR* 1.3 71.2 - - - +
349D TYR* 1.3 64.0 + - - +
351D GLN* 4.2 2.3 - - - +
352D SER* 3.1 27.5 + - - -
377D VAL* 4.0 10.5 - - + +
381D LYS* 3.4 89.0 - - + +
383D GLY 4.6 0.2 - - - -
385D GLN* 3.6 39.9 - - + +
4201R ASP* 3.4 34.7 + - - -
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Residues in contact with TYR 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C PHE* 3.8 14.1 - + + -
282C ILE 4.3 4.3 - - - -
283C GLN* 3.2 17.5 + - + +
330D GLY* 3.4 37.1 + - - -
331D MET 3.6 11.9 + - - -
332D ALA* 3.3 29.8 - - + -
347D THR 3.1 0.4 - - - -
348D TRP* 1.3 83.6 - - - +
350D ILE* 1.3 69.2 + - + +
352D SER* 3.5 2.1 - - - -
353D LEU* 2.7 40.7 + - + +
370D LEU* 3.6 20.6 - - + +
373D VAL* 3.7 25.1 - - + -
377D VAL* 4.5 3.8 - - - -
385D GLN* 3.8 9.1 - - - +
387D PRO* 4.1 15.9 - - + -
389D PRO* 5.7 0.9 - - - +
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Residues in contact with ILE 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ASP* 3.4 31.6 - - + +
189C LEU* 3.8 28.5 - - + -
235C LEU* 4.1 12.6 - - + -
281C PHE* 4.9 8.3 - - + -
283C GLN* 3.8 26.7 - - + +
347D THR* 3.1 19.9 + - - +
349D TYR* 1.3 86.9 - - + +
351D GLN* 1.3 65.2 + - - +
353D LEU* 3.0 18.4 + - + +
354D CYS* 2.9 26.6 + - - -
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Residues in contact with GLN 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C LEU* 3.7 22.2 + - - +
185C ASP* 3.2 22.8 + - - +
188C ALA* 3.9 14.1 - - - +
345D GLU* 2.9 29.1 + - + +
346D GLY* 4.0 2.9 - - - -
347D THR 3.1 19.8 + - - +
348D TRP* 4.2 2.5 - - - +
350D ILE* 1.3 79.3 - - - +
352D SER* 1.3 58.0 + - - +
354D CYS* 3.2 4.1 + - - +
355D GLN* 2.8 47.6 + - - +
358D ARG* 5.4 3.6 + - - -
381D LYS* 6.4 1.1 - - - -
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Residues in contact with SER 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D TRP 3.1 19.2 + - - -
349D TYR 3.5 2.5 - - - -
351D GLN* 1.3 79.7 - - - +
353D LEU* 1.3 63.0 + - - +
355D GLN* 3.6 14.1 - - - +
356D SER* 2.8 27.8 + - - -
373D VAL* 3.6 22.4 - - - +
376D GLU* 3.8 24.4 - - - +
377D VAL* 4.1 5.8 - - - -
381D LYS* 5.3 5.8 - - - -
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Residues in contact with LEU 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LEU* 4.9 7.0 - - + -
281C PHE* 3.4 54.1 - - + -
349D TYR* 2.7 24.8 + - + +
350D ILE* 3.0 23.3 + - + +
352D SER* 1.3 73.4 - - - +
354D CYS* 1.3 55.0 + - - +
356D SER* 3.7 1.7 - - - -
357D LEU* 2.8 68.1 + - + +
366D ILE* 5.4 1.3 - - + -
369D ILE* 4.9 3.6 - - + -
370D LEU* 4.5 15.3 - - + -
373D VAL* 4.1 15.2 - - + +
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Residues in contact with CYS 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C ALA* 3.6 32.8 - - + -
189C LEU* 3.7 23.1 - - - -
192C THR* 3.3 26.9 - - - +
350D ILE* 2.9 22.7 + - - +
351D GLN* 3.7 4.9 - - - +
353D LEU* 1.3 70.3 - - - +
355D GLN* 1.3 66.6 - - - +
357D LEU* 3.4 7.6 - - - +
358D ARG* 2.8 37.1 + - - +
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Residues in contact with GLN 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D GLN* 2.8 46.1 + - + +
352D SER* 3.6 12.4 - - - +
354D CYS* 1.3 73.5 - - - +
356D SER* 1.3 65.9 + - - +
358D ARG* 3.2 22.1 + - - +
359D GLU* 3.3 22.2 + - - +
381D LYS* 5.6 7.7 - - - +
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Residues in contact with SER 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D SER* 2.8 17.6 + - - -
353D LEU 3.7 2.9 - - - -
355D GLN* 1.3 77.7 - - - +
357D LEU* 1.3 64.3 + - - +
359D GLU* 3.4 5.0 + - - +
360D ARG* 2.9 32.1 + - - +
369D ILE* 3.3 26.3 + - - +
372D GLU* 2.8 29.9 + - - +
373D VAL* 4.2 10.8 - - - -
376D GLU* 6.5 0.7 - - - -
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Residues in contact with LEU 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C THR* 3.8 18.2 - - + -
193C PHE* 3.7 27.1 - - + -
196C LEU* 4.6 2.9 - - + -
281C PHE* 5.1 1.6 - - + -
353D LEU* 2.8 54.9 + - + +
354D CYS* 3.4 5.8 - - - +
356D SER* 1.3 73.5 - - - +
358D ARG* 1.3 57.7 + - - +
360D ARG* 4.7 0.2 - - - -
361D CYS* 3.0 61.3 + - - +
366D ILE* 5.1 4.7 - - + -
369D ILE* 3.9 19.7 - - + -
400D PHE* 4.4 14.6 - - + -
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Residues in contact with ARG 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C ALA* 4.8 10.6 - - - +
191C THR* 4.3 17.5 - - - +
192C THR* 3.8 26.9 + - + +
195C GLU* 3.8 29.7 + - - +
351D GLN* 5.4 3.4 + - - -
354D CYS* 2.8 34.3 + - - +
355D GLN* 3.7 11.9 - - - +
357D LEU* 1.3 74.8 - - - +
359D GLU* 1.3 55.9 + - - +
362D PRO* 2.9 26.0 - - - +
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Residues in contact with GLU 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D GLN* 3.3 21.0 + - - +
356D SER* 3.6 8.0 - - - +
358D ARG* 1.3 75.0 - - - +
360D ARG* 1.3 64.1 + - + +
362D PRO* 3.0 43.1 + - - +
372D GLU* 3.7 18.0 - - - +
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Residues in contact with ARG 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU 5.0 2.6 + - - -
150A ASP* 2.7 39.0 + - - +
356D SER* 2.9 26.0 + - - +
359D GLU* 1.3 79.4 + - + +
361D CYS* 1.3 58.1 + - - +
362D ARG* 2.7 55.6 + - - +
363D GLY 3.2 4.5 + - - -
364D ASP* 2.8 45.2 + - + +
368D THR* 3.8 14.4 - - - +
369D ILE* 3.7 21.3 - - + -
372D GLU* 2.5 43.6 + - - +
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Residues in contact with CYS 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C LEU* 4.0 15.0 - - + -
357D LEU* 3.0 46.9 + - - +
360D ARG* 1.3 72.7 - - - +
362D PRO* 1.3 73.0 - - + +
363D GLY* 2.8 15.5 + - - +
364D ASP 4.5 8.5 - - - -
369D ILE* 3.8 10.3 - - - +
399D VAL* 5.9 0.2 - - - -
400D PHE* 3.4 44.8 - - - +
401D PRO* 4.7 5.7 - - - +
402D SER* 4.7 0.8 + - - -
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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