Contacts of the helix formed by residues 340 - 351 (chain D) in PDB entry 3FCS
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 VAL 340 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D TYR* 3.3 36.3 - - + +
130D SER 5.6 2.2 - - - +
131D ILE* 4.7 5.4 - - + -
134D LEU* 3.6 26.9 - - + -
247D VAL* 5.1 1.1 - - + -
249D THR* 4.4 6.7 - - + -
309D ALA* 5.4 2.0 - - + -
333D LEU* 3.8 22.2 - - + -
337D SER* 3.5 18.8 + - - +
338D SER 3.4 1.7 - - - +
339D ASN* 1.3 79.0 + - - +
341D LEU* 1.3 69.3 + - - +
343D LEU* 3.4 5.4 - - + +
344D ILE* 3.2 27.4 + - + +
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Residues in contact with LEU 341 (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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134D LEU* 3.9 15.7 - - + -
137D LYS* 3.2 41.1 - - + +
138D LEU* 3.2 42.8 - - + -
141D GLN* 4.1 22.2 - - + -
338D SER 5.0 2.9 + - - +
339D ASN 3.3 0.8 - - - -
340D VAL* 1.3 83.8 - - + +
342D GLN* 1.3 66.3 + - - +
344D ILE* 3.1 11.5 + - - +
345D VAL* 3.4 11.6 + - + +
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Residues in contact with GLN 342 (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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141D GLN* 5.5 4.2 + - - -
339D ASN* 3.6 10.6 + - + +
340D VAL 3.6 0.2 - - - -
341D LEU* 1.3 81.1 - - - +
343D LEU* 1.3 63.3 + - - +
345D VAL* 3.3 17.2 + - - +
346D ASP* 2.9 57.6 + - - +
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Residues in contact with LEU 343 (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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247D VAL* 5.9 0.2 - - + -
307D ILE* 4.3 14.4 - - + -
309D ALA* 4.0 20.6 - - + -
331D GLY* 3.8 37.0 - - - +
332D VAL 4.1 13.9 - - - +
333D LEU* 4.3 12.1 - - + +
339D ASN* 3.2 14.7 + - - +
340D VAL* 3.4 10.3 - - + +
342D GLN* 1.3 79.1 - - - +
344D ILE* 1.3 65.0 + - + +
346D ASP* 3.0 9.6 + - - +
347D ALA* 2.7 45.6 + - + +
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Residues in contact with ILE 344 (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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114D ILE* 4.6 12.1 - - + -
116D TYR* 4.4 18.6 - - + -
134D LEU* 5.0 3.4 - - + -
138D LEU* 4.0 34.8 - - + -
142D MET* 4.6 7.2 - - + -
245D LEU* 4.6 11.9 - - + -
247D VAL* 4.0 34.8 - - + -
307D ILE* 4.8 3.5 - - + +
340D VAL* 3.3 18.2 - - + +
341D LEU* 3.1 6.3 + - - +
343D LEU* 1.3 88.3 - - + +
345D VAL* 1.3 53.6 + - - +
347D ALA* 3.1 5.8 + - - +
348D TYR* 2.8 33.6 + - - +
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Residues in contact with VAL 345 (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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141D GLN* 4.3 22.2 - - + +
142D MET* 3.5 28.9 - - + -
145D LEU* 4.3 15.7 - - + +
341D LEU* 3.4 12.5 + - + +
342D GLN* 3.3 19.2 + - - +
343D LEU 3.2 0.6 - - - -
344D ILE* 1.3 78.3 - - - +
346D ASP* 1.3 70.3 - - - +
348D TYR* 3.3 9.0 + - - +
349D GLY* 3.1 19.2 + - - -
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Residues in contact with ASP 346 (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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342D GLN* 2.9 45.9 + - - +
343D LEU* 3.0 10.5 + - - +
345D VAL* 1.3 80.2 - - - +
347D ALA* 1.3 53.8 + - - +
349D GLY* 3.2 3.1 + - - +
350D LYS* 2.7 37.3 + - - +
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Residues in contact with ALA 347 (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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307D ILE* 3.5 35.9 - - + -
329D THR* 4.0 8.8 + - - +
330D VAL 6.5 0.7 - - - -
343D LEU* 2.7 20.4 + - + +
344D ILE* 3.3 10.5 - - - +
346D ASP* 1.3 73.2 - - - +
348D TYR* 1.3 52.0 + - - +
350D LYS* 3.5 7.8 - - - +
351D ILE* 2.7 41.6 + - - +
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Residues in contact with TYR 348 (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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110D TYR* 4.1 11.1 + - - +
112D VAL* 3.3 32.0 - - + +
142D MET* 5.1 7.6 - - - -
145D LEU* 3.9 33.8 + - + -
146D THR* 5.5 0.2 - - - -
243D SER* 4.1 16.2 + - - -
245D LEU* 3.5 37.9 - - + -
307D ILE* 4.8 0.4 - - - +
344D ILE 2.8 15.1 + - - +
345D VAL* 3.5 10.8 - - - +
346D ASP 3.2 0.2 - - - -
347D ALA* 1.3 72.5 - - - +
349D GLY* 1.3 57.1 + - - +
351D ILE* 3.2 9.2 + - + +
352D ARG* 2.9 52.2 + - + +
391D ILE* 3.9 25.2 - - + +
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Residues in contact with GLY 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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345D VAL 3.1 10.0 + - - -
346D ASP* 3.2 3.8 + - - -
348D TYR* 1.3 83.3 - - - +
350D LYS* 1.3 56.6 + - - +
352D ARG* 3.8 4.5 - - - +
353D SER* 3.0 26.7 + - - -
389D LEU 5.2 0.7 - - - +
391D ILE* 5.6 5.6 - - - -
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Residues in contact with LYS 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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319D GLN* 5.6 4.9 - - - +
329D THR* 4.0 24.4 - - + +
330D VAL* 3.8 25.4 + - - +
346D ASP 2.7 21.5 + - - +
347D ALA* 3.5 8.3 - - - +
349D GLY* 1.3 71.8 - - - +
351D ILE* 1.3 65.9 - - - +
353D SER* 3.1 21.8 - - - -
354D LYS* 3.8 5.0 + - - +
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Residues in contact with ILE 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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245D LEU* 3.8 14.1 - - + -
305D ASN* 3.4 40.4 - - + +
306D LEU 5.7 0.4 - - - +
307D ILE* 3.6 30.3 - - + -
327D GLY* 5.5 1.8 - - - +
328D THR 5.3 1.6 - - - -
329D THR* 3.8 22.2 - - + +
347D ALA 2.7 28.3 + - - +
348D TYR* 3.5 5.6 - - - +
350D LYS* 1.3 73.5 - - - +
352D ARG* 1.3 83.6 + - + +
353D SER 3.2 3.6 + - - -
354D LYS* 3.3 19.6 + - - +
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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