Contacts of the helix formed by residues 281 - 292 (chain A) in PDB entry 4FV3
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 ASP 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A ASN* 3.5 33.8 + - - +
220A LEU* 5.3 0.2 - - - +
279A ASN 3.9 1.2 + - - -
280A ALA* 1.3 73.7 - - - +
282A SER* 1.3 67.3 + - - +
283A LYS* 2.8 42.8 + - - +
284A ALA* 3.2 19.7 + - + +
285A LEU* 3.3 12.8 + - - +
310A TYR* 3.9 9.6 - - - -
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Residues in contact with SER 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ALA 3.7 3.1 + - - -
281A ASP* 1.3 74.6 + - - +
283A LYS* 1.4 64.0 + - - +
285A LEU* 3.4 11.2 + - - +
286A ASP* 3.1 26.0 + - - +
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Residues in contact with LYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ASP* 2.8 20.1 + - - +
282A SER* 1.4 76.1 + - - +
284A ALA* 1.4 62.5 + - - +
286A ASP* 3.3 3.9 + - - -
287A LEU 3.1 18.0 + - - -
308A HIS* 3.1 17.3 - - + -
309A PRO* 4.2 33.1 + - + +
310A TYR* 3.7 20.8 - - + +
312A GLU* 5.4 4.6 + - - -
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ASN* 4.7 0.4 - - - +
216A LEU* 3.6 12.1 - - + +
220A LEU* 4.7 16.4 - - + -
280A ALA* 5.1 0.9 - - + -
281A ASP* 3.2 21.4 + - + +
283A LYS* 1.4 78.7 - - - +
285A LEU* 1.4 56.6 + - + +
287A LEU* 3.6 1.6 + - - +
288A LEU* 3.0 26.2 + - - +
310A TYR* 3.5 41.8 - - + +
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LEU* 3.9 10.5 - - + -
273A TRP* 3.7 40.5 - - + +
274A ASN* 3.8 15.3 - - + +
277A PHE* 3.8 33.9 - - + +
280A ALA* 3.7 23.3 - - + +
281A ASP 3.3 12.9 + - - +
282A SER* 3.8 11.0 - - - +
283A LYS 3.3 0.2 - - - -
284A ALA* 1.4 72.6 - - - +
286A ASP* 1.3 60.8 + - - +
288A LEU* 3.6 10.6 - - + +
289A ASP* 3.0 27.9 + - - +
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Residues in contact with ASP 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A SER 3.1 13.6 + - - +
283A LYS* 3.3 10.5 + - - +
285A LEU* 1.3 77.0 - - - +
287A LEU* 1.4 59.8 + - - +
289A ASP* 3.4 10.6 - - - +
290A LYS* 3.1 47.8 + - - +
308A HIS* 2.8 25.2 + - + +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 3.7 28.9 - - + -
132A LEU* 4.8 2.9 - - + -
283A LYS 3.1 10.7 + - - +
284A ALA 3.9 4.5 - - - +
286A ASP* 1.4 74.7 - - - +
288A LEU* 1.3 63.8 + - - +
290A LYS* 3.2 2.7 + - - +
291A MET* 3.0 34.5 + - + +
300A ILE* 3.8 28.5 - - + -
305A ALA* 4.0 24.5 - - + +
308A HIS* 3.5 35.1 + - + +
310A TYR* 4.3 7.2 - - + -
311A LEU* 4.1 9.9 - - + -
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLY* 3.1 29.8 - - - +
216A LEU* 3.8 14.8 - - + +
217A ALA* 3.9 13.0 - - + +
220A LEU* 4.3 6.7 - - + -
273A TRP* 3.6 30.5 - - + -
277A PHE* 3.7 19.3 - - + -
284A ALA 3.0 18.4 + - - +
285A LEU* 3.6 19.1 - - + +
287A LEU* 1.3 74.9 - - - +
289A ASP* 1.3 51.2 + - - +
291A MET* 3.1 4.4 + - - +
292A LEU* 2.8 53.0 + - + +
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Residues in contact with ASP 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A LYS* 3.3 20.4 + - - -
273A TRP* 2.8 39.1 + - + +
285A LEU 3.0 11.5 + - - +
286A ASP* 3.4 14.5 - - - +
287A LEU 3.3 0.2 - - - -
288A LEU* 1.3 75.0 - - - +
290A LYS* 1.3 64.2 + - - +
292A LEU 3.5 4.0 - - - +
293A THR* 3.0 23.9 + - - -
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Residues in contact with LYS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ASP* 3.1 41.8 + - - +
287A LEU 3.2 7.7 + - - +
289A ASP* 1.3 80.4 + - - +
291A MET* 1.3 61.3 + - - +
293A THR* 2.9 18.2 + - - -
298A LYS 4.9 0.4 - - - +
299A ARG* 3.7 0.5 - - - +
300A ILE* 3.2 48.8 + - + +
308A HIS* 4.1 16.8 - - + -
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Residues in contact with MET 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 4.3 9.4 - - + -
132A LEU* 4.8 9.6 - - - -
209A ILE* 4.0 14.6 - - + +
210A TRP* 3.9 9.9 - - - -
212A VAL* 4.0 22.0 - - - -
213A GLY* 3.8 24.0 - - - -
216A LEU* 3.4 35.7 - - + -
287A LEU* 3.0 35.3 + - + +
288A LEU* 3.8 3.6 - - - +
290A LYS* 1.3 75.1 - - - +
292A LEU* 1.3 59.4 + - - +
293A THR 3.3 2.2 - - - -
299A ARG* 3.2 25.3 + - - -
300A ILE* 3.6 20.2 - - + -
305A ALA* 5.0 2.0 - - + -
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A TRP* 3.5 55.6 - - + +
213A GLY* 3.7 13.9 - - - +
214A CYS* 3.8 3.8 - - - +
217A ALA* 4.7 0.4 - - + -
225A ILE* 4.0 17.5 - - + -
226A PHE* 4.0 8.1 - - + -
242A LEU* 3.4 25.3 - - + +
273A TRP* 3.7 26.6 - - + -
288A LEU* 2.8 41.0 + - + +
289A ASP* 3.5 7.5 - - - +
290A LYS 3.4 0.2 - - - -
291A MET* 1.3 76.0 - - - +
293A THR* 1.3 58.5 + - - -
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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