Contacts of the helix formed by residues 320 - 333 (chain L) in PDB entry 2FIE
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 SER 320 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202L ILE* 3.8 4.7 - - - +
203L LYS 3.3 15.4 + - - -
204L LYS 3.3 18.2 - - - -
205L LYS* 3.8 0.2 - - - -
206L GLY 3.6 4.3 + - - -
259L GLY* 3.6 6.8 - - - -
260L GLY 2.7 30.8 + - - -
319L GLY* 1.3 70.1 - - - -
321L PRO* 1.3 59.5 - - - -
323L ASP* 2.9 25.9 + - - +
324L VAL* 2.9 31.2 + - - +
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Residues in contact with PRO 321 (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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202L ILE* 4.4 0.7 - - + -
203L LYS 3.8 9.2 - - - +
204L LYS* 3.7 13.5 - - + +
292L GLY 3.6 24.5 - - - +
293L GLY* 4.0 10.3 - - - -
294L MET* 4.1 21.5 - - + -
319L GLY 3.4 4.9 - - - +
320L SER* 1.3 85.2 - - - +
322L ASP* 1.3 60.0 + - - +
324L VAL* 2.8 1.8 + - + +
325L LEU* 2.6 45.5 + - + +
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Residues in contact with ASP 322 (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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204L LYS* 3.2 40.0 + - - +
205L LYS* 3.9 30.9 + - + +
321L PRO* 1.3 82.8 - - - +
323L ASP* 1.3 56.5 + - - +
325L LEU* 3.7 10.5 + - - +
326L GLU* 3.0 28.9 + - - +
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Residues in contact with ASP 323 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205L LYS* 3.4 11.7 + - - +
206L GLY* 2.8 29.4 + - - -
226L TYR* 3.4 16.0 + - - +
240L TYR* 2.8 35.0 + - - -
260L GLY* 3.9 6.1 - - - +
261L ILE* 3.5 24.0 - - + +
320L SER* 2.9 19.6 + - - +
322L ASP* 1.3 73.3 - - - +
324L VAL* 1.3 64.4 + - - +
326L GLU* 3.5 6.0 + - - +
327L PHE 3.1 17.5 + - - -
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Residues in contact with VAL 324 (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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261L ILE* 4.0 10.1 - - + -
294L MET* 3.6 33.4 - - + +
296L THR* 3.8 29.2 - - + -
317L ILE* 4.5 7.0 - - + +
318L LEU* 3.8 6.3 - - - +
319L GLY* 3.5 32.3 - - - +
320L SER 2.9 17.8 + - - +
321L PRO 2.8 6.5 + - - +
323L ASP* 1.3 73.4 - - - +
325L LEU* 1.3 61.2 + - - +
327L PHE* 3.2 3.8 + - - +
328L LEU* 2.9 28.3 + - + +
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Residues in contact with LEU 325 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294L MET* 3.8 26.2 - - + -
321L PRO* 2.6 32.4 + - + +
322L ASP* 3.9 9.4 - - - +
324L VAL* 1.3 74.2 - - - +
326L GLU* 1.3 55.9 + - - +
328L LEU* 3.1 12.9 + - + +
329L LYS* 2.8 29.3 + - - +
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Residues in contact with GLU 326 (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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205L LYS* 3.1 27.4 + - - -
226L TYR* 4.0 13.1 - - + -
229L ARG* 4.8 15.9 + - - +
230L LYS* 3.3 26.8 + - - +
234L PRO* 6.0 1.4 - - - +
322L ASP 3.0 17.9 + - - +
323L ASP* 3.6 7.9 - - - +
324L VAL 3.2 0.2 - - - -
325L LEU* 1.3 75.7 - - - +
327L PHE* 1.3 62.6 + - - +
329L LYS* 3.2 29.2 + - - +
330L VAL* 3.1 26.8 + - + +
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Residues in contact with PHE 327 (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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222L ALA* 4.7 3.6 - - + -
223L VAL* 4.2 25.1 - - + -
226L TYR* 3.8 41.6 - + + -
261L ILE* 4.1 5.8 - - + -
263L LEU* 4.2 15.7 - - + -
265L PRO* 5.2 3.1 - - + -
296L THR* 4.8 0.7 - - + -
298L GLY* 4.8 2.5 - - - -
317L ILE* 3.6 44.0 - - + -
323L ASP 3.1 13.2 + - - +
324L VAL 3.5 8.3 - - - +
326L GLU* 1.3 77.1 - - - +
328L LEU* 1.3 66.3 + - + +
330L VAL* 3.1 4.7 + - - +
331L TYR* 2.8 64.0 + + + +
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Residues in contact with LEU 328 (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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294L MET* 4.1 25.4 - - + -
296L THR* 3.9 33.4 - - + +
298L GLY* 3.8 27.4 - - - +
324L VAL* 2.9 17.5 + - + +
325L LEU* 3.1 17.5 + - + +
327L PHE* 1.3 79.2 - - + +
329L LYS* 1.3 59.6 + - - +
330L VAL 3.3 0.2 - - - -
331L TYR* 3.7 7.6 - - + +
332L GLU* 3.0 36.9 + - - +
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Residues in contact with LYS 329 (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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229L ARG* 5.0 14.8 - - - +
325L LEU 2.8 11.1 + - - +
326L GLU* 3.3 31.6 - - - +
328L LEU* 1.3 76.4 - - - +
330L VAL* 1.3 61.5 - - - +
332L GLU* 3.4 12.4 + - - +
333L LYS* 3.3 18.7 + - - +
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Residues in contact with VAL 330 (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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222L ALA* 3.4 30.4 - - - +
225L GLU* 4.1 19.7 - - - +
226L TYR* 4.1 24.9 - - + +
229L ARG* 4.3 26.7 - - - +
326L GLU* 3.3 16.6 - - + +
327L PHE* 3.1 8.4 + - + +
329L LYS* 1.3 78.0 - - + +
331L TYR* 1.3 64.4 + - - +
333L LYS* 3.2 14.2 + - - +
334L HIS* 3.2 16.2 + - + -
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Residues in contact with TYR 331 (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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220L ASP* 4.5 12.6 - - - -
222L ALA* 3.8 18.0 - - + +
223L VAL* 6.1 0.2 - - + -
265L PRO* 6.5 0.7 - - + -
297L THR 4.7 3.8 + - - -
298L GLY* 3.4 37.0 - - - -
299L LYS* 4.0 25.8 - - + +
327L PHE* 2.8 46.2 + + + +
328L LEU* 3.7 11.7 - - + +
330L VAL* 1.3 72.9 - - - +
332L GLU* 1.3 65.7 + - + +
334L HIS* 3.2 14.0 + - - +
335L SER* 3.2 30.4 + - - -
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Residues in contact with GLU 332 (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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328L LEU* 3.0 23.7 + - - +
329L LYS* 3.5 10.3 - - - +
330L VAL 3.2 0.2 - - - -
331L TYR* 1.3 83.4 - - + +
333L LYS* 1.3 60.5 + - - +
334L HIS 3.3 0.7 + - - -
335L SER* 3.4 22.5 + - - +
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Residues in contact with LYS 333 (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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225L GLU* 3.6 30.3 + - - +
229L ARG* 4.1 11.6 - - - +
329L LYS 3.3 9.8 + - - +
330L VAL* 3.2 14.1 + - - +
331L TYR 3.1 0.6 - - - -
332L GLU* 1.3 78.7 - - - +
334L HIS* 1.3 72.7 + - + +
335L SER 3.6 2.1 - - - +
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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