Contacts of the helix formed by residues 280 - 291 (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 GLU 280 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97L GLU* 3.6 2.5 - - - +
118L ASP* 4.3 6.5 - - - +
121L ASP* 3.4 17.6 - - - +
135L ILE* 4.4 7.9 - - + -
248L MET* 3.9 20.1 - - - +
275L LEU* 3.2 16.9 - - + +
276L ARG* 2.5 74.5 + - - +
278L LEU 3.6 0.8 - - - -
279L TYR* 1.3 89.7 - - + +
281L CYS* 1.3 66.3 + - - +
283L PRO* 3.6 3.5 - - - +
284L MET* 2.9 33.6 + - - +
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Residues in contact with CYS 281 (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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248L MET* 4.8 2.0 - - - -
275L LEU* 4.0 15.0 - - - -
276L ARG 3.3 22.4 + - - -
277L LEU* 3.8 11.9 - - + +
280L GLU* 1.3 72.4 - - - +
282L ASN* 1.3 57.5 - - - +
284L MET* 2.9 6.9 + - - +
285L ALA* 2.5 38.9 + - - +
302L VAL* 3.7 17.0 - - + -
314L ALA* 4.1 8.7 - - + -
316L VAL* 3.2 34.1 - - + -
318L LEU* 5.5 0.3 - - - +
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Residues in contact with ASN 282 (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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139L TYR* 3.4 22.4 + - - +
154L GLN 4.4 1.6 - - - +
155L PRO* 4.8 0.3 - - - +
156L GLY* 3.5 25.9 + - - +
159L LEU* 3.7 9.8 - - + +
277L LEU* 3.1 25.0 + - - +
278L LEU* 3.8 13.5 - - - +
281L CYS* 1.3 75.5 - - - +
283L PRO* 1.3 68.4 - - + +
285L ALA* 4.2 0.9 - - - -
286L TYR* 2.7 34.0 + - - +
302L VAL* 3.3 33.5 + - - +
303L LEU* 3.7 2.3 - - - +
305L VAL 5.5 0.8 + - - +
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Residues in contact with PRO 283 (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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135L ILE* 3.4 30.1 - - + -
136L PHE 3.8 26.0 - - - +
137L GLY* 4.1 6.1 - - - +
159L LEU* 4.5 1.1 - - + -
162L ALA* 4.3 12.9 - - + +
163L GLY* 4.6 3.8 - - - +
278L LEU 3.5 18.6 - - - +
279L TYR* 4.0 3.1 - - - -
280L GLU 3.6 10.3 - - - +
281L CYS 3.4 3.8 - - - -
282L ASN* 1.3 93.6 - - + +
284L MET* 1.3 57.8 + - - +
286L TYR* 3.2 2.1 + - - +
287L VAL* 3.0 34.3 + - - +
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Residues in contact with MET 284 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135L ILE* 3.6 24.9 - - + -
164L TYR* 3.8 25.8 - - + -
248L MET* 3.5 43.7 - - + -
249L VAL* 3.6 21.5 - - + -
252L VAL* 3.5 27.4 - - + +
280L GLU 2.9 24.0 + - - +
281L CYS 2.9 6.0 + - - +
283L PRO* 1.3 74.2 - - - +
285L ALA* 1.3 60.7 + - - +
287L VAL* 3.6 4.1 + - - +
288L MET* 3.2 28.6 + - - +
318L LEU* 4.3 9.0 - - + -
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Residues in contact with ALA 285 (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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281L CYS 2.5 19.9 + - - +
282L ASN 3.8 2.0 - - - +
284L MET* 1.3 72.1 - - - +
286L TYR* 1.3 58.1 + - - +
288L MET* 3.6 2.5 + - - +
289L GLU* 3.1 31.7 + - - +
295L ALA* 3.4 27.0 - - + +
302L VAL* 3.4 30.3 - - + -
303L LEU* 4.1 9.1 - - + +
318L LEU* 4.7 3.3 - - + +
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Residues in contact with TYR 286 (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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156L GLY 4.0 7.2 - - - -
157L ARG* 5.5 3.1 - - - -
159L LEU* 3.5 49.5 + - + -
160L VAL 4.2 5.2 + - - -
161L ALA 4.9 1.1 - - - -
162L ALA* 4.0 14.1 - - + -
176L ALA* 3.3 29.4 - - + -
177L MET* 3.5 21.7 - - - -
178L ASP* 3.8 2.8 + - - -
282L ASN 2.7 18.9 + - - +
283L PRO 3.6 2.7 - - - +
285L ALA* 1.3 76.7 - - - +
287L VAL* 1.3 65.7 + - - +
289L GLU* 4.1 0.7 - - - +
290L LYS* 3.1 53.4 + - + +
303L LEU* 3.8 17.0 - - + +
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Residues in contact with VAL 287 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162L ALA 4.6 0.4 - - - -
163L GLY* 4.1 22.9 - - - +
164L TYR* 4.5 15.0 - - + -
174L VAL* 4.4 10.1 - - + -
176L ALA* 3.6 22.9 - - + +
181L VAL* 3.6 13.5 - - + +
252L VAL* 6.3 1.1 - - + -
256L LEU* 4.2 24.2 - - + -
283L PRO 3.0 21.0 + - - +
284L MET* 3.9 6.1 - - - +
286L TYR* 1.3 73.4 - - + +
288L MET* 1.3 72.5 + - + +
290L LYS* 3.2 4.3 + - - +
291L ALA* 2.9 20.8 + - - +
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Residues in contact with MET 288 (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* 3.7 21.5 - - - -
252L VAL* 4.1 16.8 - - + +
255L THR* 4.7 1.1 - - + -
256L LEU* 3.3 53.2 - - + +
284L MET 3.2 18.4 + - - +
285L ALA* 3.7 6.5 - - - +
287L VAL* 1.3 81.4 - - + +
289L GLU* 1.3 52.0 + - - +
291L ALA* 2.7 24.9 + - - +
292L GLY 3.0 0.2 + - - -
293L GLY* 2.7 22.8 + - - -
294L MET 4.3 14.1 - - - +
318L LEU* 3.9 24.7 - - + -
319L GLY* 4.0 17.7 - - - +
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Residues in contact with GLU 289 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157L ARG* 2.5 33.5 + - - -
285L ALA 3.1 13.7 + - - +
286L TYR 4.2 2.0 - - - +
288L MET* 1.3 79.4 - - - +
290L LYS* 1.3 61.2 + - + +
292L GLY* 3.1 15.4 + - - -
293L GLY 3.7 18.8 - - - +
294L MET* 4.9 5.2 - - - -
295L ALA* 4.5 10.8 + - - +
301L ALA* 4.5 9.2 - - - +
303L LEU* 3.2 27.7 - - + +
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Residues in contact with LYS 290 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176L ALA* 4.4 2.5 - - + -
177L MET 3.7 13.7 - - - +
178L ASP* 3.7 31.4 + - - +
180L GLY* 4.8 10.9 - - - +
181L VAL* 3.8 15.7 - - + +
199L ASP* 5.4 0.5 - - - +
200L VAL 4.5 0.9 - - - +
201L LYS* 4.1 13.2 + - - -
286L TYR* 3.1 59.2 + - + +
287L VAL 3.6 4.7 - - - +
288L MET 3.1 0.6 - - - -
289L GLU* 1.3 76.2 - - + +
291L ALA* 1.3 57.5 + - - +
292L GLY 3.0 7.8 + - - -
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Residues in contact with ALA 291 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181L VAL* 3.9 7.2 - - + +
200L VAL 3.5 21.3 - - - +
201L LYS* 3.5 10.6 - - - +
202L ILE* 3.0 27.8 + - + +
256L LEU* 3.6 28.5 - - + -
287L VAL 2.9 12.4 + - - +
288L MET* 2.7 9.4 + - - +
290L LYS* 1.3 75.5 - - - +
292L GLY* 1.3 61.9 + - - +
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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