Contacts of the helix formed by residues 272 - 290 (chain C) in PDB entry 4LCC
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 272 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 4.3 21.8 + - - +
268C ASN* 2.7 35.9 + - - +
269C TRP 3.2 0.4 + - - -
271C GLU* 1.3 94.8 - - + +
273C GLU* 1.3 67.4 + - - +
274C CYS 3.3 1.5 + - - -
275C ILE* 3.3 6.3 + - - +
276C ALA* 3.3 21.7 + - - +
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Residues in contact with GLU 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY* 3.8 7.4 - - - -
29A PHE 3.2 31.2 + - - +
30A ASN* 3.9 13.9 - - - +
93A SER* 3.2 32.0 + - - +
268C ASN* 3.2 1.7 + - - +
269C TRP* 2.9 45.8 + - + +
272C GLU* 1.3 77.3 - - - +
274C CYS* 1.3 60.8 + - - +
276C ALA* 3.5 9.9 + - - +
277C TRP* 2.9 39.6 + - - +
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Residues in contact with CYS 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 3.9 15.0 - - - -
210C GLY* 3.9 0.9 - - - -
211C CYS* 2.0 55.9 - - - -
269C TRP* 2.6 48.6 + - + +
270C LEU* 3.5 7.9 - - - +
273C GLU* 1.3 70.3 - - - +
275C ILE* 1.3 59.1 + - - +
277C TRP* 2.9 14.1 + - - +
278C LEU* 2.8 24.9 + - - +
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Residues in contact with ILE 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C CYS* 3.4 29.1 - - + -
212C GLU 4.7 6.5 - - - +
213C LEU* 4.4 8.7 - - + -
219C ILE* 3.6 37.0 - - + -
270C LEU 3.8 3.1 - - - +
271C GLU 3.5 24.0 - - - +
272C GLU 3.3 5.4 + - - +
274C CYS* 1.3 74.7 - - - +
276C ALA* 1.3 57.6 + - - +
278C LEU* 3.2 7.0 + - + +
279C LYS* 2.9 58.1 + - + +
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Residues in contact with ALA 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C GLU 3.3 9.5 + - - +
273C GLU* 3.5 16.4 - - - +
274C CYS 3.2 0.2 - - - -
275C ILE* 1.3 80.3 - - - +
277C TRP* 1.3 63.0 + - + +
279C LYS* 3.3 9.3 + - - +
280C ARG* 3.0 23.4 + - - +
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Residues in contact with TRP 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A SER* 3.1 24.6 + - - -
94A ASN* 4.2 3.1 - - - -
118C LEU* 4.1 13.5 - - + -
120C TYR* 5.7 2.5 - + - -
167C LEU* 5.8 1.1 - - + -
171C HIS* 4.2 16.6 - + - -
175C TYR* 3.7 24.7 - + - -
269C TRP* 4.5 13.9 - + - +
273C GLU* 2.9 47.2 + - + +
274C CYS* 2.9 10.4 + - - +
276C ALA* 1.3 78.8 - - + +
278C LEU* 1.3 62.7 + - - +
280C ARG* 3.2 37.5 + - - +
281C PHE* 3.2 51.3 + + + -
401C 1XL 4.4 11.8 + - - -
402C SO4 3.6 18.6 - - - -
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Residues in contact with LEU 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C HIS* 4.2 2.7 - - + +
117C SER* 3.7 47.1 - - - +
118C LEU* 3.7 16.3 - - + +
141C VAL* 3.9 16.6 - - + -
211C CYS* 4.0 14.6 - - - +
212C GLU* 4.4 0.9 - - - -
213C LEU* 4.1 26.2 - - + +
274C CYS 2.8 11.4 + - - +
275C ILE* 3.4 11.9 - - + +
277C TRP* 1.3 77.2 - - - +
279C LYS* 1.3 63.6 + - + +
280C ARG 3.2 0.7 + - - -
281C PHE* 3.3 6.2 + - + +
282C LEU* 3.1 38.1 + - + +
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Residues in contact with LYS 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C LEU* 3.6 32.5 - - + -
219C ILE* 6.2 0.2 - - - -
275C ILE* 2.9 35.1 + - + +
276C ALA* 3.3 6.9 + - - +
278C LEU* 1.3 75.8 - - + +
280C ARG* 1.3 60.6 + - - +
282C LEU* 3.6 13.6 + - + +
283C GLU* 3.4 25.1 + - - +
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Residues in contact with ARG 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A SER* 5.3 0.8 + - - -
166C ASN 5.9 0.2 + - - -
167C LEU* 4.0 19.7 - - - +
276C ALA 3.0 13.1 + - - +
277C TRP* 3.4 34.8 - - - +
278C LEU 3.1 0.4 - - - -
279C LYS* 1.3 76.4 - - - +
281C PHE* 1.3 68.2 + - + +
283C GLU* 3.5 6.3 + - - +
284C TYR* 3.0 58.6 + - + -
402C SO4 2.7 43.2 + - - -
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Residues in contact with PHE 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 4.1 24.0 - - + -
120C TYR* 3.7 23.3 - - - -
141C VAL* 4.9 9.6 - - + -
146C ILE* 4.4 6.5 - - + -
147C THR* 6.0 2.7 - - + -
162C TRP* 3.1 21.6 - - + -
163C MET* 3.5 29.4 - - + -
167C LEU* 4.7 11.7 - - + -
171C HIS* 6.1 3.4 - + - -
277C TRP* 3.2 52.3 + + + -
278C LEU* 3.8 5.4 - - - +
280C ARG* 1.3 78.8 - - + +
282C LEU* 1.3 56.1 + - - +
284C TYR* 3.1 11.9 + + - +
285C GLY 2.6 31.5 + - - -
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Residues in contact with LEU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C HIS* 4.0 36.6 - - + +
141C VAL* 4.0 18.4 - - + -
142C ASP* 4.7 0.2 - - - +
213C LEU* 5.9 4.5 - - + -
278C LEU* 3.1 24.0 - - + +
279C LYS* 3.8 16.4 - - + +
280C ARG 3.2 0.6 - - - -
281C PHE* 1.3 74.2 - - - +
283C GLU* 1.3 58.4 + - + +
285C GLY 2.9 0.6 + - - +
286C LYS* 2.5 39.9 + - - -
289C LEU* 3.6 28.0 - - + -
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Residues in contact with GLU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C LYS 3.4 11.7 + - - +
280C ARG* 3.7 10.5 - - - +
282C LEU* 1.3 79.8 - - + +
284C TYR* 1.3 68.0 + - + +
286C LYS* 3.9 16.8 + - - +
287C ASP* 5.0 1.4 - - - +
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Residues in contact with TYR 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C TRP* 3.7 24.7 - - + +
163C MET* 4.8 2.0 - - - -
166C ASN* 3.1 49.0 + - + +
167C LEU* 3.3 28.9 - - + +
280C ARG* 3.0 55.6 + - + +
281C PHE* 3.1 18.8 + + - +
282C LEU 3.0 0.6 - - - -
283C GLU* 1.3 86.3 - - + +
285C GLY* 1.3 56.9 + - - +
286C LYS 3.3 2.3 + - - -
287C ASP* 4.0 10.7 - - - +
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Residues in contact with GLY 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C TRP* 3.5 31.9 - - - -
281C PHE 2.6 15.9 + - - -
282C LEU 3.2 3.4 - - - -
284C TYR* 1.3 71.5 - - - +
286C LYS* 1.3 63.9 + - - +
287C ASP* 3.0 4.7 + - - -
288C ALA* 3.2 4.5 + - - +
289C LEU* 3.0 31.1 + - - +
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Residues in contact with LYS 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C LEU 2.5 19.2 + - - +
283C GLU* 3.9 18.6 - - - +
284C TYR 3.3 3.0 + - - -
285C GLY* 1.3 72.5 - - - +
287C ASP* 1.3 65.5 + - - +
289C LEU* 4.2 2.5 - - - -
290C GLN* 3.2 43.4 + - - +
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Residues in contact with ASP 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C GLU 5.0 1.0 - - - +
284C TYR 4.0 12.7 - - - +
285C GLY* 3.0 2.2 - - - -
286C LYS* 1.3 83.8 + - - +
288C ALA* 1.3 63.9 + - + +
290C GLN* 4.8 0.2 - - - +
291C ARG* 3.6 18.7 + - - +
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C HIS* 6.2 2.5 - - + -
162C TRP* 4.6 19.7 - - + +
285C GLY 3.2 5.5 + - - +
287C ASP* 1.3 80.3 - - + +
289C LEU* 1.3 69.5 + - + +
291C ARG* 2.9 46.3 + - - +
319C TYR* 3.3 4.7 - - - +
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Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C HIS* 5.3 4.9 - - + +
141C VAL* 4.5 9.2 - - + +
142C ASP* 4.0 20.0 - - + +
144C HIS* 4.1 26.0 - - + +
162C TRP* 4.7 16.2 - - + -
282C LEU* 3.6 33.4 - - + -
285C GLY* 3.0 24.6 + - - +
286C LYS* 4.9 2.0 - - - +
288C ALA* 1.3 79.4 - - + +
290C GLN* 1.3 62.9 + - + +
291C ARG 3.4 1.8 + - - +
319C TYR* 3.5 28.3 + - - +
320C PRO* 5.3 4.3 - - - +
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Residues in contact with GLN 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C HIS* 5.9 4.8 + - - +
286C LYS* 3.2 35.4 + - - +
287C ASP 4.4 0.7 - - - -
288C ALA 3.3 0.4 - - - -
289C LEU* 1.3 78.9 - - + +
291C ARG* 1.3 64.4 + - - +
292C THR* 3.8 8.1 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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