Contacts of the helix formed by residues 273 - 290 (chain C) in PDB entry 3L49
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 GLN 273 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C SER* 4.9 0.6 + - - -
271C ALA 5.0 1.8 - - - +
272C GLN* 1.3 78.2 - - - +
274C PRO* 1.3 65.3 - - - +
275C SER* 3.4 2.9 - - - -
276C GLU* 3.2 30.6 + - + +
277C ILE* 3.2 28.2 + - - +
300C ALA* 4.5 3.3 - - + +
301C PRO* 3.3 52.3 + - - +
302C ALA* 5.0 1.4 - - - +
303C VAL* 5.6 5.9 - - - +
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Residues in contact with PRO 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ASP* 5.4 0.4 - - - +
45C TRP* 3.4 59.8 - - + +
48C LYS* 3.7 29.2 - - + +
49C ALA* 3.3 16.9 - - + +
250C ASP 5.1 1.3 - - - +
272C GLN 3.4 12.3 - - - +
273C GLN* 1.3 84.6 - - - +
275C SER* 1.3 61.4 + - - +
277C ILE* 3.5 5.6 + - + +
278C GLY 3.2 18.4 + - - -
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Residues in contact with SER 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LYS* 4.0 24.7 + - - +
52C ALA* 3.3 19.5 - - - +
273C GLN 3.4 1.0 - - - -
274C PRO* 1.3 77.3 - - - +
276C GLU* 1.3 63.2 - - - +
279C LYS* 3.3 21.5 + - - +
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Residues in contact with GLU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C GLN* 3.2 37.8 + - + +
275C SER* 1.3 77.2 - - - +
277C ILE* 1.3 54.7 - - - +
279C LYS* 3.1 28.7 + - - +
280C LEU* 2.8 65.4 + - - +
300C ALA* 3.9 10.9 - - + +
301C PRO* 5.4 1.1 - - + -
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Residues in contact with ILE 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C TRP* 3.7 26.0 - - + -
49C ALA* 5.1 0.4 - - + -
118C VAL* 3.6 30.3 - - + -
129C THR* 3.5 24.8 - - + +
130C THR* 4.0 17.0 - - - +
131C SER* 3.7 23.3 - - - +
272C GLN* 4.3 1.6 - - - +
273C GLN 3.2 20.8 + - - +
274C PRO* 3.7 7.4 - - + +
276C GLU* 1.3 78.3 - - - +
278C GLY* 1.3 56.4 - - - +
280C LEU* 3.4 1.2 + - - -
281C ALA* 2.9 29.8 + - - +
300C ALA* 3.7 16.6 - - + -
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Residues in contact with GLY 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA* 3.7 12.8 - - - -
52C ALA* 3.9 8.5 - - - -
53C GLN* 3.5 28.2 - - - +
118C VAL* 4.9 0.2 - - - -
274C PRO 3.2 10.9 + - - -
276C GLU 3.3 0.2 - - - -
277C ILE* 1.3 77.5 - - - +
279C LYS* 1.3 61.8 + - - +
281C ALA* 3.5 1.8 + - - +
282C VAL* 3.4 27.4 + - - +
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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
----------------------------------------------------------
52C ALA* 4.0 4.7 - - + +
56C GLU* 3.4 43.3 - - + +
59C ARG* 6.1 0.2 - - - +
275C SER 3.3 15.0 + - - +
276C GLU* 3.1 36.7 + - - +
278C GLY* 1.3 75.1 - - - +
280C LEU* 1.3 78.6 + - - +
282C VAL 3.7 0.5 + - - -
283C GLN* 2.7 51.0 + - - +
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Residues in contact with LEU 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C THR* 3.7 16.8 - - + -
276C GLU* 2.8 41.1 + - - +
279C LYS* 1.3 88.6 - - - +
281C ALA* 1.3 66.1 + - - +
283C GLN* 3.3 10.7 + - + +
284C ASN* 3.1 26.9 + - - -
298C THR* 4.2 24.2 - - + -
299C PHE 4.2 6.7 - - - +
300C ALA* 4.0 24.2 - - + +
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Residues in contact with ALA 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLN* 4.9 0.9 - - + -
92C ILE* 4.3 15.3 - - + -
116C PHE* 4.7 4.0 - - + -
117C THR 4.6 2.7 - - - +
118C VAL* 3.7 24.7 - - + -
127C ASN* 5.2 0.4 - - - -
129C THR* 3.4 17.2 + - - +
277C ILE 2.9 17.0 + - - +
278C GLY 3.7 5.4 - - - +
279C LYS 3.4 0.4 - - - -
280C LEU* 1.3 76.7 - - - +
282C VAL* 1.3 61.0 + - - +
284C ASN* 3.2 7.9 + - - +
285C VAL* 3.1 25.0 + - - +
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Residues in contact with VAL 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 4.1 7.9 - - + -
34C ILE* 6.3 0.2 - - + -
53C GLN* 3.7 27.1 - - + +
56C GLU* 3.7 26.9 - - + -
57C ILE* 3.7 26.5 - - + +
60C LEU* 4.1 7.9 - - + -
92C ILE* 3.8 17.7 - - + -
278C GLY 3.4 13.8 + - - +
279C LYS 3.9 1.1 - - - +
280C LEU 3.3 0.4 - - - -
281C ALA* 1.3 72.6 - - - +
283C GLN* 1.3 60.0 + - - +
285C VAL* 3.2 10.1 + - + +
286C ALA* 2.9 28.4 + - - +
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Residues in contact with GLN 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLU* 3.3 25.2 + - - +
59C ARG* 4.3 7.5 + - - +
60C LEU* 3.5 18.2 - - - +
279C LYS* 2.7 40.7 + - - +
280C LEU* 3.3 18.8 - - + +
282C VAL* 1.3 77.6 - - - +
284C ASN* 1.3 57.9 + - - +
286C ALA* 3.4 5.5 + - - +
287C ARG* 3.0 30.7 + - - +
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Residues in contact with ASN 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C PHE* 3.5 9.9 - - + -
127C ASN* 2.9 33.7 + - + +
129C THR* 3.1 12.5 + - - -
280C LEU 3.1 14.0 + - - -
281C ALA 3.2 8.0 + - - +
283C GLN* 1.3 76.3 - - - +
285C VAL* 1.3 63.1 + - - +
287C ARG* 4.3 5.5 - - - -
288C HIS* 3.2 24.6 + - - +
294C VAL* 3.5 21.4 - - + +
295C LYS 5.2 1.2 + - - -
298C THR* 2.8 30.7 + - - +
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Residues in contact with VAL 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 4.4 3.1 - - + -
34C ILE* 3.9 24.0 - - + -
90C ALA* 3.7 24.7 - - + -
92C ILE* 3.8 23.6 - - + -
116C PHE* 3.5 32.1 - - + -
281C ALA 3.1 14.6 + - - +
282C VAL* 3.2 10.5 + - + +
284C ASN* 1.3 75.5 - - - +
286C ALA* 1.3 63.2 + - - +
288C HIS* 3.4 2.4 + - - +
289C LEU* 3.1 34.6 + - + +
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Residues in contact with ALA 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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28C SER* 3.7 30.8 + - - +
29C LEU* 3.7 21.9 - - + +
60C LEU* 4.0 12.6 - - + -
282C VAL 2.9 16.7 + - - +
283C GLN* 3.4 7.6 + - - +
285C VAL* 1.3 75.4 - - - +
287C ARG* 1.3 61.8 + - - +
289C LEU* 3.8 2.5 + - - +
290C ALA* 3.4 20.8 + - - +
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Residues in contact with ARG 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C GLN 3.0 17.4 + - - +
284C ASN* 3.8 6.1 - - - +
286C ALA* 1.3 76.7 - - - +
288C HIS* 1.3 58.3 + - - +
290C ALA* 3.0 18.6 + - - +
292C GLN* 3.2 64.9 + - - +
293C GLU* 2.5 37.9 + - - +
294C VAL* 3.8 16.8 - - + +
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Residues in contact with HIS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C PRO* 3.6 28.8 - - + +
116C PHE* 3.6 17.3 - + + -
126C ILE* 3.7 25.8 - - + +
284C ASN 3.2 15.2 + - - +
285C VAL 3.9 1.1 - - - +
287C ARG* 1.3 79.9 - - - +
289C LEU* 1.3 76.3 + - + +
291C GLY* 2.9 20.4 + - - -
292C GLN 3.9 13.4 + - - -
294C VAL* 4.1 9.5 - - + +
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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
----------------------------------------------------------
28C SER 5.7 2.5 - - - +
29C LEU* 3.9 25.8 - - + -
32C LYS* 4.3 22.8 + - + +
34C ILE* 4.0 11.2 - - + -
89C ASP* 3.6 43.1 - - + +
90C ALA* 4.7 2.9 - - + -
114C PRO* 4.4 2.9 - - + -
285C VAL* 3.1 19.6 + - + +
286C ALA* 4.3 3.6 - - - +
288C HIS* 1.3 91.4 - - + +
290C ALA* 1.3 57.1 + - - +
291C GLY 3.1 5.0 + - - -
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Residues in contact with ALA 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C SER* 5.6 5.4 + - - +
286C ALA 3.4 12.8 + - - +
287C ARG 3.0 11.9 + - - +
289C LEU* 1.3 76.4 - - - +
291C GLY* 1.3 61.7 + - - +
292C GLN* 3.4 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
------------------------------------------------------------
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