Contacts of the helix formed by residues 270 - 284 (chain C) in PDB entry 3B1D
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 270 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C GLU* 6.0 0.2 - - - +
241C THR 3.6 10.9 + - - -
242C LYS* 4.6 3.6 + - - +
269C VAL* 1.3 80.0 - - - +
271C SER* 1.3 64.8 + - - +
272C LEU* 3.9 4.5 + - - +
273C GLY* 3.0 25.3 + - - -
274C TYR* 3.2 12.6 + - - -
240D GLY 3.3 15.3 - - - -
241D THR* 4.4 5.8 - - - -
242D LYS* 3.6 24.6 - - - +
270D SER* 4.3 11.9 + - - -
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Residues in contact with SER 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C TYR* 3.3 34.6 + - - -
59C GLY 3.7 1.2 + - - -
61C THR* 2.7 37.9 + - - +
269C VAL 3.9 0.8 + - - -
270C SER* 1.3 72.3 - - - +
272C LEU* 1.3 57.8 + - - +
274C TYR* 3.2 7.2 + - - +
275C ILE* 3.0 32.9 + - - +
240D GLY* 2.9 22.8 + - - -
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Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 3.7 36.3 - - + -
52C TYR* 4.6 14.1 - - + -
241C THR* 4.3 18.6 - - + +
270C SER* 3.3 6.2 + - - +
271C SER* 1.3 75.2 - - - +
273C GLY* 1.3 60.1 + - - +
275C ILE* 4.1 22.0 - - + +
276C ALA* 2.8 35.7 + - + +
52D TYR* 3.8 30.1 - - + -
240D GLY 4.7 0.6 + - - -
272D LEU* 4.0 29.2 - - + -
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Residues in contact with GLY 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C THR* 3.1 25.1 + - - -
242C LYS 4.0 2.2 - - - -
243C ASN* 3.3 31.7 + - - +
269C VAL* 4.1 0.2 - - - -
270C SER* 3.0 18.0 + - - -
272C LEU* 1.3 78.5 - - - +
274C TYR* 1.3 61.4 + - - +
276C ALA* 4.5 0.7 - - - +
277C THR* 3.5 12.1 + - - -
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Residues in contact with TYR 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C THR* 3.8 18.9 + - - -
62C TYR* 3.5 30.3 - - - +
63C ALA* 3.6 26.6 + - + +
64C SER 5.9 0.4 - - - +
67C LEU* 3.4 29.8 - - + +
90C PHE* 4.4 10.2 - - + +
243C ASN* 4.0 7.0 - - - +
267C HIS 5.0 2.6 + - - -
268C GLU* 4.8 2.4 - - - -
269C VAL* 3.6 51.7 + - + +
270C SER 3.2 13.7 + - - -
271C SER* 3.2 5.4 + - - +
273C GLY* 1.3 77.1 - - - +
275C ILE* 1.3 65.2 + - + +
278C GLU* 3.2 24.4 + - - +
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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
----------------------------------------------------------
48C ALA* 3.7 33.2 - - + +
52C TYR* 3.5 39.3 - - + -
55C GLN* 4.1 11.0 - - - +
271C SER* 3.0 23.3 + - - +
272C LEU* 3.3 11.9 + - + +
274C TYR* 1.3 78.4 - - + +
276C ALA* 1.3 56.0 + - - +
278C GLU* 3.4 6.3 + - - +
279C THR* 2.8 38.9 + - - +
16D HIS* 6.3 2.9 - - + -
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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
----------------------------------------------------------
45C VAL* 4.1 16.8 - - + +
48C ALA* 5.6 0.7 - - - -
49C ILE* 5.9 0.2 - - + -
238C ILE* 3.8 12.5 - - + +
241C THR* 3.8 30.7 - - + +
272C LEU* 2.8 26.1 + - + +
273C GLY 4.5 0.4 - - - +
275C ILE* 1.3 76.3 - - - +
277C THR* 1.3 56.1 + - - +
279C THR* 3.4 5.0 + - - -
280C ALA* 2.9 31.7 + - - +
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Residues in contact with THR 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 3.9 14.6 - - + -
71C VAL* 4.5 5.2 - - + -
90C PHE* 4.9 2.2 - - + -
232C ALA* 4.1 28.4 + - + +
233C THR* 5.4 1.2 - - - +
238C ILE* 4.3 4.1 - - - +
241C THR* 5.3 1.4 + - - -
243C ASN* 3.5 27.5 + - - +
244C SER* 5.7 1.3 - - - +
245C TYR* 5.3 4.0 - - + -
273C GLY 3.5 17.7 + - - -
274C TYR 4.1 1.8 - - - -
275C ILE 3.4 0.2 - - - -
276C ALA* 1.3 74.3 - - - +
278C GLU* 1.3 67.2 + - - +
280C ALA* 3.3 1.2 + - - +
281C TYR* 3.0 40.3 + - + +
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Residues in contact with GLU 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C SER* 4.0 5.0 + - - -
66C GLU* 3.3 17.7 - - - +
67C LEU* 3.7 40.7 + - + +
70C ALA* 3.9 7.0 - - + -
274C TYR 3.2 16.1 + - - +
275C ILE* 3.9 6.4 - - - +
277C THR* 1.3 79.3 - - - +
279C THR* 1.3 58.9 + - - +
281C TYR* 3.9 1.0 - - - +
282C ARG* 2.8 61.9 + - - +
16D HIS* 5.1 5.0 + - - -
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Residues in contact with THR 279 (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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42C MET* 3.8 0.3 - - - +
44C GLU* 3.4 43.7 - - + +
45C VAL* 3.7 10.5 - - + +
48C ALA* 3.5 17.2 - - + +
275C ILE* 2.8 23.9 + - - +
276C ALA 3.7 3.8 - - - -
278C GLU* 1.3 77.5 - - - +
280C ALA* 1.3 62.6 + - - +
283C TYR* 3.0 41.1 + - + +
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Residues in contact with ALA 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C MET* 3.8 14.6 - - - -
45C VAL* 4.1 3.6 - - + +
74C TRP* 4.5 0.3 - - - -
232C ALA* 4.2 3.8 - - + -
236C PHE* 3.5 41.5 - - + -
238C ILE* 4.2 9.2 - - + -
276C ALA 2.9 18.3 + - - +
277C THR 3.8 3.4 - - - +
278C GLU 3.3 0.2 - - - -
279C THR* 1.3 76.7 - - - +
281C TYR* 1.3 57.6 + - - +
284C GLY* 2.8 30.8 + - - -
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Residues in contact with TYR 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ALA* 4.0 15.4 - - + +
71C VAL* 4.0 25.1 - - + -
74C TRP* 3.3 73.3 + + + +
203C GLN* 4.5 2.4 + - - -
204C ASP* 4.4 3.7 + - - -
231C SER 3.3 13.9 + - - -
232C ALA* 3.9 20.6 - - + -
236C PHE* 4.1 10.1 - + - -
245C TYR* 2.7 44.6 + + - -
277C THR* 3.0 23.8 + - + +
278C GLU 4.0 2.5 - - - +
280C ALA* 1.3 79.1 - - - +
282C ARG* 1.3 59.8 + - - +
284C GLY 4.5 0.7 + - - -
285C LYS* 4.7 4.9 - - - +
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Residues in contact with ARG 282 (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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66C GLU* 2.9 37.8 + - - +
69C GLN* 4.2 9.7 - - - +
70C ALA* 4.0 17.0 - - + +
73C ASP* 5.0 7.1 + - - -
278C GLU* 2.8 46.3 + - - +
281C TYR* 1.3 77.5 - - - +
283C TYR* 1.3 103.3 + - + +
284C GLY 3.8 0.2 - - - -
285C LYS* 5.9 2.5 - - - +
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Residues in contact with TYR 283 (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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4C TYR* 5.4 2.3 + - - -
42C MET* 3.6 12.9 - - + +
44C GLU* 4.0 26.0 - - + +
279C THR* 3.0 40.2 + - + +
282C ARG* 1.3 111.2 - - + +
284C GLY* 1.3 62.0 + - - +
285C LYS 3.5 3.2 + - - -
286C PRO* 3.8 11.9 - - - +
287C TRP* 5.2 1.0 + - - +
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Residues in contact with GLY 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C MET* 3.5 19.5 - - - -
74C TRP* 5.1 0.2 - - - -
236C PHE* 3.4 15.4 - - - -
280C ALA 2.8 20.3 + - - -
281C TYR 4.5 0.8 + - - -
282C ARG 3.8 1.0 - - - -
283C TYR* 1.3 78.7 - - - +
285C LYS* 1.3 65.3 + - - +
286C PRO* 3.4 1.1 - - - -
287C TRP* 3.2 6.2 + - - +
288C LEU* 3.0 19.2 + - - +
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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