Contacts of the helix formed by residues 272 - 281 (chain A) in PDB entry 3SPY
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 ASP 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A GLY 3.2 3.6 - - - +
217A ASN* 2.9 30.0 + - - +
218A VAL* 3.1 22.1 + - + -
219A GLU* 3.0 35.6 + - + +
220A SER* 4.0 2.9 + - - -
270A VAL* 3.8 5.1 + - - +
271A LEU* 1.3 72.4 - - - +
273A TYR* 1.3 63.7 + - - +
274A ILE* 3.4 14.0 + - - +
275A ASP* 3.0 24.2 + - - +
276A LEU* 2.9 23.4 + - - +
359A PHE* 4.4 3.9 - - - -
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Residues in contact with TYR 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A THR* 3.6 14.8 - - + +
215A GLY 2.9 22.1 + - - +
216A TRP* 3.9 18.6 - + + -
271A LEU 3.2 4.2 + - - -
272A ASP* 1.3 70.9 - - - +
274A ILE* 1.3 56.9 + - - +
276A LEU* 3.7 14.6 - - + -
277A TYR* 2.8 30.7 + - + +
331A VAL* 3.8 23.8 - - + -
334A ILE* 3.7 21.8 - - + -
335A ASP* 2.4 53.6 + - + -
338A ARG* 4.1 2.8 - - - +
340A PHE* 3.4 34.9 + + + +
341A ILE* 3.9 11.9 - - + -
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Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A TRP* 3.7 33.3 - - + +
217A ASN* 3.6 37.5 - - - +
272A ASP* 3.4 21.6 + - - +
273A TYR* 1.3 77.4 - - - +
275A ASP* 1.3 73.8 + - - +
277A TYR* 3.4 2.3 + - - +
278A LYS* 2.9 50.9 + - - +
288A TYR* 3.7 31.2 - - + +
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Residues in contact with ASP 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A GLU* 4.0 14.4 - - - +
260A ARG* 5.5 3.3 + - - -
272A ASP* 3.0 25.9 + - + +
274A ILE* 1.3 90.5 - - - +
276A LEU* 1.3 66.0 + - - +
278A LYS* 3.3 16.9 + - - +
279A LYS* 3.0 24.8 + - - +
359A PHE* 3.7 18.2 - - + -
2T C 5.4 1.9 + - - -
3T G 3.2 28.2 + - + +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LEU* 3.8 25.8 - - + +
272A ASP 2.9 12.3 + - - +
273A TYR* 3.6 25.1 - - + +
275A ASP* 1.3 75.9 - - - +
277A TYR* 1.3 57.0 + - - +
279A LYS* 3.3 0.6 + - - -
280A PHE* 2.9 50.3 + - + +
340A PHE* 4.2 15.0 - - + +
341A ILE* 3.7 30.7 - - + -
344A SER* 3.4 24.5 - - - +
358A VAL* 5.1 2.2 - - + -
359A PHE* 3.8 19.9 - - + -
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Residues in contact with TYR 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A TRP* 4.2 11.0 - + + -
273A TYR* 2.8 23.1 + + + +
274A ILE 3.5 4.3 - - - +
276A LEU* 1.3 72.9 - - - +
278A LYS* 1.3 63.9 + - - +
281A SER* 2.8 54.8 + - - -
283A THR* 3.5 11.3 + - - -
285A GLN* 3.0 23.9 + - + -
288A TYR* 4.0 17.3 - + - -
293A ILE* 3.8 32.9 - - + +
296A PHE* 3.8 1.6 - - - -
297A GLU* 2.4 40.0 + - + +
334A ILE* 4.6 11.0 - - + -
338A ARG* 4.0 4.3 + - - -
340A PHE* 3.9 17.4 - + - -
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Residues in contact with LYS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ILE* 2.9 39.1 + - - +
275A ASP* 3.3 18.7 + - - +
277A TYR* 1.3 77.6 - - - +
279A LYS* 1.3 61.6 + - - +
281A SER* 4.7 2.9 + - - -
282A PHE* 5.0 3.1 + - - -
283A THR 5.1 6.2 - - - +
288A TYR* 3.8 51.3 - - + +
1T T 6.2 2.0 + - - -
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ASP 3.0 16.3 + - - +
276A LEU 3.9 2.2 - - - +
278A LYS* 1.3 79.4 - - - +
280A PHE* 1.3 95.3 + - + +
281A SER 3.7 0.2 - - - -
282A PHE* 3.9 20.4 + - - -
347A MET* 5.2 4.0 - - - +
358A VAL 3.2 25.0 + - - +
359A PHE* 4.0 34.6 + - + +
361A PRO* 4.3 17.0 - - - +
558A ASN* 4.0 1.4 - - - +
561A ALA* 6.1 3.2 - - - +
562A LEU* 6.4 0.4 - - - +
3T G 6.5 0.7 - - + -
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Residues in contact with PHE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A LEU* 2.9 45.0 + - + +
279A LYS* 1.3 115.7 - - + +
281A SER* 1.3 61.9 + - - +
282A PHE* 3.4 9.9 - - - -
338A ARG* 4.8 0.7 + - - -
340A PHE* 3.4 36.0 - - + -
343A LEU* 3.5 24.0 - - + -
344A SER* 3.6 13.7 - - - -
347A MET* 4.5 12.3 - - + -
358A VAL* 4.5 11.4 - - + -
359A PHE* 5.5 0.2 - + - -
554A THR* 5.5 0.5 - - - -
557A ILE* 4.5 2.1 - - - +
558A ASN* 3.1 43.6 + - + +
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Residues in contact with SER 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A TYR* 2.8 48.7 + - - -
278A LYS* 4.7 1.4 + - - -
280A PHE* 1.3 78.3 - - - +
282A PHE* 1.3 70.1 + - - +
283A THR* 3.0 26.9 + - - +
338A ARG* 3.3 31.5 + - - +
340A PHE* 3.6 6.2 - - - -
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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
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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