Contacts of the helix formed by residues 272 - 279 (chain A) in PDB entry 3RSG
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 ASN 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A VAL* 3.5 25.5 - - + +
268A PRO 3.2 5.5 + - - -
269A PHE* 3.5 29.5 - - - -
270A PRO 3.5 1.2 - - - -
271A GLN* 1.3 77.2 - - - +
273A LEU* 1.3 79.4 + - - +
274A ILE 3.1 1.3 + - - -
275A ALA* 3.2 9.2 + - - +
276A THR* 4.1 1.2 + - - -
284A SER* 2.8 53.8 + - - +
285A VAL 3.8 4.9 - - - +
286A PRO* 3.4 23.8 - - - +
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Residues in contact with LEU 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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269A PHE* 4.2 22.4 - - + -
270A PRO* 3.0 17.9 + - + +
272A ASN* 1.3 92.4 - - - +
274A ILE* 1.3 65.8 + - + +
275A ALA 3.2 0.2 - - - -
276A THR* 3.3 15.2 + - - +
277A SER* 3.1 23.8 + - - -
284A SER* 5.6 0.7 - - - +
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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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245A SER* 4.0 35.0 - - - +
246A GLY* 5.1 2.7 - - - -
249A VAL* 4.0 10.8 - - + -
270A PRO 4.9 1.6 - - - +
271A GLN* 3.2 22.7 - - + +
272A ASN 3.1 0.2 - - - -
273A LEU* 1.3 79.2 - - + +
275A ALA* 1.3 58.8 + - - +
277A SER* 2.9 23.1 + - - +
278A ARG* 3.4 11.1 + - + +
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Residues in contact with ALA 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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248A PRO* 5.6 0.9 - - + -
249A VAL* 3.8 22.5 - - + +
265A LEU* 3.6 30.5 - - + -
267A VAL* 6.1 0.2 - - + -
271A GLN 4.3 0.2 + - - -
272A ASN* 3.2 12.3 + - - +
273A LEU 3.2 1.0 - - - -
274A ILE* 1.3 81.1 - - - +
276A THR* 1.3 57.5 + - + +
278A ARG* 3.2 3.1 + - - +
279A PHE* 2.8 32.7 + - - +
282A LEU* 4.1 8.4 - - + +
284A SER* 3.8 6.1 - - - +
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Residues in contact with THR 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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272A ASN 4.1 0.5 + - - -
273A LEU* 3.3 26.5 + - - +
275A ALA* 1.3 74.3 - - - +
277A SER* 1.3 63.9 + - - +
278A ARG 3.1 1.0 + - - -
279A PHE 3.5 7.2 - - - +
280A PRO* 3.4 28.9 - - + +
282A LEU* 3.3 28.5 - - + +
283A ILE* 4.8 0.2 - - - -
284A SER* 4.0 22.9 - - - +
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Residues in contact with SER 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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273A LEU 3.1 13.2 + - - -
274A ILE* 2.9 25.6 + - - +
276A THR* 1.3 78.9 + - - +
278A ARG* 1.3 60.2 + - - +
280A PRO* 5.2 2.1 - - - +
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Residues in contact with ARG 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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249A VAL* 4.3 9.2 - - + -
274A ILE* 3.4 10.0 + - + +
275A ALA 3.2 7.0 + - - +
276A THR 3.1 0.2 - - - -
277A SER* 1.3 85.2 + - - +
279A PHE* 1.3 103.2 + - + +
280A PRO* 3.8 6.0 - - - +
475A SER* 5.3 9.5 + - - -
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Residues in contact with PHE 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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249A VAL* 3.8 14.6 - - + -
250A LEU* 6.2 0.9 - - + -
253A MET* 3.2 55.2 - - + -
257A LYS* 6.0 2.9 - - - -
275A ALA 2.8 18.9 + - - +
276A THR* 3.5 3.8 - - - -
278A ARG* 1.3 123.6 - - + +
280A PRO* 1.3 64.3 - - + +
281A GLU* 3.1 15.9 - - - +
282A LEU* 3.1 18.6 + - + +
475A SER* 5.7 7.6 - - - -
478A LEU* 4.6 15.5 - - + -
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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