Contacts of the helix formed by residues 275 - 279 (chain A) in PDB entry 3GG0
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 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A VAL 3.7 0.4 + - - -
274A THR* 1.3 71.4 - - - +
276A THR* 1.3 62.9 + - + +
277A GLU 3.4 0.7 + - - -
278A VAL* 3.7 7.4 + - - +
279A ILE* 3.4 21.5 + - + +
301A ILE* 4.0 18.8 - - + -
302A ASP 3.1 12.2 + - - +
303A ASP* 3.8 12.7 + - - +
304A PHE* 3.3 21.6 - - + -
305A GLY* 3.3 18.7 + - - -
306A ALA 3.5 0.7 + - - -
307A GLY* 2.7 39.3 + - - +
308A TYR 3.7 0.7 + - - -
309A SER* 2.8 35.7 - - - +
310A GLY* 3.4 3.6 - - - -
313A LEU* 5.3 4.4 - - + +
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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
----------------------------------------------------------
274A THR* 3.1 6.9 + - + -
275A GLU* 1.3 78.1 - - + +
277A GLU* 1.3 90.6 + - - +
279A ILE* 3.2 26.9 - - - +
280A THR* 3.5 7.6 + - - -
303A ASP* 6.0 1.6 - - + +
306A ALA* 5.8 1.8 - - + -
307A GLY* 3.8 29.4 - - - +
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Residues in contact with GLU 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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212A TYR* 5.7 1.2 + - - -
241A LEU* 4.9 12.1 - - + +
242A PRO* 3.7 36.1 - - + +
246A TYR* 5.3 1.4 + - - -
274A THR* 3.0 24.6 + - - +
276A THR* 1.3 102.7 + - - +
278A VAL* 1.3 63.1 + - - +
279A ILE 3.4 0.4 - - - -
280A THR* 3.1 23.7 + - - +
281A CYS 4.6 0.7 + - - -
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Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PRO* 4.6 4.3 - - + -
246A TYR* 6.0 0.4 - - - -
273A VAL* 3.6 29.8 - - + -
274A THR 3.3 18.8 - - - +
275A GLU* 3.7 5.8 + - - +
277A GLU* 1.3 75.9 - - - +
279A ILE* 1.3 59.4 + - + +
280A THR 3.1 9.3 + - - -
281A CYS 3.6 19.2 + - - +
282A PHE* 4.0 7.8 - - + -
285A PHE* 3.7 28.2 - - + +
301A ILE* 4.4 8.3 - - + -
313A LEU* 4.8 5.6 - - + -
317A PHE* 3.6 33.2 - - + -
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Residues in contact with ILE 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 GLU* 3.4 16.8 - - + +
276A THR* 3.2 25.6 - - - +
278A VAL* 1.3 73.6 - - + +
280A THR* 1.3 64.8 + - - +
281A CYS 3.5 0.2 - - - -
282A PHE* 3.7 25.7 - - + -
307A GLY 4.5 4.9 - - - +
309A SER* 3.3 40.6 - - - +
313A LEU* 3.8 21.3 - - + -
279B ILE* 6.2 0.4 - - + -
308B TYR* 4.0 28.8 - - + -
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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