Contacts of the helix formed by residues 274 - 283 (chain F) in PDB entry 1G2D
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 THR 274 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D C 3.9 12.0 + - + -
57D T 3.8 27.2 + - + +
58D A 6.3 0.4 - - - -
252F GLN* 4.0 16.8 - - + +
255F ARG* 4.0 12.1 - - - +
263F PHE* 3.4 12.6 - - - +
272F PHE* 4.1 2.4 - - - +
273F ALA* 1.3 85.2 - - + +
275F LEU* 1.3 64.1 + - - +
276F HIS* 4.3 3.7 + - - +
277F THR* 2.8 31.1 + - - -
278F ARG* 3.4 18.7 + - - +
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Residues in contact with LEU 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E T 3.9 9.2 - - + -
75E A 3.4 57.9 - - + +
76E T 4.1 5.8 - - + +
255F ARG* 5.3 0.2 - - - +
263F PHE* 3.6 32.4 - - + -
274F THR* 1.3 71.0 - - - +
276F HIS* 1.3 66.1 + - - +
278F ARG* 3.2 33.7 + - - +
279F ASP* 3.0 39.8 + - - +
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Residues in contact with HIS 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D C 4.2 3.4 - - - +
57D T 5.2 0.9 - - - +
76E T 3.7 32.9 + + + +
77E A 3.3 36.9 + + - +
78E G 3.1 33.1 + - - -
274F THR* 3.5 3.4 + - - +
275F LEU* 1.3 75.6 - - - +
277F THR* 1.3 66.0 + - - +
279F ASP* 4.1 10.4 - - + +
280F ARG* 2.9 54.4 + - + +
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Residues in contact with THR 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D C 3.7 27.0 - - + +
55D G 3.8 10.8 - - + +
56D C 3.1 23.9 + - - -
272F PHE* 3.5 26.7 - - + -
273F ALA 5.5 0.7 - - - +
274F THR* 2.8 28.1 + - - -
275F LEU 3.3 0.4 - - - -
276F HIS* 1.3 76.6 - - - +
278F ARG* 1.3 58.1 + - - +
280F ARG* 4.0 11.8 + - - +
281F HIS* 3.0 30.0 + - - +
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Residues in contact with ARG 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F PHE* 3.7 37.2 - - + +
264F ALA 3.0 42.2 + - - +
265F CYS 4.2 0.4 - - - +
266F ASP* 5.4 2.2 + - - -
272F PHE* 3.8 19.7 - - + +
274F THR 3.4 3.6 + - - +
275F LEU* 3.2 28.6 + - - +
276F HIS 3.2 0.6 - - - -
277F THR* 1.3 77.1 - - - +
279F ASP* 1.3 91.1 + - - +
281F HIS* 3.2 3.5 + - - +
282F THR* 3.1 36.4 + - - +
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Residues in contact with ASP 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E A 5.8 1.0 - - - +
76E T 4.4 6.4 - - - +
275F LEU* 3.0 37.7 + - - +
276F HIS* 3.7 11.2 - - + +
278F ARG* 1.3 103.0 + - - +
280F ARG* 1.3 61.3 + - - +
282F THR* 2.9 22.4 + - - -
283F LYS* 3.6 16.2 - - - +
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Residues in contact with ARG 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D C 3.6 35.3 - - + +
55D G 2.8 49.3 + - - -
56D C 3.6 7.4 - - - +
78E G 3.0 18.9 + - - -
79E C 3.4 10.7 - - - +
276F HIS* 2.9 34.7 + - + +
277F THR* 4.0 10.6 + - - +
279F ASP* 1.3 77.0 - - - +
281F HIS* 1.3 62.2 + - - +
283F LYS* 3.2 33.0 - - + +
284F ILE* 4.1 6.1 + - - +
287F ARG* 4.8 4.4 + - - +
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Residues in contact with HIS 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D C 2.8 43.9 + - + +
265F CYS* 3.5 8.7 - - + -
268F CYS* 3.6 6.8 - - - -
270F ARG* 4.6 5.2 - - + -
272F PHE* 3.3 32.9 - + + -
277F THR 3.0 20.3 + - - +
278F ARG 3.2 3.8 + - - +
280F ARG* 1.3 73.1 - - - +
282F THR* 1.3 65.5 + - + +
283F LYS 3.0 5.2 - - - -
284F ILE* 3.0 46.3 + - + +
285F HIS* 3.3 2.4 + + - -
306F ZN 2.2 36.3 - - - -
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Residues in contact with THR 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265F CYS* 3.3 26.7 - - + -
266F ASP* 4.1 13.0 - - - +
267F ILE* 4.2 10.0 - - + +
278F ARG* 3.1 27.5 + - - +
279F ASP* 2.9 20.4 + - - -
281F HIS* 1.3 75.8 - - - +
283F LYS* 1.3 61.7 + - - +
285F HIS* 3.2 31.6 + - - +
286F LEU* 4.1 6.3 - - - +
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Residues in contact with LYS 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F ASP* 3.6 20.2 - - - +
280F ARG* 3.2 24.0 - - + +
281F HIS 3.0 1.0 - - - -
282F THR* 1.3 76.0 + - - +
284F ILE* 1.3 61.9 + - - +
285F HIS 3.2 0.7 - - - -
286F LEU* 3.3 33.1 + - + +
287F ARG* 3.5 26.3 + - - +
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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