Contacts of the helix formed by residues 241 - 251 (chain B) in PDB entry 3GBA
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 GLY 241 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238B GLN 3.0 14.8 + - - -
239B GLU 3.2 1.8 + - - -
240B GLU* 1.3 78.1 - - - +
242B LYS* 1.3 58.7 + - - +
243B LEU 3.4 2.9 - - - -
244B HIS* 3.3 14.8 + - - +
245B MET* 3.0 25.7 + - - +
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Residues in contact with LYS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLU* 3.4 35.3 + - - +
237B LEU* 2.9 24.5 + - + +
240B GLU* 3.9 37.2 + - + +
241B GLY* 1.3 77.0 - - - +
243B LEU* 1.3 61.3 + - - +
245B MET* 3.3 23.9 + - + +
246B MET* 3.0 38.3 + - - +
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 3.9 20.0 + - - +
39B LEU* 4.3 15.3 - - + -
105B PHE* 3.8 24.0 - - + +
234B ILE* 4.1 17.9 - - + +
237B LEU* 3.5 15.5 + - + -
238B GLN* 3.5 49.4 - - + +
241B GLY 3.4 0.2 - - - -
242B LYS* 1.3 76.9 - - - +
244B HIS* 1.3 58.0 + - - +
246B MET* 3.7 16.8 - - - +
247B LYS* 3.0 29.3 + - - +
259B SO4 3.7 6.9 + - - +
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Residues in contact with HIS 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B GLN* 5.3 3.4 + - - +
241B GLY* 3.3 15.7 + - - +
242B LYS 3.2 0.2 - - - -
243B LEU* 1.3 76.3 - - - +
245B MET* 1.3 67.1 + - - +
247B LYS* 3.3 1.6 + - - +
248B GLU* 2.9 57.9 + - + +
259B SO4 2.7 41.0 + - - +
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Residues in contact with MET 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLU* 4.4 13.7 - - - +
241B GLY 3.0 12.3 + - - +
242B LYS* 3.3 38.3 + - + +
244B HIS* 1.3 80.5 - - - +
246B MET* 1.3 65.9 + - + +
248B GLU* 3.4 6.0 + - - +
249B LYS* 3.0 31.5 + - + +
252B ARG* 5.0 1.0 + - - -
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Residues in contact with MET 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 3.5 39.0 - - + +
38B ASP* 4.3 14.8 - - + +
39B LEU* 3.5 47.3 - - + +
42B GLU* 4.7 13.2 - - + -
237B LEU* 5.5 0.9 - - - -
242B LYS* 3.0 25.1 + - - +
243B LEU* 3.7 15.0 - - + +
245B MET* 1.3 83.7 - - + +
247B LYS* 1.3 66.8 + - - +
249B LYS* 3.4 6.6 + - + -
250B TRP* 3.2 32.8 + - + +
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Residues in contact with LYS 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 3.9 3.5 - - + -
106B MET* 3.7 31.7 - - + +
192B THR* 5.2 5.2 - - - +
195B GLU* 3.6 18.1 + - - +
243B LEU 3.0 17.4 + - - +
244B HIS 3.7 3.6 - - - +
246B MET* 1.3 77.8 - - - +
248B GLU* 1.3 62.2 + - + +
250B TRP 3.3 0.5 + - - -
251B TRP* 2.9 77.9 + - + +
259B SO4 3.7 29.9 + - - +
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B HIS* 2.9 52.2 + - + +
245B MET* 3.7 5.4 - - - +
247B LYS* 1.3 77.1 - - + +
249B LYS* 1.3 63.1 + - - +
251B TRP* 5.3 1.6 - - - -
252B ARG* 3.2 52.5 + - - +
259B SO4 4.9 1.7 + - - +
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Residues in contact with LYS 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ASP* 2.9 36.0 + - - +
245B MET* 3.0 20.4 + - + +
246B MET* 3.6 7.9 - - + +
247B LYS 3.2 0.2 - - - -
248B GLU* 1.3 79.4 - - - +
250B TRP* 1.3 87.4 + - + +
252B ARG* 3.4 28.8 + - - +
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Residues in contact with TRP 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PRO* 3.7 15.9 - - + +
18B MET* 3.4 31.4 - - + -
33B GLU* 4.0 22.2 - - + -
34B GLY* 3.4 27.4 - - - -
35B TYR* 3.5 25.3 - + + +
38B ASP* 2.9 25.8 + - - -
196B TYR* 3.7 22.5 - - - -
246B MET* 3.2 24.5 + - - -
249B LYS* 1.3 109.6 - - + +
251B TRP* 1.3 79.8 + - + +
252B ARG 3.3 4.4 + - - +
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Residues in contact with TRP 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PRO* 3.8 18.4 - - + -
16B TYR* 3.4 45.5 - + - -
35B TYR* 3.8 25.1 - + - -
106B MET* 4.1 6.1 - - + -
192B THR* 3.0 26.8 + - - -
195B GLU* 3.7 30.5 + - + +
196B TYR* 3.6 25.5 - - + +
199B GLN* 2.8 25.3 + - - +
247B LYS* 2.9 47.9 + - + +
248B GLU* 4.0 3.1 - - - -
250B TRP* 1.3 90.9 - - + +
252B ARG* 1.3 59.9 + - - +
253B GLY 3.5 0.3 + - - -
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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