Contacts of the helix formed by residues 241 - 247 (chain B) 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 LEU 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B PHE* 5.4 8.1 - - + -
211B ARG* 6.2 2.9 - - + -
212B TYR* 4.1 20.4 - - + -
215B ASP* 3.1 10.4 + - + +
240B LEU* 1.3 79.3 - - - +
242B PRO* 1.3 73.7 - - + +
243B GLY 4.2 4.7 - - - +
244B SER* 3.2 26.3 + - - +
245B LEU* 3.5 5.0 + - - +
273B VAL* 4.8 0.9 - - - -
274B THR* 5.0 2.7 - - + +
277B GLU* 3.4 27.1 - - - +
501B C2E 3.5 21.8 - - - +
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Residues in contact with PRO 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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240B LEU 3.8 4.2 - - - +
241B LEU* 1.3 85.5 - - + +
243B GLY* 1.3 57.7 - - - +
245B LEU 3.0 3.8 + - - -
246B TYR* 2.8 29.0 + - - +
273B VAL* 4.5 4.0 - - + -
274B THR* 4.9 2.0 - - - +
277B GLU* 3.4 44.9 - - + +
278B VAL* 4.5 12.8 - - + -
281B CYS* 3.9 24.2 - - - -
285B PHE* 3.3 27.3 - - + -
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Residues in contact with GLY 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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212B TYR* 3.6 22.9 - - - +
241B LEU* 3.2 3.0 - - - +
242B PRO* 1.3 80.2 - - - +
244B SER* 1.3 56.4 + - - +
246B TYR* 4.1 4.0 - - - -
247B HIS* 2.8 53.8 + - - +
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Residues in contact with SER 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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212B TYR* 3.5 33.0 - - - +
213B ARG* 5.9 0.2 - - - -
215B ASP* 2.7 35.1 + - - +
216B LEU* 4.1 15.1 - - - +
240B LEU* 4.2 11.0 - - - -
241B LEU* 3.2 19.0 + - - +
243B GLY* 1.3 75.8 - - - +
245B LEU* 1.3 60.4 + - - +
247B HIS 5.1 0.2 - - - -
248B HIS* 3.9 17.2 + - - +
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Residues in contact with LEU 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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216B LEU* 4.2 2.2 - - + -
240B LEU* 3.8 26.2 - - + -
241B LEU 3.5 8.3 + - - +
242B PRO 3.0 6.9 + - - +
244B SER* 1.3 76.3 - - - +
246B TYR* 1.3 64.6 + - - +
247B HIS 3.5 0.2 - - - -
248B HIS* 3.9 5.8 + - - +
251B ALA* 3.4 30.9 + - + +
252B VAL* 5.1 0.7 - - + +
255B LEU* 3.8 18.6 - - + -
271B ILE* 4.2 21.8 - - + -
273B VAL* 4.5 4.5 - - + -
285B PHE* 3.9 21.3 - - + -
288B VAL* 3.6 31.3 - - + +
292B LEU* 4.5 13.5 - - + -
299B LEU* 6.2 0.4 - - + -
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Residues in contact with TYR 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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242B PRO* 2.8 17.0 + - + +
243B GLY* 4.0 5.2 - - - +
245B LEU* 1.3 79.3 - - - +
247B HIS* 1.3 92.3 + + - +
248B HIS 3.2 10.8 + - - +
281B CYS* 5.9 6.1 - - - -
284B GLN* 3.4 54.3 + - + +
285B PHE* 4.4 9.4 - + + -
287B LYS* 4.8 11.1 - - + -
288B VAL* 4.3 14.9 - - + +
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Residues in contact with HIS 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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212B TYR* 3.4 38.2 + + + -
243B GLY* 2.8 36.8 + - - +
244B SER 5.1 0.4 - - - -
246B TYR* 1.3 98.5 - + - +
248B HIS* 1.3 58.4 + - - +
249B PRO* 4.3 3.6 - - - +
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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