Contacts of the strand formed by residues 269 - 274 (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 VAL 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B PHE* 3.8 33.7 - - + -
236B LEU* 3.5 9.6 - - + +
238B ILE* 4.4 4.3 - - + -
259B LEU* 3.8 25.4 - - + -
264B LEU* 4.3 11.7 - - + -
265B ARG 3.8 9.2 - - - +
266B PRO 3.2 10.8 + - - +
267B ASP 3.2 1.9 - - - +
268B GLN* 1.3 82.1 - - - +
270B LEU* 1.3 61.6 + - - +
271B ILE* 4.3 15.9 - - + -
297B MET* 3.5 18.3 - - + +
298B LYS* 2.9 24.2 + - - +
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Residues in contact with LEU 270 (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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235B GLN* 4.1 22.7 - - - +
236B LEU 2.9 11.8 + - - +
237B ALA* 3.4 15.8 - - + -
238B ILE* 3.0 28.6 + - - +
268B GLN 3.9 0.4 + - - -
269B VAL* 1.3 74.5 - - - +
271B ILE* 1.3 64.0 + - - +
272B GLU* 3.7 17.3 - - + +
298B LYS* 3.3 28.0 - - + +
299B LEU 4.1 4.3 - - - +
300B ALA* 3.6 33.4 - - + +
320B ASP* 5.0 1.6 - - + -
321B LYS* 4.1 26.7 - - + +
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Residues in contact with ILE 271 (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 ILE* 3.6 30.3 - - + +
240B LEU* 3.8 29.6 - - + -
245B LEU* 4.2 13.0 - - + -
255B LEU* 4.0 20.9 - - + -
269B VAL* 4.3 9.6 - - + -
270B LEU* 1.3 74.3 - - - +
272B GLU* 1.3 66.9 - - - +
273B VAL* 4.6 4.7 - - + -
292B LEU* 4.2 27.8 - - + -
297B MET* 4.4 6.7 - - + -
298B LYS 2.8 16.7 + - - +
299B LEU* 3.5 8.4 - - + +
300B ALA 2.8 27.6 + - - +
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Residues in contact with GLU 272 (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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176B ILE* 4.8 0.7 - - - +
188B GLU* 2.8 6.2 - - - +
237B ALA* 3.3 21.7 - - + +
238B ILE 2.8 16.0 + - - +
239B ASN* 3.3 13.5 - - - +
240B LEU 3.0 28.1 + - - +
270B LEU* 3.7 20.0 - - + +
271B ILE* 1.3 72.0 - - - +
273B VAL* 1.3 60.6 + - - +
300B ALA* 3.6 9.6 - - + -
302B ASP* 2.9 11.4 - - + +
321B LYS* 5.6 0.5 + - - -
323B LYS* 2.7 34.2 + - - +
502B MN 2.1 36.7 + - - -
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Residues in contact with VAL 273 (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 3.3 20.6 - - - +
242B PRO* 4.5 6.5 - - + -
245B LEU* 4.5 10.3 - - + -
271B ILE* 4.6 4.9 - - + -
272B GLU* 1.3 73.5 - - - +
274B THR* 1.3 59.6 + - - +
278B VAL* 3.8 22.0 - - + -
285B PHE* 4.3 26.0 - - + -
289B LEU* 5.5 0.9 - - + -
299B LEU* 3.8 24.9 - - + -
300B ALA 3.0 13.1 + - - +
301B ILE* 3.5 8.2 - - + +
302B ASP* 2.7 29.0 + - - -
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Residues in contact with THR 274 (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 4.8 1.9 + - - -
241B LEU* 5.0 3.0 - - + +
242B PRO* 4.9 1.1 - - - +
273B VAL* 1.3 72.0 - - - +
275B GLU* 1.3 66.2 + - - +
276B THR* 4.6 4.9 - - - -
277B GLU* 2.7 44.4 + - - +
278B VAL* 3.2 18.4 + - - +
302B ASP* 3.4 13.0 - - + +
303B ASP* 3.3 28.0 - - + +
501B C2E 4.9 9.0 - - - +
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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