Contacts of the strand formed by residues 229 - 234 (chain D) in PDB entry 1GPM
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 LYS 229 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227D ASP 4.7 4.5 - - - +
228D ASP* 1.3 77.3 - - - +
230D VAL* 1.3 60.6 + - - +
254D ASN* 3.4 22.2 - - + +
327D GLU* 3.1 38.3 + - - +
328D ASP* 3.0 51.4 + - + +
329D VAL* 3.8 8.0 - - + -
330D LYS 3.1 23.6 + - - -
331D TRP* 3.3 6.9 + - - -
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Residues in contact with VAL 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D VAL* 3.7 24.0 - - + -
229D LYS* 1.3 77.4 - - - +
231D ILE* 1.3 62.4 + - - +
247D LEU* 4.4 7.0 - - + -
251D ILE* 3.7 26.7 - - + -
254D ASN 2.9 9.3 + - - +
255D LEU* 3.5 13.2 - - + +
256D THR* 3.1 26.7 + - - +
329D VAL* 4.6 2.9 - - - -
331D TRP* 3.4 26.2 - - + +
333D ALA* 3.7 30.7 - - + +
373D VAL* 4.8 2.0 - - + -
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Residues in contact with ILE 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D VAL* 1.3 73.7 - - - +
232D LEU* 1.3 64.8 + - - +
256D THR* 3.5 6.5 - - - +
258D VAL* 3.6 24.5 - - + -
319D PHE* 3.5 25.4 - - + +
323D ALA* 3.9 17.9 - - + +
326D LEU* 3.7 21.5 - - + -
329D VAL* 3.5 22.4 - - + +
331D TRP 2.8 20.4 + - - +
332D LEU* 3.4 19.2 - - + +
333D ALA 2.9 25.1 + - - -
370D MET* 4.0 10.3 - - + -
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Residues in contact with LEU 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D ILE* 1.3 77.0 - - - +
233D GLY* 1.3 75.8 + - - +
234D LEU* 5.1 1.8 - - + -
240D SER* 4.2 6.3 - - - +
243D THR* 4.0 16.4 - - + -
244D ALA* 3.5 42.8 - - + +
247D LEU* 4.3 9.6 - - + -
255D LEU* 4.0 12.6 - - + -
256D THR 3.1 8.2 + - - +
257D CYS* 3.2 14.3 - - - -
258D VAL 2.8 26.2 + - - -
319D PHE* 4.2 3.4 - - - -
332D LEU* 4.7 0.7 - - - -
333D ALA* 3.2 32.5 - - + +
334D GLN* 4.5 4.3 - - - +
527D AMP 4.8 3.8 - - - +
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Residues in contact with GLY 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D LEU* 1.3 77.3 - - - +
234D LEU* 1.3 55.8 + - - -
240D SER* 3.7 7.1 - - - -
258D VAL 3.5 6.5 - - - -
315D PHE* 5.3 0.2 - - - -
319D PHE* 3.7 20.0 - - - -
332D LEU* 5.0 1.6 - - - +
333D ALA 4.5 2.4 + - - -
527D AMP 2.7 48.7 + - - -
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Residues in contact with LEU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D LEU* 3.3 2.8 + - + -
233D GLY* 1.3 70.3 - - - -
235D SER* 1.3 62.3 + - - +
236D GLY 4.3 4.9 - - - +
240D SER* 4.0 27.8 - - - +
241D SER* 4.2 11.4 - - - +
244D ALA* 4.4 7.4 - - + -
257D CYS* 4.1 29.6 - - + -
258D VAL 3.0 12.1 + - - +
259D PHE* 3.0 27.6 - - + -
273D VAL* 3.7 27.1 - - + -
277D PHE* 3.9 27.4 - - + -
283D LEU* 5.4 0.2 - - + -
285D ILE* 4.3 11.2 - - + -
527D AMP 3.0 9.1 - - - -
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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