Contacts of the strand formed by residues 269 - 274 (chain G) in PDB entry 1GLE
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 CYS 269 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263G ASN* 4.4 6.3 - - - +
264G THR 3.1 6.7 - - - -
265G TYR* 3.3 38.4 - - - -
268G GLY* 1.3 72.4 - - - -
270G PHE* 1.3 68.8 + - - +
271G MET 4.1 0.4 - - - -
304G GLY 3.5 3.1 - - - +
306G VAL* 2.7 51.9 + - + +
309G ALA* 3.7 17.9 - - + -
384G ILE* 4.1 6.3 - - - -
387G GLN* 6.3 0.4 - - - -
388G THR* 4.2 9.4 - - - +
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Residues in contact with PHE 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G ARG* 4.1 7.6 - - - -
103G TRP* 4.3 11.4 - + - -
135G TYR* 3.8 12.8 - + - -
246G GLN* 2.8 45.3 - - + +
262G LYS* 3.1 10.6 + - - -
263G ASN* 3.1 4.2 + - - -
264G THR* 2.8 35.4 + - + -
266G GLY 5.8 0.2 - - - -
268G GLY* 3.4 18.8 - - - -
269G CYS* 1.3 97.9 - - - +
271G MET* 1.3 58.4 - - - +
272G LEU* 3.4 10.8 - - + -
303G GLU* 4.2 2.5 - - - -
304G GLY 3.4 1.8 - - - +
305G ALA* 3.7 29.2 - - + -
306G VAL 3.9 4.9 - - - -
307G PHE* 5.8 0.2 - + - -
503G G3H 3.7 28.5 - - - -
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Residues in contact with MET 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261G ALA* 5.5 4.7 - - + -
262G LYS 3.3 16.4 - - - +
263G ASN* 2.9 28.0 + - + +
269G CYS 4.1 0.2 + - - -
270G PHE* 1.3 72.3 - - - +
272G LEU* 1.3 64.1 + - - +
303G GLU* 3.2 1.7 - - - -
304G GLY 2.8 36.1 + - - -
388G THR* 4.0 8.5 - - + +
391G VAL* 3.6 25.4 - - + -
392G LEU* 3.4 43.7 - - + -
395G MET* 3.2 36.4 - - + +
403G LEU* 5.8 2.0 - - - -
406G LEU* 4.5 12.3 - - + -
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Residues in contact with LEU 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246G GLN* 4.0 27.1 - - + +
247G GLN* 4.2 11.7 - - + +
250G LEU* 3.5 27.4 - - + +
260G MET 3.9 0.2 - - - +
261G ALA* 3.1 24.4 - - - +
262G LYS* 3.1 20.4 + - - +
270G PHE* 3.4 18.6 - - + +
271G MET* 1.3 95.7 - - - +
273G MET* 1.3 62.1 + - - +
289G THR* 5.7 2.0 - - + -
291G ALA* 6.2 0.2 - - + -
301G ALA* 5.4 4.7 - - + -
302G LEU 3.1 4.3 - - - +
303G GLU* 3.3 32.3 - - + +
395G MET* 3.9 3.6 - - - -
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Residues in contact with MET 273 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250G LEU* 4.5 0.9 - - - -
259G GLY* 3.5 29.8 - - - +
260G MET 3.2 8.1 - - - +
261G ALA* 3.7 13.9 - - + -
272G LEU* 1.3 76.5 - - - +
274G ASN* 1.3 77.5 + - - +
275G THR* 3.3 10.6 + - + +
301G ALA* 3.1 6.3 - - - -
302G LEU* 2.9 35.1 + - + +
395G MET* 4.1 20.8 - - + +
399G SER* 4.1 25.1 - - - +
401G ILE* 4.3 14.1 - - + -
403G LEU* 4.3 18.4 - - + -
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Residues in contact with ASN 274 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250G LEU* 4.3 8.7 - - + +
255G CYS 4.6 0.9 - - - -
256G VAL 3.4 18.3 - - - +
257G LYS 3.2 25.6 - - - +
258G GLU* 3.4 0.7 - - - -
259G GLY 2.7 30.1 + - - -
260G MET 2.8 12.6 + - - +
273G MET* 1.3 72.7 - - - +
275G THR* 1.3 63.5 + - - +
276G GLY* 2.5 38.3 + - - -
291G ALA* 4.6 5.3 - - - +
292G CYS 3.4 16.8 + - - -
299G ASN* 3.2 23.2 + - - +
300G TYR 3.9 7.1 + - - +
301G ALA* 4.3 2.5 - - - -
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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