Contacts of the helix formed by residues 245 - 253 (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 ASP 245 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10G ASP* 4.1 5.4 - - - +
11G GLN 4.5 1.0 - - - +
12G GLY* 4.6 0.3 - - - -
80G THR* 3.3 13.0 - - + +
81G ASN 2.9 35.7 + - - +
82G GLN* 3.6 2.9 + - - -
83G ARG* 3.8 1.2 - - - +
243G ALA 3.4 1.8 + - - -
244G GLY* 1.3 69.5 - - - -
246G GLN* 1.3 77.6 + - - +
248G ALA 2.8 11.8 + - - -
249G ALA* 3.0 8.9 + - - +
439G THR* 3.4 28.2 - - + +
502G ZN 3.7 4.4 - - - -
503G G3H 2.3 57.2 + - - +
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Residues in contact with GLN 246 (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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83G ARG* 3.3 34.1 - - - +
244G GLY 3.5 0.8 - - - -
245G ASP* 1.3 95.9 + - - +
247G GLN* 1.3 56.5 + - - +
249G ALA* 3.0 8.7 + - - +
250G LEU* 3.0 23.0 + - - +
262G LYS* 2.5 35.2 + - - +
264G THR* 3.2 21.2 - - - +
270G PHE* 2.8 51.0 - - + +
272G LEU* 4.0 12.6 - - + -
439G THR* 5.4 3.2 + - - -
503G G3H 3.8 10.5 + - - -
504G ADP 5.6 0.4 + - - -
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Residues in contact with GLN 247 (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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83G ARG* 3.3 28.7 + - - +
184G THR* 3.6 32.0 + - + +
188G ARG* 4.4 3.3 - - - +
243G ALA* 4.8 3.6 - - + -
244G GLY* 3.1 17.1 - - - +
246G GLN* 1.3 72.3 - - - +
248G ALA* 1.3 59.0 + - - +
249G ALA 2.9 5.6 - - - -
250G LEU* 3.5 10.6 - - - +
251G PHE* 3.0 24.4 + - - +
272G LEU* 4.2 8.2 - - + +
289G THR* 3.6 22.2 + - + +
290G ILE 2.7 30.2 + - - +
291G ALA* 4.0 12.7 - - + +
292G CYS* 5.4 6.4 + - - -
303G GLU* 5.0 0.2 + - - -
446G LEU* 6.0 0.2 - - - +
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Residues in contact with ALA 248 (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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80G THR* 3.2 34.3 - - + -
243G ALA* 4.2 12.5 - - + +
244G GLY 2.9 5.9 + - - +
245G ASP 2.8 7.8 + - - +
247G GLN* 1.3 74.7 - - - +
249G ALA* 1.3 59.7 + - - +
251G PHE* 3.9 7.0 - - - -
252G GLY 3.2 5.4 + - - -
438G VAL 3.6 0.9 - - - +
439G THR 3.4 14.7 - - - +
442G GLY* 3.2 23.6 - - - -
443G ALA* 4.1 11.2 - - - +
446G LEU* 5.4 0.9 - - - -
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Residues in contact with ALA 249 (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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245G ASP 3.0 4.9 + - - +
246G GLN* 3.0 11.2 + - - +
247G GLN 2.9 0.8 - - - -
248G ALA* 1.3 77.5 - - - +
250G LEU* 1.3 67.6 + - - +
251G PHE 3.0 1.6 - - - -
253G GLN* 3.0 29.2 + - - +
262G LYS* 4.4 3.1 - - - +
264G THR* 4.1 17.0 - - - +
409G ASP* 4.3 2.2 - - - +
438G VAL* 3.6 16.6 - - + +
439G THR* 3.4 26.7 - - - +
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Residues in contact with LEU 250 (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 3.0 12.3 + - - +
247G GLN* 3.2 12.3 + - - +
249G ALA* 1.3 79.3 - - - +
251G PHE* 1.3 54.4 + - - +
253G GLN* 3.2 6.2 + - - +
255G CYS* 2.7 71.5 + - + -
256G VAL 4.8 3.1 - - - +
260G MET 4.5 1.3 - - - +
262G LYS* 4.1 17.7 - - + +
272G LEU* 3.5 42.8 - - + +
273G MET 4.4 0.9 - - - +
274G ASN* 4.3 14.6 - - + +
291G ALA* 4.5 21.5 - - + -
292G CYS 6.0 0.4 - - - +
301G ALA* 4.9 2.0 - - + -
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Residues in contact with PHE 251 (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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247G GLN 3.0 16.9 + - - +
248G ALA* 4.0 7.2 - - - +
250G LEU* 1.3 73.1 - - - +
252G GLY* 1.3 57.9 + - - +
253G GLN 3.0 1.3 - - - -
254G LEU* 2.5 35.5 + - - +
255G CYS* 4.4 2.7 - - - +
256G VAL* 3.8 28.9 - - + +
292G CYS* 4.2 19.1 - - + +
293G GLY 4.2 14.4 - - - -
294G PRO* 4.3 12.1 - - + -
442G GLY 3.7 9.2 - - - -
445G TYR* 3.5 28.9 - + + -
446G LEU* 3.1 41.7 - - + -
449G LEU* 4.6 6.7 - - + -
457G LEU* 4.4 13.2 - - + -
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Residues in contact with GLY 252 (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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248G ALA 3.2 11.2 + - - -
249G ALA 3.3 2.6 + - - -
251G PHE* 1.3 79.5 - - - +
253G GLN* 1.3 60.0 + - - +
254G LEU* 3.0 10.5 + - - +
438G VAL* 4.2 13.3 - - - +
441G LEU* 4.8 6.0 - - - +
442G GLY* 3.9 20.9 - - - -
445G TYR* 4.3 16.5 + - - -
464G ALA* 5.1 6.8 - - - +
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Residues in contact with GLN 253 (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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249G ALA 3.0 16.3 + - - +
250G LEU 3.4 9.9 - - - +
251G PHE 3.0 1.4 - - - -
252G GLY* 1.3 75.0 - - - +
254G LEU* 1.3 72.7 + - - +
255G CYS* 3.5 18.2 + - - -
260G MET* 4.6 1.7 - - - +
262G LYS* 4.1 11.2 - - + +
407G ARG* 3.1 53.8 + - + +
408G VAL* 3.3 14.1 + - - +
409G ASP* 2.5 44.3 + - - +
433G PRO* 3.7 7.5 - - - +
438G VAL* 4.1 11.1 - - + +
464G ALA* 5.7 3.1 - - - +
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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