Contacts of the strand formed by residues 297 - 306 (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 GLU 297 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219G ARG* 4.1 16.6 - - - +
220G SER* 5.9 0.4 - - - -
291G ALA 4.4 0.2 - - - -
292G CYS* 3.1 5.9 - - - -
293G GLY* 2.5 52.7 + - - -
294G PRO* 3.5 8.1 - - - +
295G THR* 2.9 28.9 + - - -
296G GLY* 1.3 76.9 - - - +
298G VAL* 1.3 76.1 + - + +
299G ASN* 3.7 5.1 - - - +
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Residues in contact with VAL 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G TYR* 4.1 37.5 - - + -
197G LEU* 4.4 24.5 - - + -
219G ARG* 6.1 2.0 - - + -
220G SER* 5.8 1.6 - - - +
277G GLU* 5.8 2.9 - - - +
290G ILE* 4.1 20.4 - - + -
291G ALA 3.7 4.9 - - - -
296G GLY 3.7 1.9 + - - +
297G GLU* 1.3 83.2 - - - +
299G ASN* 1.3 71.1 + - - +
300G TYR* 4.9 13.0 - - + -
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Residues in contact with ASN 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256G VAL 3.7 6.3 + - - -
274G ASN* 3.2 32.0 + - - +
276G GLY* 3.1 19.6 + - - +
277G GLU* 5.2 1.7 - - - +
290G ILE* 3.2 10.2 - - - +
291G ALA 2.7 33.9 + - - +
292G CYS 3.6 7.4 - - - +
293G GLY* 3.1 28.1 - - - -
294G PRO* 4.9 0.8 - - - +
297G GLU* 3.4 6.2 - - - +
298G VAL* 1.3 84.5 - - - +
300G TYR* 1.3 72.3 + - - +
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Residues in contact with TYR 300 (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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194G ILE* 2.6 51.4 + - + -
195G HIS* 3.9 6.6 + + - -
197G LEU* 3.6 13.4 - - + +
274G ASN* 3.9 6.2 - - - +
275G THR* 3.0 19.2 + - - +
276G GLY 2.8 9.8 + - - +
277G GLU* 3.8 20.4 - - + -
278G LYS 3.4 17.7 - - - +
279G ALA* 3.7 30.1 - - + -
288G THR* 5.0 1.8 - - + -
289G THR 3.4 6.3 - - - -
290G ILE* 3.9 23.6 - - + -
291G ALA* 4.3 0.9 - - - +
298G VAL* 4.9 9.0 - - + -
299G ASN* 1.3 79.7 - - - +
301G ALA* 1.3 68.3 + - - +
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Residues in contact with ALA 301 (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* 4.9 4.7 - - + -
272G LEU* 5.4 3.4 - - + -
273G MET 3.1 19.7 - - - +
274G ASN* 4.3 0.7 - - - -
275G THR* 3.3 8.1 + - - -
287G LEU 3.4 1.4 - - - +
288G THR* 3.5 5.0 - - - +
289G THR* 2.8 43.9 + - + +
291G ALA* 4.2 16.2 - - + -
300G TYR* 1.3 82.2 - - - +
302G LEU* 1.3 69.4 - - - +
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Residues in contact with LEU 302 (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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271G MET 3.6 0.7 - - - +
272G LEU* 3.1 5.9 - - - +
273G MET* 2.9 35.3 + - + +
275G THR* 4.3 8.1 - - + -
280G VAL* 3.8 49.1 - - + +
282G SER* 4.7 9.6 - - - -
286G LEU* 5.1 5.8 - - + -
287G LEU 3.6 12.8 - - - +
288G THR* 3.9 4.7 - - + +
301G ALA* 1.3 77.9 - - - +
303G GLU* 1.3 59.4 + - - +
395G MET* 3.9 21.3 - - - +
398G ASP* 4.1 25.1 - - + +
399G SER* 4.6 14.8 - - - -
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Residues in contact with GLU 303 (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* 2.6 37.8 + - - -
135G TYR* 4.1 2.9 + - - -
188G ARG* 2.9 22.0 + - - -
247G GLN* 5.0 0.3 + - - -
270G PHE* 4.2 3.0 - - - -
271G MET 3.2 3.4 - - - -
272G LEU* 3.3 30.2 - - + +
286G LEU* 3.1 9.5 - - - +
287G LEU* 2.8 53.0 + - + +
289G THR* 4.2 9.7 - - + +
302G LEU* 1.3 75.8 - - - +
304G GLY* 1.3 71.9 + - - +
305G ALA* 4.1 5.5 - - - +
395G MET* 5.1 0.9 - - - -
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Residues in contact with GLY 304 (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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269G CYS 3.5 1.9 - - - +
270G PHE* 3.4 6.6 - - - -
271G MET* 2.8 37.1 + - - +
286G LEU* 3.3 19.7 - - - +
303G GLU* 1.3 76.0 - - - +
305G ALA* 1.3 62.9 + - - -
306G VAL* 5.2 0.2 - - - -
353G ALA* 4.3 0.2 - - - -
391G VAL* 3.5 18.1 - - - +
395G MET* 4.7 0.8 - - - +
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Residues in contact with ALA 305 (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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135G TYR* 3.9 27.4 - - + +
269G CYS 3.8 2.9 - - - -
270G PHE* 3.7 21.5 - - + -
287G LEU* 4.8 0.7 - - + -
303G GLU* 4.0 9.4 + - + +
304G GLY* 1.3 74.3 - - - +
306G VAL* 1.3 60.3 + - - +
307G PHE* 4.2 4.3 - - + -
352G GLY* 3.6 1.8 - - - -
353G ALA* 2.6 42.6 + - - +
356G TRP* 4.4 9.0 - - + -
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Residues in contact with VAL 306 (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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268G GLY* 3.2 2.4 - - - -
269G CYS* 2.7 56.2 + - + +
270G PHE* 3.9 4.0 - - - -
305G ALA* 1.3 77.2 - - - +
307G PHE* 1.3 65.4 + - - +
308G MET 3.7 8.7 - - - +
309G ALA* 5.6 0.2 - - + -
352G GLY* 5.3 2.2 - - - +
353G ALA 4.2 12.6 - - - +
387G GLN* 3.4 63.0 - - + +
388G THR* 5.1 0.9 - - - +
391G VAL* 4.7 12.1 - - + -
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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