Contacts of the strand formed by residues 278 - 283 (chain G) in PDB entry 1QDU
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 278 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230G PHE* 3.5 12.3 - - + +
265G PHE* 2.9 37.0 - - + +
266G THR 3.9 9.9 - - - -
267G GLY* 5.4 0.4 - - - -
273G LEU* 2.9 34.8 + - + +
274G ALA* 4.5 1.2 - - - +
275G GLY 4.4 2.0 - - - +
276G LYS 2.6 31.7 + - - +
277G PRO* 1.3 74.3 - - - +
279G VAL* 1.3 61.9 + - - +
280G PHE* 4.0 7.1 - - + -
323H ASP 5.7 0.9 - - - -
325H ALA 4.3 10.6 + - - -
326H ASP* 2.9 12.7 + - - +
327H PHE* 3.5 38.1 - - + -
328H LEU* 3.1 24.3 + - - +
394H LEU* 5.2 0.2 - - - +
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Residues in contact with VAL 279 (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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229G CYS* 4.5 7.9 - - - -
230G PHE 2.8 11.4 + - - +
231G ILE* 3.4 17.6 - - + -
232G CYS* 2.9 23.1 + - - +
277G PRO* 4.9 0.7 - - + -
278G LYS* 1.3 75.5 - - - +
280G PHE* 1.3 75.4 + - - +
281G PHE* 3.3 44.0 - - + -
328H LEU* 3.6 20.6 - - + +
366H ILE* 6.1 0.7 - - + -
394H LEU* 5.9 0.4 - - + -
398H LEU* 4.0 26.5 - - + -
400H PHE* 4.7 3.6 - - + -
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Residues in contact with PHE 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215G LEU* 5.3 1.1 - - + -
230G PHE* 4.6 5.2 - + - -
232G CYS* 3.2 35.7 - - + -
234G ILE* 5.0 3.8 - - + -
258G ILE* 6.2 0.2 - - + -
261G LEU* 4.4 8.3 - - + -
262G THR* 3.6 39.9 - - + -
265G PHE* 3.7 25.4 - + - -
278G LYS* 4.0 15.9 - - + -
279G VAL* 1.3 82.0 - - - +
281G PHE* 1.3 59.3 + - - +
282G ILE* 3.8 9.9 - - + -
327H PHE* 3.8 24.0 - + - -
328H LEU 2.9 9.6 + - - +
329H LEU* 3.5 19.1 - - + +
330H GLY* 2.6 34.1 + - - -
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Residues in contact with PHE 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G LEU* 4.9 0.4 - - + -
193G PHE* 3.7 28.7 - + - -
231G ILE* 4.0 3.6 - - + -
232G CYS 2.8 9.9 + - - -
233G CYS* 3.3 26.8 - - + +
234G ILE 2.9 27.4 + - - +
235G LEU* 4.8 1.6 - - - +
279G VAL* 3.3 29.6 - - + -
280G PHE* 1.3 77.9 - - - +
282G ILE* 1.3 62.4 + - - +
283G GLN* 5.5 0.4 - - - -
328H LEU* 5.3 1.1 - - + -
330H GLY* 3.6 10.1 - - - +
349H TYR* 3.6 23.6 - - + -
350H ILE* 5.0 5.2 - - + -
353H LEU* 3.7 33.0 - - + -
357H LEU* 5.3 1.1 - - + -
366H ILE* 4.8 13.7 - - + -
370H LEU* 4.5 15.7 - - + -
400H PHE* 5.9 2.9 - + - -
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Residues in contact with ILE 282 (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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232G CYS 5.1 0.2 - - - +
234G ILE* 3.6 21.5 - - + +
243G ILE* 3.6 27.4 - - + -
258G ILE* 4.2 20.6 - - + -
261G LEU* 5.8 0.2 - - + -
280G PHE* 3.8 18.2 - - + -
281G PHE* 1.3 80.6 - - - +
283G GLN* 1.3 62.6 + - - +
284G ALA* 3.9 11.9 - - + +
286G GLN* 5.5 0.2 - - - +
329H LEU* 3.3 27.4 - - + -
330H GLY 3.1 7.8 + - - +
331H MET* 3.9 24.2 - - + -
332H ALA* 3.2 26.5 + - - +
349H TYR* 3.9 2.5 - - - -
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Residues in contact with GLN 283 (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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179G ARG* 4.3 5.4 - - - +
185G ASP* 4.3 1.8 - - - +
234G ILE 2.8 16.1 + - - +
235G LEU* 3.8 13.7 - - + -
236G SER 3.1 22.7 + - - +
282G ILE* 1.3 73.2 - - - +
284G ALA* 1.3 60.2 + - - +
332H ALA* 3.9 3.6 - - + -
339H SER* 3.0 26.7 + - - -
340H TYR 4.6 0.7 - - - +
347H THR* 2.8 47.4 + - + +
349H TYR* 3.4 18.7 + - - +
350H ILE* 3.8 13.9 - - + -
385H GLN* 4.7 0.2 + - - -
4403W ASP* 3.1 18.1 + - - +
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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