Contacts of the strand formed by residues 268 - 276 (chain G) in PDB entry 3QS7
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 LEU 268 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260G LEU* 4.0 20.9 - - + -
262G LEU* 3.9 18.6 - - + +
266G GLU 3.7 3.6 + - - -
267G PRO* 1.3 71.7 - - - +
269G TRP* 1.4 68.5 + - - +
270G ILE* 3.7 31.6 - - + -
316G PHE* 3.0 10.4 - - - +
317G VAL* 2.9 48.8 + - + +
320G VAL* 3.7 18.1 - - + +
324G ASP 5.2 0.4 - - - +
328G TYR* 4.0 26.5 - - + +
342G VAL* 4.1 15.9 - - + -
344G ILE* 5.4 0.7 - - + -
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Residues in contact with TRP 269 (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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173G PHE* 3.0 62.8 + + + +
174G ARG* 4.1 0.9 - - - -
175G LYS* 3.7 28.0 - - + -
182G LEU* 3.5 28.7 - - + -
244G LEU* 4.5 11.9 - - + -
245G PHE* 3.4 25.3 + - - +
260G LEU* 4.7 2.4 - - - +
267G PRO* 3.5 23.6 + - + +
268G LEU* 1.4 83.2 + - - +
270G ILE* 1.3 65.0 + - - +
271G ARG 4.2 0.4 - - - -
314G PHE* 3.6 28.5 - + + -
315G ALA 3.6 3.4 - - - -
316G PHE* 3.6 38.1 - + + -
317G VAL 5.0 0.4 + - - -
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Residues in contact with ILE 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G LEU* 5.8 0.2 - - - -
245G PHE* 3.4 31.6 - - + -
247G ILE* 3.8 11.0 - - + -
260G LEU* 4.5 4.7 - - + -
268G LEU* 3.7 36.6 - - + -
269G TRP* 1.3 75.9 - - - +
271G ARG* 1.3 60.4 + - - +
285G TRP* 3.3 29.9 - - + -
314G PHE* 3.2 3.5 - - - -
315G ALA* 2.9 63.5 + - + +
316G PHE 5.9 0.2 - - - -
328G TYR* 4.8 16.6 - - + -
340G ALA* 5.5 1.6 - - + -
342G VAL* 5.4 2.9 - - + -
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Residues in contact with ARG 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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229G ILE* 5.9 1.6 - - + -
244G LEU* 3.6 31.5 - - + +
245G PHE 2.9 8.6 + - - +
246G THR* 3.3 5.8 - - - -
247G ILE* 2.9 26.9 + - - +
269G TRP 4.2 0.4 - - - -
270G ILE* 1.3 72.3 - - - +
272G CYS* 1.3 61.1 + - - +
273G LYS* 3.9 2.3 + - + -
285G TRP* 4.5 1.1 - - - -
312G ILE* 4.3 13.0 - - + -
314G PHE* 3.7 17.0 - - + -
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Residues in contact with CYS 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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247G ILE* 3.4 9.4 - - + -
249G LEU* 3.7 19.5 - - - -
270G ILE 3.8 0.4 + - - -
271G ARG* 1.3 74.4 - - - +
273G LYS* 1.4 56.5 + - - +
283G LEU* 3.5 13.0 - - + +
285G TRP* 3.7 10.3 - - + -
311G ARG 3.4 1.9 - - - +
312G ILE* 3.3 6.1 - - - -
313G LEU 2.9 46.0 + - - +
330G CYS* 2.0 50.0 - - + -
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Residues in contact with LYS 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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226G GLY* 5.3 13.2 - - - +
246G THR* 6.1 3.6 - - - -
247G ILE 2.9 9.4 + - - +
248G ASP* 3.3 12.5 - - + +
249G LEU 2.9 25.3 + - - -
250G ASN* 3.9 2.3 + - - +
271G ARG* 3.9 4.5 + - + +
272G CYS* 1.4 73.3 - - - +
274G ALA* 1.3 60.0 + - - +
275G VAL* 5.5 2.2 - - + -
310G ILE* 5.1 8.7 - - + -
311G ARG 3.3 6.5 - - - +
312G ILE* 4.7 9.6 - - + +
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Residues in contact with ALA 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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249G LEU* 4.2 13.2 - - + -
250G ASN* 4.3 4.9 - - - +
272G CYS 4.2 0.2 + - - -
273G LYS* 1.3 75.6 - - - +
275G VAL* 1.3 63.4 + - - +
281G PHE* 3.6 12.7 - - + -
283G LEU* 3.8 28.5 - - + -
310G ILE* 3.6 3.0 - - - +
311G ARG 3.0 30.2 + - - -
335G HIS* 3.9 15.7 - - + -
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Residues in contact with VAL 275 (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 ASN* 3.3 25.6 - - + +
273G LYS* 5.5 2.0 - - + -
274G ALA* 1.3 76.8 - - - +
276G HIS* 1.3 64.0 + - - +
304G SER* 5.3 2.5 - - - +
308G THR* 4.0 19.3 - - + -
309G MET 3.5 10.8 - - - +
310G ILE* 3.9 28.3 - - + -
335G HIS* 3.1 19.0 + - - -
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Residues in contact with HIS 276 (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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274G ALA 4.2 0.4 - - - -
275G VAL* 1.3 75.8 - - - +
277G VAL* 1.3 71.8 + - + +
278G ASN* 2.8 39.3 + - + +
280G GLY 3.9 16.8 + - - -
281G PHE* 3.7 26.7 - + + -
308G THR* 3.2 7.8 - - - +
309G MET 2.9 32.0 + - - +
334G LYS* 3.6 26.5 - - + +
335G HIS* 3.6 16.2 - + - +
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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