Contacts of the strand formed by residues 278 - 283 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C PHE* 3.4 11.2 - - + +
265C PHE* 3.0 35.2 - - + +
266C THR 4.3 7.9 - - - -
267C GLY* 5.1 0.4 - - - +
273C LEU* 3.0 35.3 + - + -
274C ALA* 4.6 1.7 - - - +
275C GLY 4.4 2.0 - - - +
276C LYS 2.5 35.5 + - - +
277C PRO* 1.3 73.9 - - - +
279C VAL* 1.3 61.9 + - - +
280C PHE* 4.1 7.6 - - + -
323D ASP 5.6 0.9 - - - -
325D ALA 4.1 12.3 + - - -
326D ASP* 2.9 14.4 + - - +
327D PHE* 3.5 38.6 - - + -
328D LEU 3.1 23.6 + - - +
394D LEU* 5.2 0.2 - - - +
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Residues in contact with VAL 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C CYS* 4.6 6.7 - - - -
230C PHE* 2.8 10.4 + - - +
231C ILE* 3.3 22.1 - - + -
232C CYS* 2.8 25.6 + - - +
277C PRO* 4.9 1.1 - - + -
278C LYS* 1.3 76.5 - - - +
280C PHE* 1.3 72.5 + - - +
281C PHE* 3.4 43.7 - - + -
328D LEU* 3.5 21.3 - - + +
366D ILE* 6.2 0.7 - - + -
394D LEU* 5.8 0.7 - - + -
398D LEU* 4.0 27.6 - - + -
400D PHE* 4.7 3.6 - - + -
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Residues in contact with PHE 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C LEU* 5.3 0.9 - - + -
230C PHE* 4.7 3.8 - + - -
232C CYS* 3.2 35.9 - - + -
234C ILE* 5.1 2.7 - - + -
261C LEU* 4.3 9.0 - - + -
262C THR* 3.4 41.3 - - + -
265C PHE* 3.7 26.0 - + - -
278C LYS* 4.1 15.0 - - + -
279C VAL* 1.3 83.1 - - - +
281C PHE* 1.3 59.2 + - - +
282C ILE* 3.6 18.4 - - + -
327D PHE* 3.7 24.0 - + - -
328D LEU 2.9 9.5 + - - +
329D LEU* 3.4 10.5 - - + -
330D GLY* 2.5 34.8 + - - -
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Residues in contact with PHE 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LEU* 4.9 0.4 - - + -
193C PHE* 3.7 27.6 - + - -
231C ILE* 4.1 13.5 - - + -
232C CYS 3.0 5.9 + - - -
233C CYS* 3.3 17.8 - - + +
234C ILE 2.9 24.6 + - - +
235C LEU* 5.2 1.2 - - - +
279C VAL* 3.4 29.2 - - + -
280C PHE* 1.3 77.0 - - - +
282C ILE* 1.3 63.9 + - - +
283C GLN* 4.0 0.6 + - - -
328D LEU* 5.4 2.0 - - + -
330D GLY* 3.6 8.1 - - - +
349D TYR* 3.6 18.2 - - + -
350D ILE* 4.9 6.1 - - + -
353D LEU* 3.5 39.5 - - + -
357D LEU* 5.2 1.3 - - + -
366D ILE* 4.8 13.7 - - + -
370D LEU* 4.3 17.7 - - + -
400D PHE* 5.9 3.1 - + - -
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Residues in contact with ILE 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C CYS 4.8 0.2 - - - +
234C ILE* 3.5 24.0 - - + +
243C ILE* 3.6 29.4 - - + -
258C ILE* 4.3 17.5 - - + -
261C LEU* 5.7 0.9 - - + -
280C PHE* 3.6 21.8 - - + -
281C PHE* 1.3 81.1 - - - +
283C GLN* 1.3 62.9 + - - +
284C ALA* 3.8 9.4 - - + +
329D LEU* 3.4 25.8 - - + -
330D GLY 3.0 16.1 + - - +
331D MET* 4.2 23.7 - - + +
332D ALA* 3.3 18.2 + - - +
349D TYR* 4.0 2.4 - - - -
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Residues in contact with GLN 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ARG* 4.0 7.6 + - - +
185C ASP* 4.2 1.6 - - - +
234C ILE 2.7 13.5 + - - +
235C LEU* 3.9 7.0 - - + -
236C SER 3.0 23.4 + - - +
282C ILE* 1.3 72.8 - - - +
284C ALA* 1.3 63.4 + - - +
332D ALA* 3.9 5.4 - - + +
339D SER* 3.2 23.8 + - - -
340D TYR 4.6 1.0 - - - +
347D THR* 2.8 40.7 + - + +
349D TYR* 3.6 18.1 + - + +
350D ILE* 3.8 21.3 - - + -
385D GLN* 4.7 0.3 + - - -
4203U ASP* 2.9 22.8 + - - +
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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
------------------------------------------------------------
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