Contacts of the strand formed by residues 278 - 283 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230K PHE* 3.4 13.2 - - + +
265K PHE* 2.9 36.3 - - + +
266K THR 4.1 8.1 - - - -
267K GLY* 5.0 0.4 - - - +
273K LEU* 3.0 35.7 + - + +
274K ALA* 4.5 1.7 - - - +
275K GLY 4.4 1.8 - - - +
276K LYS 2.6 31.7 + - - +
277K PRO* 1.3 72.8 - - - +
279K VAL* 1.3 63.0 + - - +
280K PHE* 4.1 8.0 - - + -
323L ASP 5.7 0.9 - - - -
325L ALA 4.1 11.2 + - - -
326L ASP* 3.0 12.9 + - - +
327L PHE* 3.6 37.1 - - + -
328L LEU 3.2 21.3 + - - +
394L LEU* 5.3 0.4 - - - +
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Residues in contact with VAL 279 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229K CYS* 4.6 11.4 - - - -
230K PHE 2.7 14.8 + - - +
231K ILE* 3.4 11.4 - - + -
232K CYS* 2.8 25.4 + - - +
277K PRO* 4.9 0.4 - - + -
278K LYS* 1.3 76.2 - - - +
280K PHE* 1.3 72.5 + - - +
281K PHE* 3.4 43.7 - - + -
328L LEU* 3.5 23.3 - - + +
366L ILE* 6.1 0.4 - - + -
398L LEU* 4.0 27.8 - - + -
400L PHE* 4.8 4.0 - - + -
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Residues in contact with PHE 280 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215K LEU* 5.2 1.3 - - + -
230K PHE* 4.7 4.5 - + - -
232K CYS* 3.2 33.9 - - + -
234K ILE* 5.1 3.1 - - + -
261K LEU* 4.3 8.1 - - + -
262K THR* 3.5 45.8 - - + -
265K PHE* 3.8 25.6 - + - -
278K LYS* 4.1 14.1 - - + -
279K VAL* 1.3 83.1 - - - +
281K PHE* 1.3 59.5 + - - +
282K ILE* 3.7 9.9 - - + -
327L PHE* 3.9 20.6 - + - -
328L LEU 2.8 11.3 + - - +
329L LEU* 3.4 18.8 - - + +
330L GLY* 2.5 34.5 + - - -
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Residues in contact with PHE 281 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189K LEU* 5.4 0.2 - - + -
193K PHE* 3.8 26.2 - + - -
231K ILE* 4.0 5.4 - - + -
232K CYS 2.9 7.7 + - - -
233K CYS* 3.3 27.8 - - + +
234K ILE 2.9 25.6 + - - +
235K LEU* 4.9 1.2 - - - +
279K VAL* 3.4 29.6 - - + -
280K PHE* 1.3 77.2 - - - +
282K ILE* 1.3 62.5 + - - +
283K GLN* 5.5 0.2 - - - -
328L LEU* 5.5 1.3 - - + -
330L GLY* 3.7 10.3 - - - +
349L TYR* 3.6 23.6 - - + -
350L ILE* 4.9 5.8 - - + -
353L LEU* 3.6 34.5 - - + -
357L LEU* 5.4 1.1 - - + -
366L ILE* 4.9 14.4 - - + -
370L LEU* 4.4 16.2 - - + -
400L PHE* 5.9 2.5 - + - -
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Residues in contact with ILE 282 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232K CYS 4.8 0.4 - - - +
234K ILE* 3.6 24.0 - - + +
243K ILE* 3.6 28.7 - - + -
258K ILE* 4.4 18.6 - - + -
261K LEU* 5.7 0.9 - - + -
280K PHE* 3.7 21.5 - - + -
281K PHE* 1.3 81.5 - - - +
283K GLN* 1.3 63.2 + - - +
284K ALA* 4.1 10.3 + - + +
286K GLN* 5.7 0.2 - - - +
329L LEU* 3.5 26.0 - - + -
330L GLY 3.1 8.9 + - - +
331L MET* 4.0 20.4 - - + -
332L ALA* 3.3 26.2 + - - +
349L TYR* 3.9 2.0 - - - -
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Residues in contact with GLN 283 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179K ARG* 4.3 4.7 + - - +
185K ASP* 4.3 2.0 - - - +
234K ILE 2.8 7.9 + - - -
235K LEU* 3.4 20.1 - - + -
236K SER 3.0 25.8 + - - +
282K ILE* 1.3 72.9 - - - +
284K ALA* 1.3 63.0 + - - +
332L ALA* 3.9 5.3 - - + +
339L SER* 2.8 28.0 + - - -
340L TYR 4.6 1.2 - - - +
347L THR* 3.0 47.5 + - + +
349L TYR* 3.6 17.2 + - - +
350L ILE* 3.8 14.1 - - + -
385L GLN* 4.7 0.5 + - - -
4603Y ASP* 3.4 13.5 + - - +
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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