Contacts of the strand formed by residues 278 - 283 (chain K) in PDB entry 3V3K
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
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Residue Dist Surf HB Arom Phob DC
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294I PHE* 5.9 0.6 - - - -
230K CYS* 3.5 7.6 - - + -
265K PHE* 3.0 40.2 + - + +
266K ASN* 4.7 2.9 - - - +
267K GLY* 5.2 5.2 - - - +
273K LEU* 2.7 49.5 + - + -
274K GLY* 4.8 0.6 - - - -
275K GLY 4.6 2.0 - - - +
276K LYS 3.1 15.5 + - - +
277K PRO* 1.3 74.8 - - - +
279K LEU* 1.3 63.5 + - - +
280K PHE* 3.3 21.8 - - + -
325K SER* 3.5 17.0 + - - -
326K ASP* 2.9 12.7 + - - +
327K ILE* 3.5 22.2 - - + -
328K PHE 3.2 21.5 + - - -
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Residues in contact with LEU 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* 4.3 6.3 - - - -
230K CYS 2.9 14.3 + - - +
231K VAL* 3.6 18.3 - - + -
232K VAL* 3.0 24.5 + - - +
277K PRO* 4.4 7.6 - - + -
278K LYS* 1.3 74.8 - - - +
280K PHE* 1.3 68.3 + - - +
281K PHE* 3.8 19.1 - - + -
328K PHE* 3.5 17.9 - - + +
366K LEU* 3.4 26.7 - - + -
394K LEU* 4.9 1.8 - - + -
398K LEU* 3.4 28.0 - - + -
400K PHE* 3.6 24.7 - - + -
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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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232K VAL* 3.3 33.2 - - + +
234K ILE* 6.1 0.7 - - + -
261K ILE* 4.1 17.3 - - + -
262K VAL* 3.8 30.7 - - + -
265K PHE* 3.6 40.4 - + + -
278K LYS* 3.3 31.2 - - + -
279K LEU* 1.3 72.6 - - - +
281K PHE* 1.3 60.1 + - - +
282K ILE* 3.9 8.9 + - + -
327K ILE* 4.5 3.1 - - + -
328K PHE* 2.8 16.9 + - - +
329K VAL* 3.5 23.8 - - + +
330K SER* 2.7 35.5 + - - +
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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* 6.1 1.3 - - + -
193K PHE* 3.9 17.7 - + - -
231K VAL* 3.8 31.0 - - + -
232K VAL 2.9 8.7 + - - +
233K VAL* 3.3 21.1 - - + +
234K ILE 2.9 25.5 + - - -
279K LEU* 3.8 21.1 - - + -
280K PHE* 1.3 72.8 - - - +
282K ILE* 1.3 62.0 + - - +
283K GLN 3.8 1.4 + - - -
328K PHE* 5.2 1.8 - + - -
330K SER* 3.8 8.5 - - - -
349K TYR* 3.4 27.8 - - + +
353K LEU* 3.6 23.1 - - + -
357K PHE* 4.5 9.0 - + - -
366K LEU* 4.0 22.2 - - + -
370K LEU* 4.3 18.6 - - + -
400K PHE* 5.0 0.4 - + - -
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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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234K ILE* 3.8 17.7 - - + +
243K VAL* 3.7 27.8 - - + -
258K VAL* 3.3 45.5 - - + -
261K ILE* 6.0 1.3 - - + -
280K PHE* 4.7 9.6 - - + +
281K PHE* 1.3 73.7 - - - +
283K GLN* 1.3 59.0 + - - +
284K ALA* 3.4 11.1 + - + +
329K VAL* 3.6 19.7 - - + -
330K SER 3.0 11.9 + - - +
331K TYR* 4.9 11.4 - - + -
332K SER* 3.2 28.3 + - - -
349K TYR* 4.8 2.7 - - - -
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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* 3.8 15.3 - - - +
185K ASP* 5.1 0.4 - - - +
234K ILE 2.9 9.0 + - - +
235K LEU* 3.5 24.9 - - + -
236K SER 2.9 27.4 + - - +
281K PHE 3.8 2.2 + - - -
282K ILE* 1.3 68.2 - - - +
284K ALA* 1.3 62.7 + - - +
332K SER* 3.3 13.2 - - - -
339K SER* 3.2 22.6 + - - -
347K SER* 2.7 32.3 + - - +
349K TYR* 3.6 9.9 - - + +
350K VAL* 4.3 7.9 - - + -
189L GLY* 2.7 35.8 + - - -
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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
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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