Contacts of the strand formed by residues 278 - 283 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E CYS* 3.5 8.3 - - + +
265E PHE* 3.1 37.0 + - + +
266E ASN* 5.2 3.8 - - - +
267E GLY 5.7 0.8 - - - +
273E LEU* 2.9 42.4 + - + -
275E GLY 4.8 0.6 - - - +
276E LYS 2.7 25.8 + - - +
277E PRO* 1.3 73.9 - - - +
279E LEU* 1.3 63.2 + - - +
280E PHE* 3.4 22.1 - - + -
323E THR 5.8 0.7 - - - -
325E SER* 3.3 28.0 + - - -
326E ASP* 2.9 14.1 + - - +
327E ILE* 3.8 12.3 - - + -
328E PHE 3.1 24.6 + - - -
294G PHE* 6.0 1.2 - - - -
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Residues in contact with LEU 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E CYS* 4.2 7.2 - - - -
230E CYS 2.8 14.4 + - - +
231E VAL* 3.5 17.3 - - + -
232E VAL* 2.9 25.0 + - - +
277E PRO* 4.3 9.2 - - + -
278E LYS* 1.3 75.2 - - - +
280E PHE* 1.3 67.0 + - - +
281E PHE* 4.0 18.6 - - + -
328E PHE* 3.4 19.5 - - + +
366E LEU* 3.5 24.9 - - + -
394E LEU* 4.9 2.0 - - + -
398E LEU* 3.5 29.4 - - + -
400E PHE* 3.7 25.6 - - + -
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Residues in contact with PHE 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E VAL* 3.4 29.6 - - + +
234E ILE* 6.3 0.4 - - + -
261E ILE* 4.1 19.3 - - + -
262E VAL* 3.9 28.5 - - + -
265E PHE* 3.5 45.3 - + + -
278E LYS* 3.4 30.5 - - + -
279E LEU* 1.3 73.7 - - - +
281E PHE* 1.3 60.1 + - - +
282E ILE* 3.9 10.6 + - + -
327E ILE* 4.4 3.1 - - + -
328E PHE* 2.7 17.0 + - - +
329E VAL* 3.5 23.8 - - + +
330E SER* 2.7 34.3 + - - +
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Residues in contact with PHE 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E LEU* 6.2 0.9 - - + -
193E PHE* 3.6 17.3 - + - -
231E VAL* 3.5 33.0 - - + -
232E VAL 3.0 8.1 + - - -
233E VAL* 3.4 25.0 - - + +
234E ILE 2.9 25.6 + - - -
279E LEU* 4.0 19.1 - - + -
280E PHE* 1.3 71.9 - - - +
282E ILE* 1.3 61.5 + - - +
283E GLN 3.5 2.8 + - - -
328E PHE* 4.7 2.5 - + - -
330E SER* 3.6 19.1 - - - -
349E TYR* 3.5 26.5 - - + +
353E LEU* 4.1 17.0 - - + -
357E PHE* 4.7 6.3 - + - -
366E LEU* 4.0 29.4 - - + -
370E LEU* 4.4 5.2 - - + -
400E PHE* 5.0 0.2 - + - -
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Residues in contact with ILE 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E VAL 5.5 0.7 - - - +
234E ILE* 3.7 16.8 - - + +
242E ALA 5.3 0.4 - - - +
243E VAL* 3.6 29.4 - - + -
258E VAL* 3.2 46.9 - - + -
261E ILE* 5.5 6.3 - - + -
262E VAL* 5.9 0.2 - - + -
280E PHE* 4.6 9.9 - - + -
281E PHE* 1.3 74.8 - - - +
283E GLN* 1.3 57.5 + - - +
284E ALA* 3.2 14.5 + - + +
329E VAL* 3.8 15.9 - - + -
330E SER 3.2 13.4 + - - +
331E TYR* 4.2 12.2 - - + -
332E SER* 3.4 21.0 + - - -
349E TYR* 4.9 0.9 - - - -
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Residues in contact with GLN 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E ARG* 3.9 12.6 - - - +
185E ASP* 5.2 0.9 - - - +
234E ILE 2.9 8.7 + - - +
235E LEU* 3.6 22.7 - - + -
236E SER 3.0 24.1 + - - +
281E PHE 3.5 2.8 + - - +
282E ILE* 1.3 67.2 - - - +
284E ALA* 1.3 60.9 + - - +
332E SER* 3.2 18.4 - - - -
339E SER* 2.9 19.9 + - - -
347E SER* 3.0 26.4 + - - +
349E TYR* 3.5 9.8 - - + +
350E VAL* 4.0 19.5 - - + -
189F GLY* 2.7 37.6 + - - -
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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