Contacts of the strand formed by residues 251 - 257 (chain E) in PDB entry 3KQG
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 TYR 251 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211D LEU* 3.8 22.9 - - - +
209E PHE* 3.7 29.5 - + + +
210E SER 3.9 7.0 + - - -
246E ALA* 3.4 37.7 - - + -
249E LEU* 3.5 20.2 - - + +
250E ILE* 1.3 74.3 - - - +
252E TRP* 1.3 62.3 + - - +
253E ILE* 3.9 0.2 - - - +
297E ASN* 3.0 4.3 - - - +
298E ILE* 2.7 40.9 + - + +
316E LEU* 3.0 45.3 - - + +
317E PHE 3.7 7.9 - - - -
318E ILE* 3.4 35.4 - - + -
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Residues in contact with TRP 252 (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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214E LYS 3.0 27.9 + - - -
215E THR 4.0 1.3 - - - -
216E TRP* 3.3 40.2 - + + +
219E ALA* 4.7 4.3 - - + -
230E LEU* 4.0 6.0 - - + +
251E TYR* 1.3 72.4 - - - +
253E ILE* 1.3 62.4 + - - +
295E CYS* 3.4 36.3 - - + -
296E GLY 3.2 26.5 - - - -
297E ASN* 3.7 7.1 - - + +
309E ALA* 3.7 20.0 - - + -
310E PRO 3.5 22.2 - - - -
311E CYS 4.2 0.4 - - - -
313E LYS 3.3 15.3 + - - -
315E PHE* 3.4 39.1 - + + +
316E LEU 2.7 10.5 + - - +
317E PHE* 4.0 8.9 - - + +
318E ILE 3.1 24.3 + - - -
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Residues in contact with ILE 253 (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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216E TRP* 3.0 23.7 + - - -
230E LEU* 3.6 11.2 - - - +
231E THR* 3.7 26.2 - - + +
233E VAL* 4.2 5.2 - - + -
242E LEU* 5.3 0.2 - - + -
251E TYR 3.5 4.4 + - - +
252E TRP* 1.3 78.2 - - - +
254E GLY* 1.3 59.0 + - - +
255E LEU* 3.0 26.3 + - + +
266E TRP* 3.9 12.3 - - + -
296E GLY 3.2 16.8 + - - +
297E ASN* 4.3 1.6 - - - -
298E ILE* 3.8 23.1 - - + +
306E TRP* 3.4 35.2 - - + +
318E ILE* 4.3 9.0 - - + -
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Residues in contact with GLY 254 (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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216E TRP* 4.1 4.8 - - - -
230E LEU* 3.6 20.3 - - - +
231E THR 2.8 23.9 + - - -
253E ILE* 1.3 70.6 - - - +
255E LEU* 1.3 61.9 + - - +
256E THR* 3.4 0.7 + - - +
265E SER 3.3 4.3 - - - +
266E TRP* 3.5 9.4 - - - -
267E VAL* 3.0 32.2 + - - +
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Residues in contact with LEU 255 (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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216E TRP* 3.2 13.7 + - - -
253E ILE* 3.0 26.6 + - + -
254E GLY* 1.3 75.8 - - - +
256E THR* 1.3 58.6 + - - +
264E TRP* 4.0 15.5 - - + -
265E SER 3.6 3.8 - - - +
266E TRP* 3.7 17.0 - - + -
272E PHE* 3.6 33.4 - - + -
281E TRP* 4.2 8.1 - - + -
295E CYS* 3.6 1.4 - - - -
296E GLY* 3.1 41.9 + - - +
306E TRP* 3.6 33.9 - - + -
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Residues in contact with THR 256 (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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216E TRP* 3.6 29.1 - - + -
254E GLY 4.2 4.5 - - - +
255E LEU* 1.3 75.9 - - - +
257E LYS* 1.3 65.5 + - - +
258E ALA* 4.0 2.7 + - + +
263E ASP 3.8 1.0 - - - +
264E TRP* 3.5 7.2 - - - -
265E SER* 2.9 56.3 + - - +
266E TRP 4.9 0.4 - - - -
267E VAL* 4.7 7.2 - - + +
294E HIS 3.6 8.6 + - - -
295E CYS* 4.7 2.9 - - - -
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Residues in contact with LYS 257 (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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256E THR* 1.3 77.0 + - - +
258E ALA* 1.3 60.6 + - - +
259E GLY 3.4 13.3 + - - +
260E MET 4.1 11.3 + - - +
261E GLU 4.5 2.4 + - - -
262E GLY 3.5 26.9 + - - +
263E ASP 3.7 4.5 - - - +
264E TRP* 3.6 43.6 - - + +
286E PRO* 5.7 2.4 - - - +
288E ASN* 4.5 15.0 - - - +
293E GLU 4.3 6.3 - - - -
294E HIS* 2.7 61.7 + - + +
308E ASP* 5.8 0.2 - - - -
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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