Contacts of the helix formed by residues 287 - 299 (chain E) in PDB entry 4KSL
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 GLU 287 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263E ARG* 2.5 30.4 + - - +
276E HIS* 3.6 16.4 - - - +
285E GLY 4.1 0.8 + - - -
286E LEU* 1.3 76.1 - - - +
288E GLN* 1.3 67.6 + - - +
289E VAL* 3.2 13.9 - - + +
290E GLU* 2.9 27.3 + - - +
291E MET* 3.3 9.2 + - - +
42F ARG* 2.5 32.1 + - - -
71F LEU 3.4 12.6 - - - +
72F ARG* 4.0 17.0 - - - +
73F LEU 3.5 12.3 - - - +
74F ARG* 4.1 11.6 - - + +
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Residues in contact with GLN 288 (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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286E LEU 3.8 0.6 + - - -
287E GLU* 1.3 72.8 - - - +
289E VAL* 1.3 64.0 + - - +
291E MET* 3.1 27.2 + - - +
292E PHE* 3.5 10.8 - - - -
306E ARG* 3.4 33.0 + - - +
319E TYR* 3.7 21.5 + - + +
337E ASP* 3.8 17.5 + - + +
340E TYR* 5.5 4.0 - - - +
7F THR* 6.2 0.5 - - - -
8F LEU* 4.3 23.1 + - + +
9F THR* 5.6 3.1 - - - +
71F LEU* 4.1 36.2 + - + +
73F LEU* 4.0 13.3 + - - +
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Residues in contact with VAL 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256E PHE* 3.8 27.4 - - + +
259E LEU* 4.5 5.2 - - + +
260E LEU* 3.9 23.3 - - + +
263E ARG* 3.5 37.0 - - - +
287E GLU* 3.7 11.7 - - + +
288E GLN* 1.3 78.8 - - - +
290E GLU* 1.3 63.0 + - - +
292E PHE* 3.4 20.7 - - - +
293E LEU* 3.9 1.7 + - - +
8F LEU* 3.7 28.1 - - + +
70F VAL* 4.8 9.6 - - + -
71F LEU 5.4 1.3 + - - +
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Residues in contact with GLU 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236E MET* 4.6 2.7 - - - +
260E LEU* 4.0 18.2 - - + -
263E ARG* 2.9 33.1 + - - +
272E LEU* 4.2 5.0 - - + +
276E HIS* 3.2 25.4 + - - +
277E LEU* 6.3 4.3 - - + -
280E VAL* 5.4 1.7 - - - +
285E GLY 4.2 3.6 - - - +
286E LEU* 3.6 25.2 - - + +
287E GLU* 2.9 31.3 + - - +
289E VAL* 1.3 73.3 - - - +
291E MET* 1.3 59.8 + - - +
292E PHE 3.2 1.6 - - - -
293E LEU* 3.1 17.0 + - + +
294E LEU* 2.9 25.5 + - - +
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Residues in contact with MET 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E ALA* 4.0 23.6 - - + -
286E LEU* 4.1 16.2 - - - +
287E GLU 3.3 12.7 + - - +
288E GLN* 3.1 16.0 + - - +
290E GLU* 1.3 74.2 - - - +
292E PHE* 1.3 61.1 + - - +
294E LEU* 3.3 9.5 + - + +
295E ALA* 2.9 29.3 + - - +
302E ILE* 4.0 32.7 - - + +
319E TYR* 3.8 25.1 - - + +
332E LEU* 4.5 5.6 - - + -
340E TYR* 3.7 41.1 - - + +
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Residues in contact with PHE 292 (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 PHE* 3.4 39.3 - + + -
288E GLN 3.5 11.7 - - - -
289E VAL* 3.4 14.6 - - - +
291E MET* 1.3 78.9 - - - +
293E LEU* 1.3 56.9 + - - +
295E ALA* 3.2 3.8 + - - +
296E TYR* 2.9 34.0 + - - -
318E VAL 4.7 2.2 - - - -
319E TYR* 3.5 30.0 - + - -
320E PRO* 3.6 20.6 - - + -
321E THR* 3.5 32.3 - - + -
8F LEU* 3.7 47.1 - - + -
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Residues in contact with LEU 293 (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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236E MET* 3.6 42.6 - - + +
239E ARG* 4.2 11.2 - - + -
240E ALA* 3.9 18.2 - - + +
243E LEU* 4.7 4.0 - - + -
256E PHE* 3.8 19.4 - - + -
260E LEU* 4.3 12.1 - - + -
272E LEU* 4.1 26.9 - - + -
277E LEU* 5.4 5.2 - - + -
289E VAL 4.7 0.2 - - - +
290E GLU* 3.1 23.5 + - + +
292E PHE* 1.3 80.0 - - - +
294E LEU* 1.3 57.8 + - - +
296E TYR* 3.4 2.6 + - - +
297E ALA* 2.9 29.3 + - - +
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Residues in contact with LEU 294 (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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130E ALA 4.1 5.8 - - - +
131E LEU* 3.6 34.8 - - + -
134E THR* 3.6 30.5 - - + +
232E VAL* 3.7 21.3 - - + -
236E MET* 3.8 14.5 - - + -
286E LEU* 4.1 8.7 - - + -
290E GLU 2.9 12.5 + - - +
291E MET* 3.5 15.3 - - + +
292E PHE 3.2 0.2 - - - -
293E LEU* 1.3 74.7 - - - +
295E ALA* 1.3 65.3 - - - +
297E ALA* 3.0 2.8 + - - +
298E VAL* 3.0 36.1 + - + +
302E ILE* 4.0 11.4 - - + -
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Residues in contact with ALA 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E MET 2.9 14.3 + - - +
292E PHE 3.4 8.3 - - - +
294E LEU* 1.3 76.7 - - - +
296E TYR* 1.3 52.9 + - - +
298E VAL* 4.5 1.8 - - - -
299E ARG* 2.7 35.0 + - - -
300E HIS 3.1 25.8 + - - +
302E ILE* 4.0 9.4 - - + -
319E TYR 3.6 25.4 - - - +
320E PRO* 4.1 6.7 - - + -
327E TRP* 3.7 2.7 - - - -
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Residues in contact with TYR 296 (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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239E ARG* 3.8 46.9 + - + -
243E LEU* 5.0 2.2 - - + -
254E PRO* 3.6 30.8 - - + +
256E PHE* 3.4 26.0 - + + -
292E PHE 2.9 25.1 + - - +
293E LEU* 3.8 7.0 - - + +
295E ALA* 1.3 76.2 - - - +
297E ALA* 1.3 63.5 + - - +
299E ARG* 3.3 23.9 + - - +
320E PRO* 3.6 33.6 - - + +
322E ASP 5.4 2.3 + - - -
324E PRO* 5.8 2.6 - - + +
327E TRP* 3.8 22.8 - + - -
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Residues in contact with ALA 297 (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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148E TRP* 4.2 0.7 - - - -
232E VAL 4.5 1.1 - - - +
235E LEU* 4.1 23.3 - - + +
236E MET* 3.6 37.7 - - + +
239E ARG* 4.8 4.5 - - - +
293E LEU 2.9 17.8 + - - +
294E LEU* 3.0 6.5 + - + +
296E TYR* 1.3 78.8 - - - +
298E VAL* 1.3 63.7 + - + +
299E ARG* 2.9 24.8 + - - +
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Residues in contact with VAL 298 (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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134E THR* 4.3 18.8 - - + -
135E LEU* 4.6 12.3 - - + -
138E ALA* 5.9 1.8 - - + -
148E TRP* 3.5 28.9 + - + -
195E LEU* 6.3 0.2 - - + -
199E TRP* 5.3 4.5 - - + -
232E VAL* 4.2 34.3 - - + -
235E LEU* 5.1 2.0 - - + -
294E LEU* 3.0 19.8 + - + +
295E ALA* 4.0 2.0 - - - +
297E ALA* 1.3 76.3 - - + +
299E ARG* 1.3 71.0 + - - +
300E HIS* 2.9 37.4 + - + +
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Residues in contact with ARG 299 (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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148E TRP* 3.3 55.6 + - + +
235E LEU* 5.3 3.0 - - - +
238E ASN* 5.4 5.1 - - - +
239E ARG* 4.1 25.1 - - - +
242E GLU* 5.5 1.6 + - - -
295E ALA 2.7 12.8 + - - -
296E TYR 3.3 12.8 + - - +
297E ALA* 2.9 26.1 + - - +
298E VAL* 1.3 81.1 - - - +
300E HIS* 1.3 62.1 + - - +
327E TRP* 3.6 44.4 - - + +
328E PRO* 3.6 9.0 - - - +
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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