Contacts of the helix formed by residues 288 - 309 (chain C) in PDB entry 1JLH
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 GLY 288 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C ARG* 3.2 28.1 - - - +
284C ALA* 2.8 20.3 + - - +
287C VAL* 1.3 87.5 - - - +
289C PHE* 1.3 64.7 + - - -
290C ASP* 3.3 3.1 - - - -
291C ASN 3.4 0.7 + - - -
292C PHE 3.3 14.7 + - - -
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Residues in contact with PHE 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ARG* 6.1 0.7 - - - -
125C LEU* 3.3 46.0 - - + -
128C MET* 3.7 12.1 - - + -
129C LYS* 3.5 52.3 - - + +
132C CYS* 4.6 9.8 - - + +
284C ALA* 3.4 19.4 + - + -
288C GLY* 1.3 70.3 - - - -
290C ASP* 1.3 66.1 + - - +
292C PHE* 3.2 19.7 + + - +
293C GLU* 3.0 52.9 + - + +
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Residues in contact with ASP 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LYS* 5.2 8.8 + - - -
288C GLY 3.3 0.8 - - - -
289C PHE* 1.3 78.7 - - - +
291C ASN* 1.3 65.6 + - - +
293C GLU* 3.2 20.0 + - - +
294C GLN* 3.1 25.4 + - - +
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Residues in contact with ASN 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C LEU* 6.1 0.4 - - - -
173C TYR* 3.7 29.4 + - - +
287C VAL* 2.7 39.6 + - + +
288C GLY 3.4 1.6 + - - -
289C PHE 3.3 0.2 - - - -
290C ASP* 1.3 79.0 - - - +
292C PHE* 1.3 64.9 + - - +
294C GLN* 3.1 12.6 + - - +
295C LEU* 2.9 19.6 + - - +
483C PRO* 3.5 31.7 - - + +
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Residues in contact with PHE 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C LEU* 3.9 20.9 - - + -
128C MET* 4.5 9.4 - - - -
275C LEU 3.8 15.7 - - - -
276C TRP 3.8 5.8 - - - -
277C SER 3.8 19.5 - - - -
280C GLY* 3.8 18.4 - - - -
283C ILE* 3.8 24.2 - - + -
284C ALA* 3.9 14.6 - - + -
287C VAL* 4.6 0.6 - - - +
288C GLY 3.3 10.8 + - - +
289C PHE* 3.2 29.1 + + - +
291C ASN* 1.3 78.8 - - - +
293C GLU* 1.3 58.4 + - - +
295C LEU* 3.1 16.2 + - + +
296C LEU* 3.0 54.8 + - + +
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Residues in contact with GLU 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ARG* 2.8 33.9 + - - +
129C LYS* 5.3 7.6 + - - +
289C PHE* 3.0 47.1 + - + +
290C ASP* 3.5 23.8 - - - +
291C ASN 3.2 0.2 - - - -
292C PHE* 1.3 75.4 - - + +
294C GLN* 1.3 54.9 + - + +
296C LEU* 3.2 10.7 + - + +
297C SER* 2.7 40.9 + - - +
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Residues in contact with GLN 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C HIS* 5.3 10.0 + - - -
290C ASP* 3.1 16.1 + - + +
291C ASN* 3.1 15.9 + - - +
293C GLU* 1.3 76.5 - - - +
295C LEU* 1.3 57.7 + - - +
297C SER* 3.1 9.1 + - - -
298C GLY 2.8 26.3 + - - -
483C PRO* 4.0 12.6 - - + -
484C PHE* 3.4 37.4 - - + +
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Residues in contact with LEU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C VAL* 4.1 22.7 - - + -
170C LEU* 4.7 2.9 - - + -
275C LEU* 4.1 20.6 - - + -
276C TRP* 3.7 14.0 - - + -
283C ILE* 4.4 4.5 - - + -
291C ASN 2.9 12.8 + - - +
292C PHE* 3.2 30.3 - - + +
294C GLN* 1.3 76.5 - - - +
296C LEU* 1.3 62.6 + - + +
298C GLY 3.3 1.0 + - - -
299C ALA 3.2 15.9 + - - -
483C PRO* 3.3 26.4 + - + +
486C LEU* 4.1 19.7 - - + -
487C GLY* 3.5 27.7 - - - +
490C VAL* 5.9 0.7 - - + -
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Residues in contact with LEU 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LEU 3.9 15.3 - - - +
103C ARG* 3.5 23.0 - - + +
105C ARG* 3.8 29.2 - - - +
125C LEU* 4.1 10.8 - - + -
276C TRP* 4.1 25.1 - - + +
292C PHE* 3.0 57.3 + - + +
293C GLU* 3.2 9.4 + - + +
295C LEU* 1.3 78.8 - - + +
297C SER* 1.3 52.0 + - - +
299C ALA* 3.1 5.2 + - - +
300C HIS* 2.8 35.0 + - - +
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Residues in contact with SER 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ARG* 3.8 25.6 + - - +
293C GLU* 2.7 28.9 + - - +
294C GLN* 3.4 13.7 + - - -
296C LEU* 1.3 73.0 - - - +
298C GLY* 1.3 57.4 + - - +
300C HIS* 3.3 3.9 + - - +
301C TRP* 2.9 28.9 + - - +
484C PHE* 3.7 16.5 - - - -
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Residues in contact with GLY 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C GLN 2.8 10.9 + - - -
295C LEU 3.8 0.9 - - - -
296C LEU 3.2 0.2 - - - -
297C SER* 1.3 78.2 - - - +
299C ALA* 1.3 61.1 + - - +
301C TRP* 3.2 5.5 + - - +
302C MET 3.1 16.8 + - - -
484C PHE* 3.2 40.8 - - - -
488C ALA* 3.4 15.7 - - - +
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Residues in contact with ALA 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ARG* 3.6 20.6 - - + +
276C TRP* 3.4 36.8 - - + -
295C LEU 3.2 4.6 + - - -
296C LEU 3.1 6.9 + - - +
298C GLY* 1.3 76.5 - - - +
300C HIS* 1.3 59.2 + - - +
302C MET* 3.2 2.8 + - - +
303C ASP* 2.8 35.0 + - - +
487C GLY 3.5 11.2 - - - +
491C ALA* 3.7 7.0 - - + -
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Residues in contact with HIS 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C VAL 5.2 0.6 + - - -
103C ARG* 3.1 25.0 + - - +
104C ASN* 3.4 27.6 - - - -
105C ARG* 3.8 19.7 - - + -
106C SER* 2.7 27.5 + - - -
296C LEU 2.8 9.4 + - - +
297C SER* 3.4 13.5 - - - +
299C ALA* 1.3 77.3 - - - +
301C TRP* 1.3 63.2 + - - +
303C ASP* 3.3 13.2 + - - +
304C GLN* 3.1 56.4 + - + +
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Residues in contact with TRP 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU* 4.0 20.6 - - + -
44C ASN 3.4 19.3 + - - -
45C THR* 3.6 46.7 + - + +
46C ASN* 5.1 5.7 - - - +
297C SER 2.9 13.5 + - - +
298C GLY 3.5 8.5 - - - +
300C HIS* 1.3 78.8 - - - +
302C MET* 1.3 79.9 + - + +
304C GLN* 3.1 12.9 + - + +
305C HIS* 3.0 53.9 + + + -
484C PHE* 3.8 16.2 - + + -
488C ALA* 5.0 1.3 - - + -
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Residues in contact with MET 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU* 4.3 6.1 - - + -
50C ILE* 4.0 22.4 - - + -
298C GLY 3.1 8.6 + - - +
299C ALA 3.6 6.7 - - - +
301C TRP* 1.3 97.4 - - + +
303C ASP* 1.3 67.5 + - - +
305C HIS* 3.2 21.5 + - - +
306C PHE* 2.9 23.2 + - - +
316C PRO* 4.2 6.3 - - - -
488C ALA* 3.4 30.5 - - + +
491C ALA* 3.8 7.6 - - + +
492C MET* 3.4 41.1 - - + +
495C HIS* 4.5 4.0 - - - +
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Residues in contact with ASP 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C PHE* 3.7 18.7 - - + -
100C VAL* 3.5 15.5 - - - +
103C ARG* 2.7 45.1 + - - +
299C ALA 2.8 18.4 + - - +
300C HIS* 3.4 12.4 + - - +
301C TRP 3.2 0.2 - - - -
302C MET* 1.3 75.7 - - - +
304C GLN* 1.3 64.3 + - - +
306C PHE* 3.5 1.4 + - - +
307C ARG* 3.0 29.6 + - - +
491C ALA* 4.0 0.7 - - - +
495C HIS* 2.7 34.5 - - - -
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Residues in contact with GLN 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C PHE* 5.2 5.6 - - - -
104C ASN* 5.2 0.2 + - - -
106C SER* 5.8 0.2 - - - -
300C HIS* 3.1 51.9 + - + +
301C TRP* 3.3 11.7 - - + +
302C MET 3.1 0.4 - - - -
303C ASP* 1.3 81.7 - - - +
305C HIS* 1.3 66.8 + - - +
307C ARG* 4.4 10.2 - - - +
308C THR* 2.9 43.5 + - + +
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Residues in contact with HIS 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU* 3.3 33.7 - - + +
301C TRP* 3.0 38.6 + + + +
302C MET* 3.2 12.2 + - - +
304C GLN* 1.3 75.5 - - - +
306C PHE* 1.3 60.2 + - - +
308C THR* 4.3 2.5 - - - -
309C THR* 2.6 55.0 + - + +
313C LYS 3.6 9.7 + - - -
314C ASN* 3.7 9.9 - - - -
315C ALA* 3.0 40.6 - - + -
316C PRO* 3.8 8.9 - - + +
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Residues in contact with PHE 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C VAL* 5.0 4.0 - - + -
80C ARG* 2.9 48.6 + - + -
83C MET* 6.1 0.4 - - - -
84C PHE* 4.2 8.1 - + - -
302C MET 2.9 16.0 + - - +
303C ASP 3.7 1.8 - - - +
305C HIS* 1.3 80.1 + - - +
307C ARG* 1.3 57.9 + - - +
314C ASN* 2.8 39.2 + - - +
316C PRO* 3.9 15.0 - - + -
317C VAL* 3.7 21.5 - - + -
495C HIS* 3.4 42.4 - + + +
498C PHE* 3.9 17.0 - + - -
499C VAL* 3.8 21.5 - - + -
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Residues in contact with ARG 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ARG* 3.4 27.6 + - - +
81C GLU* 2.8 39.3 + - - +
84C PHE* 3.4 51.8 + - + +
85C ASN* 3.2 24.0 + - - -
303C ASP 3.0 19.1 + - - +
304C GLN* 3.1 12.8 + - - +
306C PHE* 1.3 78.8 - - - +
308C THR* 1.3 65.3 + - + +
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Residues in contact with THR 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C GLN* 2.9 35.1 + - + +
305C HIS* 4.0 2.6 + - - -
307C ARG* 1.3 86.4 - - + +
309C THR* 1.3 64.2 + - - +
310C PRO* 3.7 7.4 - - - +
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Residues in contact with THR 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLU* 5.4 1.0 - - - +
80C ARG* 4.5 5.2 + - - -
305C HIS* 2.6 44.5 + - + +
306C PHE 4.4 0.3 - - - +
307C ARG 3.7 1.0 - - - -
308C THR* 1.3 80.8 + - - +
310C PRO* 1.3 82.2 - - + +
311C LEU* 3.3 1.7 + - - +
313C LYS* 3.3 33.7 - - + +
314C ASN* 2.9 23.9 + - - +
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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
------------------------------------------------------------
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