Contacts of the helix formed by residues 289 - 310 (chain D) in PDB entry 1JIQ
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 289 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ARG* 3.3 28.7 - - - +
285D ALA 2.8 17.1 + - - +
288D VAL* 1.3 82.5 - - - +
290D PHE* 1.3 66.3 + - - -
291D ASP* 3.3 3.6 - - - -
292D ASN 3.2 4.1 + - - -
293D PHE* 3.1 17.7 + - - +
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Residues in contact with PHE 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D ARG* 6.0 0.2 - - - -
126D LEU* 3.4 48.7 - - + -
129D MET* 3.9 14.1 - - + -
130D LYS* 3.5 49.6 - - + +
133D CYS* 4.5 11.9 - - + +
137D ARG* 4.9 0.2 - - - +
285D ALA* 3.5 12.3 + - + -
289D GLY* 1.3 70.8 - - - -
291D ASP* 1.3 58.9 + - - +
293D PHE* 3.1 23.5 + + - +
294D GLU* 2.9 63.9 + - + +
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Residues in contact with ASP 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D LYS* 5.0 9.9 + - - -
289D GLY* 3.3 1.9 - - - -
290D PHE* 1.3 78.5 - - - +
292D ASN* 1.3 66.4 + - - +
294D GLU* 3.3 19.3 + - - +
295D GLN* 3.1 26.0 + - - +
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Residues in contact with ASN 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D LEU* 6.0 0.4 - - - -
174D TYR* 3.7 25.3 - - - +
288D VAL* 2.9 40.8 + - + +
289D GLY 3.2 2.8 + - - -
291D ASP* 1.3 78.8 + - - +
293D PHE* 1.3 59.8 + - - +
295D GLN* 3.1 13.2 + - - +
296D LEU* 3.0 24.1 + - - +
484D PRO* 3.5 31.8 - - + +
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Residues in contact with PHE 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D LEU* 3.9 22.0 - - + -
129D MET* 4.0 10.8 - - + -
276D LEU 3.7 24.9 - - - -
277D TRP 3.8 8.5 - - - -
278D SER 3.8 12.8 - - - -
281D GLY* 3.8 15.9 - - - -
284D ILE* 3.9 21.8 - - + -
285D ALA* 4.1 12.1 - - + -
288D VAL* 4.4 3.3 - - - +
289D GLY 3.1 13.1 + - - +
290D PHE* 3.4 31.0 - + - +
292D ASN* 1.3 76.1 - - - +
294D GLU* 1.3 59.1 + - - +
296D LEU* 3.1 22.3 + - + +
297D LEU* 2.9 43.3 + - + +
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Residues in contact with GLU 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D ARG* 3.0 34.9 + - - +
130D LYS* 5.1 8.3 + - - +
290D PHE* 2.9 48.5 + - + +
291D ASP* 3.6 20.7 - - - +
293D PHE* 1.3 76.7 - - - +
295D GLN* 1.3 59.7 + - + +
297D LEU* 3.3 11.5 + - + +
298D SER* 2.8 32.7 + - - +
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Residues in contact with GLN 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D HIS* 4.9 10.9 + - - -
291D ASP 3.1 19.0 + - - +
292D ASN* 3.1 17.5 + - - +
294D GLU* 1.3 76.1 - - - +
296D LEU* 1.3 64.3 + - - +
298D SER* 3.1 9.0 + - - -
299D GLY 2.9 20.3 + - - -
484D PRO* 4.1 5.6 - - + -
485D PHE* 3.3 44.0 - - + +
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Residues in contact with LEU 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D VAL* 4.1 20.9 - - + -
171D LEU* 4.7 3.6 - - + -
276D LEU* 3.9 23.6 - - + -
277D TRP* 3.8 14.6 - - + -
284D ILE* 4.4 2.9 - - + -
292D ASN 3.0 12.0 + - - +
293D PHE* 3.2 32.3 - - + +
295D GLN* 1.3 75.0 - - - +
297D LEU* 1.3 62.4 + - - +
299D GLY 3.2 2.1 + - - -
300D ALA 3.2 16.8 + - - -
484D PRO* 3.4 25.7 + - + +
487D LEU* 4.2 19.1 - - + -
488D GLY* 3.5 28.7 - - - +
491D VAL* 6.0 0.4 - - + -
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Residues in contact with LEU 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LEU 4.2 8.7 - - - +
104D ARG* 3.5 28.7 - - + +
106D ARG* 3.9 30.1 - - - +
126D LEU* 3.9 23.1 - - + -
277D TRP* 3.4 39.7 - - + +
293D PHE* 2.9 32.2 + - + +
294D GLU* 3.5 10.8 - - + +
296D LEU* 1.3 76.8 - - + +
298D SER* 1.3 58.6 + - - +
300D ALA* 3.2 6.7 + - - +
301D HIS* 2.8 25.8 + - - +
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Residues in contact with SER 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ARG* 3.8 24.7 + - - +
294D GLU* 2.8 29.0 + - - +
295D GLN* 3.1 13.3 + - - -
297D LEU* 1.3 72.9 - - - +
299D GLY* 1.3 57.9 + - - +
301D HIS* 3.3 3.1 + - - +
302D TRP* 2.9 23.9 + - - +
485D PHE* 3.6 20.1 - - - -
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Residues in contact with GLY 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D GLN 2.9 10.9 + - - -
296D LEU 3.2 1.1 + - - -
298D SER* 1.3 72.9 - - - +
300D ALA* 1.3 65.4 + - - +
302D TRP* 3.2 4.5 + - - +
303D MET 3.1 17.7 + - - -
485D PHE* 3.3 41.6 - - - -
489D ALA* 3.4 17.0 - - - +
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Residues in contact with ALA 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ARG* 3.6 20.6 - - - +
277D TRP* 3.4 35.9 - - + -
296D LEU 3.2 4.2 + - - -
297D LEU 3.2 8.5 + - - +
299D GLY* 1.3 77.0 - - - +
301D HIS* 1.3 58.0 + - - +
303D MET* 3.2 3.6 + - - +
304D ASP* 2.8 34.7 + - - +
488D GLY 3.5 11.0 - - - +
492D ALA* 3.8 7.0 - - + -
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Residues in contact with HIS 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D VAL 5.2 1.0 + - - -
104D ARG* 3.1 23.7 + - - +
105D ASN* 3.4 26.9 - - + -
106D ARG* 3.8 19.5 - - + -
107D SER* 3.5 22.9 + - - -
297D LEU 2.8 10.0 + - - +
298D SER* 3.5 12.3 - - - +
300D ALA* 1.3 75.9 - - - +
302D TRP* 1.3 61.6 + - - +
304D ASP* 3.2 15.4 + - + +
305D GLN* 3.1 61.8 + - + +
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Residues in contact with TRP 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 3.9 22.4 - - + -
45D ASN 3.6 19.3 + - - -
46D THR* 3.6 41.2 + - + +
47D ASN* 5.4 3.8 - - - +
298D SER 2.9 14.1 + - - +
299D GLY 3.2 9.2 + - - +
301D HIS* 1.3 74.9 - - - +
303D MET* 1.3 85.3 + - + +
305D GLN* 3.2 16.9 + - + +
306D HIS* 3.0 54.9 + - + -
485D PHE* 3.8 16.4 - + + -
489D ALA* 5.0 1.3 - - + -
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Residues in contact with MET 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 4.1 7.9 - - + -
51D ILE* 4.0 21.5 - - + -
299D GLY 3.1 9.5 + - - +
300D ALA 3.6 6.7 - - - +
302D TRP* 1.3 98.9 - - + +
304D ASP* 1.3 67.1 + - - +
306D HIS* 3.2 21.3 + - - +
307D PHE* 3.0 22.3 + - - +
317D PRO* 4.4 5.6 - - - -
489D ALA* 3.6 22.4 - - + +
492D ALA* 3.9 6.3 - - + +
493D MET* 3.6 46.4 - - + +
496D HIS* 4.7 3.6 - - + -
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Residues in contact with ASP 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D PHE* 3.6 18.0 - - + -
101D VAL* 3.6 16.4 - - - +
104D ARG* 2.8 43.0 + - - +
300D ALA 2.8 20.3 + - - +
301D HIS* 3.2 16.5 + - - +
303D MET* 1.3 73.3 - - - +
305D GLN* 1.3 57.8 + - + +
307D PHE* 3.4 3.8 + - - +
308D ARG* 3.0 27.4 + - - +
492D ALA* 4.1 1.0 - - - +
496D HIS* 2.6 34.3 + - - -
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Residues in contact with GLN 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D PHE* 5.8 0.7 - - + -
107D SER* 5.6 1.9 - - - -
301D HIS* 3.1 59.4 + - + +
302D TRP* 3.6 14.5 - - + +
303D MET 3.2 0.4 - - - -
304D ASP* 1.3 75.8 - - + +
306D HIS* 1.3 65.2 + - - +
308D ARG* 4.2 6.1 - - - -
309D THR* 2.7 38.9 + - + +
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Residues in contact with HIS 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D LEU* 3.5 28.9 - - + +
302D TRP* 3.0 42.7 + + + +
303D MET* 3.5 14.4 - - - +
305D GLN* 1.3 75.7 - - - +
307D PHE* 1.3 65.3 + - - +
309D THR* 4.1 2.2 - - - -
310D THR* 2.6 50.9 + - + -
314D LYS 3.8 12.6 - - - -
315D ASN* 3.7 5.0 - - - -
316D ALA* 3.0 24.9 + - - +
317D PRO* 3.8 20.0 - - + -
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Residues in contact with PHE 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D VAL* 5.1 3.6 - - + -
81D ARG* 2.9 52.4 + - + -
84D MET* 4.5 1.3 - - + -
85D PHE* 4.1 9.9 - + - -
303D MET 3.0 16.4 + - - +
304D ASP 3.6 2.7 - - - +
306D HIS* 1.3 78.1 - - - +
308D ARG* 1.3 58.4 + - - +
315D ASN* 2.9 32.1 - - - +
317D PRO* 3.7 11.4 - - + -
318D VAL* 3.8 11.0 - - + -
496D HIS* 3.3 45.3 - + + -
499D PHE* 3.9 16.6 - + - -
500D VAL* 3.8 32.3 - - + -
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Residues in contact with ARG 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ARG* 3.2 28.6 + - - +
82D GLU* 2.8 39.3 + - - +
85D PHE* 3.5 47.2 + - + +
86D ASN* 3.3 26.5 - - - +
304D ASP 3.0 17.1 + - - +
305D GLN* 3.2 8.0 + - - +
307D PHE* 1.3 79.4 - - - +
309D THR* 1.3 63.6 + - + +
310D THR 3.7 0.4 - - - -
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Residues in contact with THR 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ARG* 5.7 0.2 - - - -
305D GLN* 2.7 27.7 + - + +
306D HIS* 3.9 3.1 + - - -
308D ARG* 1.3 85.4 - - + +
310D THR* 1.3 65.7 + - - +
311D PRO* 3.7 6.8 - - - +
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Residues in contact with THR 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D GLU* 5.1 1.6 - - - +
81D ARG* 4.7 5.5 + - - -
306D HIS* 2.6 42.1 + - + -
307D PHE 4.6 0.9 - - - +
308D ARG 3.7 0.8 - - - -
309D THR* 1.3 80.5 + - - +
311D PRO* 1.3 78.1 - - + +
312D LEU* 3.3 2.8 + - - +
314D LYS* 3.3 39.9 - - + +
315D ASN* 3.0 22.7 + - - +
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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