Contacts of the helix formed by residues 288 - 309 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ARG* 3.2 28.1 - - - +
284D ALA* 2.8 22.4 + - - +
287D VAL* 1.3 79.7 - - - +
289D PHE* 1.3 66.9 + - - -
290D ASP* 3.2 2.9 - - - -
291D ASN 3.3 0.7 + - - -
292D PHE* 3.1 18.2 + - - +
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Residues in contact with PHE 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ARG* 6.0 0.4 - - - -
125D LEU* 3.4 43.7 - - + -
128D MET* 4.0 9.9 - - + -
129D LYS* 3.5 53.8 - - + +
132D CYS* 4.6 11.0 - - + +
136D ARG* 5.1 0.2 - - - +
284D ALA* 3.5 19.1 + - + -
288D GLY* 1.3 70.3 - - - -
290D ASP* 1.3 62.3 + - - +
292D PHE* 3.0 21.4 + + - +
293D GLU* 2.9 65.7 + - + +
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Residues in contact with ASP 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D LYS* 5.2 8.1 + - - -
288D GLY* 3.2 1.3 - - - -
289D PHE* 1.3 81.0 - - - +
291D ASN* 1.3 64.1 + - - +
293D GLU* 3.3 20.6 + - - +
294D GLN* 3.2 25.3 + - - +
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Residues in contact with ASN 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D LEU* 5.5 0.6 - - - +
173D TYR* 3.7 27.4 + - - +
287D VAL* 2.8 40.6 + - + +
288D GLY 3.3 1.4 + - - -
289D PHE 3.2 0.2 - - - -
290D ASP* 1.3 77.1 - - - +
292D PHE* 1.3 66.6 + - - +
294D GLN* 3.1 13.5 + - - +
295D LEU* 3.0 20.1 + - - +
483D PRO* 3.6 30.6 - - + +
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Residues in contact with PHE 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D LEU* 4.0 9.2 - - + -
128D MET* 3.9 17.9 - - + -
275D LEU 3.8 15.9 - - - -
276D TRP 3.8 17.7 - - - -
277D SER 3.9 12.6 - - - -
280D GLY* 4.0 11.9 - - - -
283D ILE* 4.2 25.1 - - + -
284D ALA* 4.0 16.4 - - + +
287D VAL* 4.6 3.7 - - - +
288D GLY 3.1 12.6 + - - +
289D PHE* 3.0 31.2 + + - +
291D ASN* 1.3 76.4 - - - +
293D GLU* 1.3 61.9 + - - +
295D LEU* 3.1 14.8 + - + +
296D LEU* 3.0 49.2 + - + +
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Residues in contact with GLU 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ARG* 3.0 33.0 + - - +
129D LYS* 4.8 9.6 + - - -
289D PHE* 2.9 47.9 + - + +
290D ASP* 3.5 23.9 - - - +
291D ASN 3.2 0.2 - - - -
292D PHE* 1.3 78.4 - - + +
294D GLN* 1.3 51.4 - - + +
296D LEU* 3.2 10.3 + - + +
297D SER* 2.8 39.0 + - - +
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Residues in contact with GLN 294 (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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47D HIS* 5.6 5.7 + - - -
290D ASP 3.2 15.2 + - - +
291D ASN* 3.1 20.1 + - - +
293D GLU* 1.3 74.5 - - - +
295D LEU* 1.3 61.5 + - - +
297D SER* 3.2 7.5 + - - -
298D GLY 2.9 25.5 + - - -
483D PRO* 3.8 14.4 - - + -
484D PHE* 3.3 40.0 - - - +
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Residues in contact with LEU 295 (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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166D VAL* 3.9 23.8 - - + -
170D LEU* 4.8 3.8 - - + -
275D LEU* 4.2 19.5 - - + -
276D TRP* 3.6 14.1 - - + -
283D ILE* 4.3 11.2 - - + -
291D ASN 3.0 11.2 + - - +
292D PHE* 3.2 23.6 - - + +
294D GLN* 1.3 76.7 - - - +
296D LEU* 1.3 61.6 + - - +
298D GLY 3.2 1.9 + - - -
299D ALA 3.2 16.1 + - - -
483D PRO* 3.4 23.1 + - + +
486D LEU* 4.1 20.0 - - + -
487D GLY* 3.4 30.7 - - - +
490D VAL* 5.7 0.7 - - + -
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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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102D LEU 4.0 15.0 - - - +
103D ARG* 3.4 29.2 - - + +
105D ARG* 4.0 26.0 - - - +
125D LEU* 4.1 10.5 - - + -
276D TRP* 3.9 28.7 - - + +
292D PHE* 3.0 57.4 + - + +
293D GLU* 3.5 9.6 - - + +
295D LEU* 1.3 78.9 - - + +
297D SER* 1.3 57.0 + - - +
299D ALA 3.1 1.9 + - - -
300D HIS* 2.9 26.2 + - - +
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Residues in contact with SER 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ARG* 3.6 29.1 + - - +
293D GLU* 2.8 27.1 + - - +
294D GLN* 3.2 10.4 + - - -
296D LEU* 1.3 74.1 - - - +
298D GLY* 1.3 58.8 + - - +
300D HIS* 3.4 3.0 + - - +
301D TRP* 3.0 23.2 + - - +
484D PHE* 3.5 21.4 - - - -
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Residues in contact with GLY 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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294D GLN 2.9 10.9 + - - -
295D LEU 3.2 1.8 + - - -
296D LEU 3.2 0.4 - - - -
297D SER* 1.3 74.3 - - - +
299D ALA* 1.3 65.1 + - - +
301D TRP* 3.3 5.0 + - - +
302D MET 3.2 15.8 + - - -
484D PHE* 3.2 39.4 - - - -
488D ALA* 3.3 17.1 - - - +
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Residues in contact with ALA 299 (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 ARG* 3.5 21.1 - - - +
276D TRP* 3.5 33.4 - - + -
295D LEU 3.2 4.6 + - - -
296D LEU 3.1 8.3 + - - +
298D GLY* 1.3 75.6 - - - +
300D HIS* 1.3 52.9 + - - +
302D MET* 3.0 5.9 + - - +
303D ASP* 2.8 38.1 + - - +
487D GLY 3.3 13.3 - - - +
491D ALA* 3.7 6.5 - - + +
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Residues in contact with HIS 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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100D VAL 5.1 0.6 + - - -
103D ARG* 3.2 24.8 + - - +
104D ASN* 3.4 31.0 - - + -
105D ARG* 3.7 20.0 - - + -
106D SER* 2.9 27.2 + - - -
296D LEU 2.9 11.1 + - - +
297D SER 3.5 6.3 - - - +
299D ALA* 1.3 78.1 - - - +
301D TRP* 1.3 61.6 + - - +
303D ASP* 3.2 14.4 + - - +
304D GLN* 3.1 57.0 + - + +
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Residues in contact with TRP 301 (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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43D LEU* 3.9 26.5 - - + -
44D ASN 3.5 20.5 + - - -
45D THR* 3.6 43.4 + - + +
46D ASN* 5.4 3.7 - - - +
50D ILE* 5.0 0.2 - - + -
297D SER 3.0 13.6 + - - +
298D GLY 3.5 9.9 - - - +
299D ALA 3.2 0.2 - - - -
300D HIS* 1.3 78.5 - - - +
302D MET* 1.3 85.5 + - + +
304D GLN* 3.2 10.9 + - + +
305D HIS* 3.1 46.0 + + + -
484D PHE* 3.8 14.8 - + + -
488D ALA* 5.1 1.6 - - + -
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Residues in contact with MET 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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43D LEU* 4.4 6.5 - - + -
50D ILE* 4.1 20.9 - - + -
298D GLY 3.2 5.5 + - - +
299D ALA 3.0 8.8 + - - +
301D TRP* 1.3 98.2 - - + +
303D ASP* 1.3 66.7 + - - +
305D HIS* 3.3 20.8 + - - -
306D PHE* 3.0 23.0 + - - +
316D PRO* 4.3 10.3 - - + -
488D ALA* 3.3 30.7 - - + +
489D LEU* 5.5 0.2 - - - -
491D ALA* 3.8 8.1 - - + +
492D MET* 3.5 39.3 - - + +
495D HIS* 4.8 1.6 - - - +
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Residues in contact with ASP 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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84D PHE* 3.9 15.8 - - + -
100D VAL* 3.8 16.2 - - + +
103D ARG* 2.8 44.6 + - - +
299D ALA 2.8 14.4 + - - +
300D HIS* 3.2 12.2 + - - +
302D MET* 1.3 77.6 - - - +
304D GLN* 1.3 67.7 + - - +
306D PHE* 3.3 5.2 + - - +
307D ARG* 3.0 26.7 + - - +
491D ALA* 4.3 0.5 - - - +
495D HIS* 2.8 35.1 - - - -
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Residues in contact with GLN 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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84D PHE* 5.1 6.5 - - - -
106D SER* 5.6 0.9 - - - -
300D HIS* 3.1 49.4 + - + +
301D TRP* 3.2 9.6 + - + +
303D ASP* 1.3 81.6 - - - +
305D HIS* 1.3 59.0 + - - +
307D ARG* 3.1 12.1 + - - +
308D THR* 2.9 45.2 + - + +
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Residues in contact with HIS 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 3.3 35.0 - - + +
301D TRP* 3.1 35.9 + + + +
302D MET* 3.6 12.9 - - - +
303D ASP 3.3 0.2 - - - -
304D GLN* 1.3 75.8 - - - +
306D PHE* 1.3 65.1 + - - +
308D THR* 4.4 2.7 - - - -
309D THR* 2.7 51.1 + - - +
313D LYS 3.9 7.3 + - - -
314D ASN* 3.9 8.5 - - - -
315D ALA* 3.1 41.7 - - + -
316D PRO* 3.9 10.1 - - - +
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Residues in contact with PHE 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D VAL* 5.1 4.0 - - + -
80D ARG* 2.9 48.1 + - + -
84D PHE* 4.0 10.8 - + - -
302D MET 3.0 17.5 + - - +
303D ASP 3.5 4.0 - - - +
305D HIS* 1.3 78.0 + - - +
307D ARG* 1.3 58.6 + - - +
314D ASN* 2.8 38.3 + - - +
316D PRO* 4.3 11.9 - - + -
317D VAL* 3.9 10.3 - - + -
495D HIS* 3.3 46.2 - + + +
498D PHE* 3.7 26.0 - + - -
499D VAL* 3.8 24.0 - - + -
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Residues in contact with ARG 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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80D ARG* 3.3 38.0 + - - +
81D GLU* 2.9 28.0 + - - +
84D PHE* 3.3 50.8 + - + +
85D ASN* 3.6 21.4 + - - +
303D ASP 3.0 16.2 + - - +
304D GLN* 3.1 13.6 + - - +
306D PHE* 1.3 79.0 - - - +
308D THR* 1.3 65.3 + - + +
309D THR 3.6 0.6 - - - +
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Residues in contact with THR 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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304D GLN* 2.9 34.7 + - + +
305D HIS* 4.4 1.4 - - - -
307D ARG* 1.3 80.4 - - + +
309D THR* 1.3 66.5 + - - +
310D PRO* 3.8 5.9 - - - +
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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
----------------------------------------------------------
77D GLU* 5.2 1.4 - - - +
80D ARG* 4.6 5.9 + - - -
305D HIS* 2.7 42.6 + - - +
306D PHE 4.5 0.7 - - - +
307D ARG 3.6 0.6 - - - +
308D THR* 1.3 79.3 + - - +
310D PRO* 1.3 84.7 - - + +
311D LEU* 3.4 1.2 + - - +
313D LYS* 3.4 34.5 - - + +
314D ASN* 3.1 20.5 + - - +
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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