Contacts of the helix formed by residues 288 - 309 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ARG* 3.1 28.7 - - - +
284B ALA 2.8 17.6 + - - +
287B VAL* 1.3 83.8 - - - +
289B PHE* 1.3 65.7 + - - -
290B ASP* 3.2 3.6 - - - -
291B ASN* 3.2 1.4 + - - +
292B PHE* 3.1 18.4 + - - +
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Residues in contact with PHE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 6.2 0.2 - - - -
125B LEU* 3.3 45.5 - - + -
126B ASP* 6.1 0.2 - - - -
128B MET* 3.6 17.0 - - + -
129B LYS* 3.5 49.1 - - + +
132B CYS* 4.6 9.8 - - + +
284B ALA* 3.4 20.4 + - + -
288B GLY* 1.3 70.0 - - - -
290B ASP* 1.3 60.7 + - - +
292B PHE* 3.2 20.2 + + - +
293B GLU* 2.9 60.9 + - + +
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Residues in contact with ASP 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LYS* 5.7 4.5 + - - -
288B GLY 3.2 1.5 - - - -
289B PHE* 1.3 78.0 - - - +
291B ASN* 1.3 65.5 + - - +
293B GLU* 3.2 20.0 + - - +
294B GLN* 3.1 26.6 + - + +
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Residues in contact with ASN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 5.6 0.6 - - - +
173B TYR* 3.5 30.4 + - - +
287B VAL* 2.8 40.4 + - + +
288B GLY 3.2 2.0 + - - -
290B ASP* 1.3 80.0 - - - +
292B PHE* 1.3 66.2 + - - +
294B GLN* 3.2 12.5 + - - +
295B LEU* 3.0 19.2 + - - +
483B PRO* 3.5 29.8 - - + +
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Residues in contact with PHE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 4.2 8.5 - - + -
128B MET* 4.1 13.7 - - + -
275B LEU 3.7 25.1 - - - -
276B TRP 3.9 2.7 - - - -
277B SER 3.9 12.1 - - - -
280B GLY* 3.7 15.5 - - - -
283B ILE* 3.7 31.2 - - + -
284B ALA* 3.9 14.8 - - + -
287B VAL* 4.6 0.4 - - - +
288B GLY 3.1 13.0 + - - +
289B PHE* 3.2 26.6 + + - +
291B ASN* 1.3 76.9 - - - +
293B GLU* 1.3 57.7 + - - +
295B LEU* 3.2 18.2 + - + +
296B LEU* 3.0 54.9 + - + +
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Residues in contact with GLU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 2.8 33.9 + - - +
129B LYS* 4.6 13.1 + - - +
289B PHE* 2.9 49.2 + - + +
290B ASP* 3.5 22.9 - - - +
291B ASN 3.2 0.2 - - - -
292B PHE* 1.3 75.2 - - - +
294B GLN* 1.3 60.2 + - + +
296B LEU* 3.3 11.3 + - + +
297B SER* 2.8 33.7 + - - +
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Residues in contact with GLN 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B HIS* 5.0 11.4 + - - -
290B ASP* 3.1 17.0 + - + +
291B ASN* 3.2 16.4 + - - +
293B GLU* 1.3 73.5 - - - +
295B LEU* 1.3 56.6 + - - +
297B SER* 3.1 8.1 + - - -
298B GLY 2.8 31.5 + - - -
483B PRO* 4.0 13.2 - - + -
484B PHE* 3.3 36.4 - - + +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B VAL* 4.0 24.5 - - + -
170B LEU* 4.7 2.9 - - + -
275B LEU* 4.3 15.5 - - + -
276B TRP* 3.7 13.1 - - + -
283B ILE* 4.3 3.6 - - + -
291B ASN 3.0 13.2 + - - +
292B PHE* 3.3 35.7 - - + +
293B GLU 3.2 0.2 - - - -
294B GLN* 1.3 76.1 - - - +
296B LEU* 1.3 63.7 + - - +
298B GLY 3.2 1.9 + - - -
299B ALA 3.2 17.2 + - - -
483B PRO* 3.3 25.7 + - + +
486B LEU* 4.2 18.8 - - + -
487B GLY* 3.4 29.6 - - - +
490B VAL* 5.9 0.7 - - + -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU 4.2 7.0 - - - +
103B ARG* 3.4 25.9 - - + +
105B ARG* 3.7 29.2 - - - +
125B LEU* 4.1 15.3 - - + -
276B TRP* 3.8 33.2 - - + +
292B PHE* 3.0 53.3 + - + +
293B GLU* 3.5 11.2 - - + +
294B GLN 3.2 0.2 - - - -
295B LEU* 1.3 76.0 - - + +
297B SER* 1.3 58.2 + - - +
299B ALA* 3.3 1.6 + - - +
300B HIS* 2.8 30.1 + - - +
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Residues in contact with SER 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 3.8 26.3 + - - +
293B GLU* 2.8 28.7 + - - +
294B GLN* 3.3 11.9 + - - -
296B LEU* 1.3 71.7 - - - +
298B GLY* 1.3 65.3 + - - +
300B HIS* 3.2 3.3 + - - +
301B TRP* 3.0 19.4 + - - +
484B PHE* 3.6 21.0 - - - -
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Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B GLN 2.8 14.7 + - - -
295B LEU 3.2 1.3 + - - -
297B SER* 1.3 72.5 - - - +
299B ALA* 1.3 61.8 + - - +
301B TRP* 3.1 13.3 + - - +
302B MET 3.2 8.8 + - - -
484B PHE* 3.1 41.4 - - - -
488B ALA* 3.5 14.4 - - - +
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ARG* 3.6 19.3 - - - +
276B TRP* 3.4 34.5 - - + -
295B LEU 3.2 5.5 + - - -
296B LEU 3.6 5.4 - - - +
298B GLY* 1.3 74.2 - - - +
300B HIS* 1.3 58.5 + - - +
302B MET* 3.1 3.6 + - - +
303B ASP* 2.8 34.5 + - - +
487B GLY 3.4 16.3 - - - +
491B ALA* 3.7 8.2 - - + +
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Residues in contact with HIS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL 5.2 0.6 + - - -
103B ARG* 3.1 25.3 + - - +
104B ASN* 3.5 27.2 - - - -
105B ARG* 3.7 24.7 - - + -
106B SER* 2.8 27.4 + - - -
296B LEU 2.8 12.7 + - - +
297B SER* 3.5 5.8 - - - +
298B GLY 3.2 0.2 - - - -
299B ALA* 1.3 77.4 - - - +
301B TRP* 1.3 58.6 + - - +
303B ASP* 3.3 10.9 + - - +
304B GLN* 2.9 65.6 + - + +
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Residues in contact with TRP 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.9 26.9 - - + -
44B ASN 3.6 18.9 + - - -
45B THR* 3.6 42.8 + - + +
46B ASN* 5.2 5.1 - - - +
297B SER 3.0 11.9 + - - +
298B GLY 3.1 8.9 + - - +
300B HIS* 1.3 77.6 - - - +
302B MET* 1.3 82.5 + - + +
304B GLN* 3.3 12.7 + - + +
305B HIS* 3.0 50.5 + + + -
484B PHE* 3.8 15.9 - + + -
488B ALA* 5.1 1.8 - - + -
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Residues in contact with MET 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 4.2 8.5 - - + -
50B ILE* 4.1 20.9 - - + -
298B GLY 3.2 6.5 + - - +
299B ALA 3.1 7.7 + - - +
301B TRP* 1.3 101.3 - - + +
303B ASP* 1.3 66.0 + - - +
305B HIS* 3.2 22.0 + - - +
306B PHE* 2.9 22.7 + - - +
316B PRO* 4.2 6.3 - - + -
488B ALA* 3.5 30.1 - - + +
491B ALA* 3.8 8.1 - - + +
492B MET* 3.6 40.2 - - + +
495B HIS* 4.8 3.4 - - - +
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Residues in contact with ASP 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PHE* 3.8 16.6 - - + -
100B VAL* 3.8 14.3 - - + +
103B ARG* 2.8 44.0 + - - +
299B ALA 2.8 16.8 + - - +
300B HIS* 3.5 11.1 + - - +
301B TRP 3.2 0.2 - - - -
302B MET* 1.3 76.3 - - - +
304B GLN* 1.3 65.8 + - - +
306B PHE* 3.2 4.5 + - - +
307B ARG* 2.9 28.9 + - - +
491B ALA* 4.2 0.7 - - - +
495B HIS* 2.8 34.7 - - - -
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Residues in contact with GLN 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B PHE* 5.2 4.9 - - - -
106B SER* 5.0 2.6 + - - -
300B HIS* 2.9 57.6 + - + +
301B TRP* 3.4 12.1 - - + +
303B ASP* 1.3 82.2 - - - +
305B HIS* 1.3 60.3 + - - +
307B ARG* 3.1 6.2 + - - +
308B THR* 2.8 46.4 + - + +
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Residues in contact with HIS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 3.5 29.5 - - + +
301B TRP* 3.0 39.3 + + + +
302B MET* 3.5 12.6 - - - +
304B GLN* 1.3 75.1 - - - +
306B PHE* 1.3 61.9 + - - +
308B THR* 4.1 2.2 - - - -
309B THR* 2.6 54.2 + - + +
313B LYS 3.6 9.5 + - - -
314B ASN* 3.8 7.2 - - - -
315B ALA* 3.1 41.7 - - + -
316B PRO* 3.7 11.5 - - + +
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Residues in contact with PHE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B VAL* 5.2 4.3 - - + -
80B ARG* 2.9 45.3 + - + -
83B MET* 5.8 0.7 - - - -
84B PHE* 4.0 10.8 - + - -
302B MET 2.9 12.8 + - - +
303B ASP 3.4 6.3 - - - +
305B HIS* 1.3 79.3 + - - +
307B ARG* 1.3 57.4 + - - +
314B ASN* 2.9 36.5 + - - +
316B PRO* 4.0 13.7 - - + -
317B VAL* 3.9 11.9 - - + -
495B HIS* 3.3 45.3 - + + +
498B PHE* 3.8 26.9 - + - -
499B VAL* 3.8 23.1 - - + -
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Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ARG* 3.4 30.1 + - - +
81B GLU* 2.9 39.0 + - - +
84B PHE* 3.5 48.6 + - + +
85B ASN* 3.2 27.5 + - - +
303B ASP 2.9 16.1 + - - +
304B GLN* 3.1 7.2 + - - +
306B PHE* 1.3 79.4 - - - +
308B THR* 1.3 63.3 + - + +
309B THR 3.7 0.2 - - - -
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Residues in contact with THR 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B GLN* 2.8 38.2 + - + +
305B HIS* 4.1 1.4 - - - -
307B ARG* 1.3 83.3 - - + +
309B THR* 1.3 64.6 + - - +
310B PRO* 3.7 7.4 - - - +
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Residues in contact with THR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU* 5.4 1.2 - - - +
80B ARG* 4.7 4.5 + - - -
305B HIS* 2.6 44.5 + - + +
306B PHE 4.3 0.7 + - - +
307B ARG 3.7 1.2 - - - -
308B THR* 1.3 80.0 + - - +
310B PRO* 1.3 84.8 - - + +
311B LEU* 3.3 1.7 + - - +
313B LYS* 3.2 35.4 - - + +
314B ASN* 2.9 24.1 + - - +
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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