Contacts of the helix formed by residues 307 - 320 (chain B) in PDB entry 5JLH
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 307 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B VAL* 4.2 14.7 - - - +
220B LEU* 4.6 8.6 - - - +
305B TYR 3.3 0.6 + - - -
306B PRO* 1.3 72.8 - - - +
308B ILE* 1.3 63.9 + - - +
309B ALA 3.3 2.7 - - - -
310B ASP* 3.4 20.0 + - - +
311B ARG* 3.1 22.3 + - - +
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Residues in contact with ILE 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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218B VAL* 3.5 24.2 - - + +
260B LEU* 5.1 5.4 - - + -
261B PHE* 4.5 10.0 - - + -
273B ILE* 5.1 5.4 - - + -
298B LEU* 4.1 15.5 - - + -
302B THR 3.9 3.1 - - - +
303B THR* 3.1 46.4 - - + +
305B TYR* 3.4 34.0 + - + +
306B PRO 3.4 1.0 + - - -
307B GLY* 1.3 76.8 - - - +
309B ALA* 1.3 65.7 + - - +
311B ARG* 3.2 4.2 + - - +
312B MET* 2.9 37.0 + - + +
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B LEU* 4.4 8.4 - - + +
307B GLY* 3.3 0.8 - - - +
308B ILE* 1.3 81.0 - - - +
310B ASP* 1.3 61.8 + - - +
312B MET* 3.3 5.5 + - - +
313B GLN* 2.9 31.4 + - - +
328B ILE* 3.9 13.7 - - + +
330B ALA* 4.3 24.2 - - + -
334B ARG* 5.2 5.1 - - - +
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Residues in contact with ASP 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 4.3 28.6 - - + +
307B GLY* 3.4 18.7 + - - +
308B ILE 3.2 0.4 - - - -
309B ALA* 1.3 81.4 - - - +
311B ARG* 1.3 59.6 - - - +
313B GLN* 3.1 12.7 + - - +
314B LYS* 2.9 28.8 + - - +
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Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B VAL* 3.5 19.1 - - + -
219B ALA 3.3 26.8 + - - +
220B LEU* 5.1 2.6 - - - +
221B ASP* 4.1 1.8 + - - +
222B PHE* 3.9 18.0 - - - +
258B GLU* 3.1 25.5 + - - -
261B PHE* 3.4 25.1 - - + +
262B GLN* 4.6 8.7 - - - +
274B HIS* 5.6 0.2 - - - -
307B GLY 3.1 11.8 + - - +
308B ILE 3.7 6.1 - - - +
310B ASP* 1.3 80.6 - - - +
312B MET* 1.3 63.4 + - - +
314B LYS* 3.2 39.8 + - - +
315B GLU* 2.8 54.8 + - - +
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Residues in contact with MET 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B MET* 5.1 4.3 - - + -
261B PHE* 3.6 10.8 - - + -
273B ILE* 3.4 31.4 - - + +
274B HIS* 3.9 12.8 - - - +
277B THR* 3.9 21.8 - - - +
296B THR* 5.3 6.3 - - + -
298B LEU* 5.0 18.4 - - + -
308B ILE* 2.9 34.4 + - + +
309B ALA* 3.6 5.6 - - - +
311B ARG* 1.3 76.4 - - - +
313B GLN* 1.3 58.4 + - - +
315B GLU* 3.3 3.4 + - - +
316B ILE* 2.9 52.3 + - + +
328B ILE* 3.6 13.2 - - + -
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Residues in contact with GLN 313 (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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309B ALA* 2.9 16.0 + - - +
310B ASP* 3.1 16.5 + - - +
312B MET* 1.3 77.0 - - - +
314B LYS* 1.3 60.1 + - - +
316B ILE* 5.0 0.4 - - - -
317B THR* 2.6 39.1 + - - +
326B ILE* 3.5 26.3 + - - +
327B LYS* 4.9 3.0 - - - +
328B ILE* 3.3 23.9 + - + +
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Residues in contact with LYS 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 3.0 31.6 - - + +
221B ASP* 4.4 8.3 + - - +
310B ASP 2.9 12.4 + - - +
311B ARG* 3.2 48.2 + - - +
313B GLN* 1.3 76.9 - - - +
315B GLU* 1.3 74.1 + - - +
317B THR* 3.8 4.3 - - - -
318B ALA* 2.9 30.0 + - - +
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Residues in contact with GLU 315 (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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261B PHE* 3.0 23.3 - - - -
274B HIS* 2.9 47.4 + - + +
311B ARG* 2.8 56.6 + - - +
312B MET* 3.9 3.0 - - - +
314B LYS* 1.3 92.9 - - - +
316B ILE* 1.3 65.7 - - - +
318B ALA* 3.1 6.9 + - - +
319B LEU* 2.9 29.8 + - - +
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Residues in contact with ILE 316 (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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274B HIS* 4.1 19.1 - - + +
277B THR* 3.9 25.6 - - + -
278B PHE* 4.4 15.9 - - + -
281B ILE* 5.9 1.6 - - + -
293B TYR* 4.2 18.6 - - + -
296B THR* 5.1 8.5 - - + +
312B MET* 2.9 42.6 + - + +
313B GLN 4.4 0.2 - - - +
315B GLU* 1.3 72.6 - - - +
317B THR* 1.3 58.9 + - - +
319B LEU* 3.1 3.0 + - - +
320B ALA* 2.8 33.7 + - + +
326B ILE* 3.6 28.0 - - + -
328B ILE* 5.0 7.2 - - + -
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Residues in contact with THR 317 (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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313B GLN* 2.6 29.9 + - - +
314B LYS* 3.8 5.2 - - - -
316B ILE* 1.3 77.7 - - - +
318B ALA* 1.3 64.3 + - - +
320B ALA* 3.4 15.5 - - - +
321B PRO 5.1 0.3 - - - -
322B SER* 4.9 17.1 + - - -
324B MET 6.0 0.7 - - - +
326B ILE* 3.9 27.2 + - + +
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Residues in contact with ALA 318 (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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314B LYS 2.9 20.2 + - - +
315B GLU* 3.4 8.3 - - - +
316B ILE 3.1 0.4 - - - -
317B THR* 1.3 79.1 - - - +
319B LEU* 1.3 67.4 + - + +
320B ALA 4.0 2.9 - - - +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B HIS* 4.0 25.8 - - + +
275B GLU* 4.4 16.4 - - + -
278B PHE* 3.3 39.1 - - + -
315B GLU* 2.9 17.7 + - + +
316B ILE* 5.2 0.2 - - - -
318B ALA* 1.3 83.2 - - + +
320B ALA* 1.3 62.3 + - - +
321B PRO* 4.7 0.3 - - - +
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PHE* 3.4 15.5 - - + -
293B TYR* 3.7 21.8 - - + -
316B ILE 2.8 21.8 + - - +
317B THR* 3.4 10.5 - - - +
318B ALA 3.5 3.0 - - - +
319B LEU* 1.3 76.3 - - - +
321B PRO* 1.3 83.3 - - + +
322B SER* 3.2 3.6 + - - -
324B MET* 6.0 0.2 - - + -
326B ILE* 4.5 6.1 - - + -
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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
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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