Contacts of the helix formed by residues 304 - 319 (chain B) in PDB entry 5J1T
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 304 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ALA* 3.8 10.9 - - - +
301B ALA 2.9 13.2 + - - +
303B GLU* 1.3 81.6 - - - +
305B ARG* 1.3 56.8 + - - +
307B THR* 3.2 4.0 + - - -
308B LEU* 2.9 29.1 + - - +
457B VAL* 5.0 0.2 - - - +
458B GLN 4.9 0.2 - - - -
459B PRO* 4.0 19.7 - - - -
464B GLU* 3.2 11.2 - - - +
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Residues in contact with ARG 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ALA 3.7 0.8 + - - -
302B ARG* 3.1 55.7 + - - +
303B GLU 3.5 1.0 - - - -
304B GLY* 1.3 78.2 - - - +
306B GLU* 1.3 79.5 + - + +
308B LEU* 3.4 4.3 + - - +
309B LYS* 3.3 27.8 + - + +
366B HIS* 4.7 10.7 + - - +
399B LEU* 3.7 46.1 - - + +
464B GLU* 3.7 5.6 + - - +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ARG* 1.3 90.2 + - + +
307B THR* 1.3 66.5 + - - +
309B LYS* 3.0 38.5 + - - +
310B CYS* 3.0 23.9 + - - +
463B ILE* 3.7 24.9 - - + +
464B GLU* 3.0 31.5 + - - +
467B GLY* 5.1 9.2 - - - -
468B CYS* 5.4 1.7 + - - +
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Residues in contact with THR 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PHE* 3.9 14.8 - - + -
269B GLN* 4.4 0.9 - - - +
304B GLY 3.2 4.7 + - - -
306B GLU* 1.3 74.5 - - - +
308B LEU* 1.3 59.6 + - - +
310B CYS* 4.4 1.1 - - - -
311B LEU* 2.8 35.0 + - - +
457B VAL* 3.7 11.0 - - + -
458B GLN 3.5 22.4 - - - +
459B PRO* 4.1 0.4 - - - -
460B VAL* 2.9 43.2 + - + +
463B ILE* 4.0 10.0 - - + +
464B GLU* 2.6 23.3 + - - -
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PHE* 3.6 42.8 - - + +
299B THR 3.8 9.0 - - - +
300B ALA* 3.9 11.2 - - + +
304B GLY 2.9 18.3 + - - +
305B ARG 3.6 5.6 - - - +
306B GLU 3.2 0.2 - - - -
307B THR* 1.3 76.9 - - - +
309B LYS* 1.3 60.3 + - + +
311B LEU* 4.2 1.1 - - - +
312B SER* 2.8 31.0 + - - -
366B HIS* 5.8 3.1 - - - +
397B THR* 3.8 21.8 - - - +
398B VAL 3.7 23.1 - - - +
399B LEU* 4.0 20.6 - - + -
457B VAL* 4.1 11.1 - - + +
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Residues in contact with LYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ARG* 3.3 11.1 + - + +
306B GLU* 3.0 44.3 + - - +
307B THR 3.3 0.2 - - - -
308B LEU* 1.3 78.7 - - + +
310B CYS* 1.3 63.4 + - - +
312B SER* 3.0 18.0 + - - -
313B HIS* 3.1 12.0 + - - +
331B ASP* 5.7 3.4 - - - +
365B HIS* 3.5 27.8 - - + +
366B HIS* 4.5 23.1 - - + +
397B THR* 6.1 0.2 - - - +
468B CYS* 6.4 0.4 - - + -
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Residues in contact with CYS 310 (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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266B PHE* 3.7 19.1 - - + -
306B GLU 3.0 17.2 + - - +
307B THR 3.7 3.1 - - - +
309B LYS* 1.3 74.9 - - - +
311B LEU* 1.3 66.2 + - - +
313B HIS* 3.4 3.4 + - - +
314B HIS* 3.0 35.6 + - - -
463B ILE* 4.1 10.5 - - + -
468B CYS* 2.1 56.1 - - + +
470B PHE* 4.0 9.9 - - - -
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LEU* 4.7 3.6 - - + -
266B PHE* 3.5 41.7 - - + -
269B GLN* 4.9 5.2 - - + +
273B LEU* 4.1 21.3 - - + -
274B TRP* 4.0 16.2 - - + -
298B PHE* 4.3 9.0 - - + -
307B THR 2.8 21.6 + - - +
308B LEU* 4.2 1.6 - - - +
310B CYS* 1.3 73.1 - - - +
312B SER* 1.3 59.6 + - - +
314B HIS* 3.2 1.7 + - - -
315B VAL* 2.9 51.7 + - + +
457B VAL* 3.9 32.5 - - + -
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Residues in contact with SER 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PHE* 4.2 12.9 - - - -
308B LEU 2.8 22.1 + - - -
309B LYS 3.0 11.6 + - - -
311B LEU* 1.3 79.2 - - - +
313B HIS* 1.3 61.1 + - - +
315B VAL* 3.3 1.2 + - - +
316B ALA* 3.0 23.6 + - - +
363B VAL* 3.9 4.9 - - - -
365B HIS* 3.3 14.7 - - - -
395B VAL* 3.8 23.2 - - - +
397B THR* 3.4 24.0 - - - +
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Residues in contact with HIS 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LYS 3.1 14.6 + - - +
310B CYS* 3.7 5.2 - - - +
312B SER* 1.3 81.6 + - - +
314B HIS* 1.3 73.8 + + - +
316B ALA* 3.3 3.1 + - - +
317B ASP* 2.8 34.5 + - + +
326B SER* 6.0 0.9 - - - -
327B PRO* 4.1 23.8 - - + +
329B GLN* 3.9 34.5 + - + -
363B VAL* 4.1 17.5 - - - +
365B HIS* 4.8 6.2 + - + -
468B CYS* 5.8 2.7 - - - -
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Residues in contact with HIS 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLN* 4.9 3.9 + - - -
262B LEU* 3.7 33.2 - - + +
265B LYS* 4.8 4.9 - - + +
266B PHE* 4.2 4.9 - + + -
310B CYS* 3.0 29.4 + - - +
311B LEU 3.2 4.2 + - - +
313B HIS* 1.3 87.3 - + - +
315B VAL* 1.3 56.6 + - - +
317B ASP* 3.8 9.8 - - + +
318B ALA* 2.9 28.9 + - - +
468B CYS* 3.8 17.2 - - - -
470B PHE* 3.1 56.9 + + - -
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PHE* 5.1 0.3 - - - -
259B PHE* 4.1 15.9 - - + -
262B LEU* 4.0 13.9 - - + -
273B LEU* 6.1 0.7 - - + -
274B TRP* 5.4 0.7 - - + -
281B LEU* 3.8 28.9 - - + +
296B ILE* 4.6 1.1 - - + -
298B PHE* 3.9 33.7 - - + -
311B LEU* 2.9 38.1 + - + +
312B SER 3.8 3.4 - - - +
314B HIS* 1.3 74.4 - - - +
316B ALA* 1.3 66.7 + - - +
318B ALA* 3.2 13.0 + - - +
319B TYR* 3.3 10.9 + - - +
395B VAL* 4.5 8.5 - - + -
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Residues in contact with ALA 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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312B SER 3.0 16.5 + - - +
313B HIS 3.7 4.0 - - - +
315B VAL* 1.3 77.6 - - - +
317B ASP* 1.3 64.7 + - - +
319B TYR* 3.3 19.9 + - - +
320B THR* 4.1 2.8 + - - -
327B PRO* 3.8 21.7 - - + +
361B ALA* 3.5 19.0 - - + +
362B ALA 4.2 2.2 - - - +
363B VAL* 4.1 11.7 - - + -
395B VAL* 3.9 21.0 - - + +
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Residues in contact with ASP 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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258B GLN* 4.1 13.2 + - - +
313B HIS* 2.8 27.0 + - + +
314B HIS* 3.8 12.4 - - + +
316B ALA* 1.3 79.8 - - - +
318B ALA* 1.3 61.8 + - - +
320B THR* 3.1 25.7 + - - +
321B SER* 3.6 0.3 + - - -
324B LYS 5.5 0.2 - - - +
325B VAL 3.9 4.3 - - - +
326B SER* 3.8 13.0 + - - -
327B PRO* 3.4 25.4 - - + +
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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
----------------------------------------------------------
255B PHE* 3.4 25.9 - - + +
258B GLN* 3.5 20.6 - - + +
259B PHE* 4.7 2.7 - - + +
262B LEU* 4.6 9.2 - - + -
314B HIS 2.9 18.7 + - - +
315B VAL* 3.2 8.4 + - - +
317B ASP* 1.3 73.1 - - - +
319B TYR* 1.3 65.9 + - - +
321B SER* 2.4 31.7 + - - +
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Residues in contact with TYR 319 (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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251B ALA* 4.9 6.1 - - - +
255B PHE* 4.2 8.0 - + - +
281B LEU* 4.2 26.7 - - + -
284B HIS* 2.3 42.5 + + - +
285B LEU* 3.5 54.6 + - + +
315B VAL 3.3 8.7 + - - +
316B ALA* 3.3 14.7 + - - +
317B ASP 3.1 1.0 - - - -
318B ALA* 1.3 78.4 - - - +
320B THR* 1.3 57.7 + - + +
321B SER 3.5 0.9 + - - -
360B LYS* 3.7 40.4 - - + -
361B ALA* 4.2 5.4 - - + -
391B ASP* 4.5 6.2 + - - -
392B VAL* 4.5 2.7 - - - -
393B ALA* 3.9 22.9 - - + -
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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