Contacts of the helix formed by residues 309 - 324 (chain B) in PDB entry 2JDQ
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 ASP 309 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B THR* 3.4 27.5 + - + +
307B HIS* 3.1 19.6 + - + +
308B ASN* 1.3 77.9 - - + +
310B TYR* 1.3 61.1 + - - +
311B LYS* 3.0 32.1 + - - +
312B VAL* 2.9 21.5 + - + +
313B VAL* 3.1 14.4 + - - +
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Residues in contact with TYR 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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308B ASN 4.0 6.4 + - - -
309B ASP* 1.3 76.2 + - - +
311B LYS* 1.3 57.8 + - - +
313B VAL* 4.2 10.1 - - + -
314B SER* 3.0 35.2 + - - -
346B LEU* 6.0 2.7 - - + -
349B SER* 3.9 16.8 - - - -
350B PRO* 3.4 29.8 - - + +
351B LYS* 3.9 37.5 - - + +
354B ILE* 3.4 20.6 - - + -
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B THR* 4.6 8.7 - - + -
269B ASP* 5.2 9.9 + - - +
272B ALA* 3.2 18.3 - - + +
276B TRP* 4.6 3.1 + - - -
309B ASP* 3.0 26.4 + - - +
310B TYR* 1.3 76.6 - - - +
312B VAL* 1.3 58.3 + - - +
314B SER* 5.4 0.4 - - - -
315B PRO* 3.0 22.0 - - - +
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B THR* 3.7 39.5 - - + +
271B LEU* 4.3 10.1 - - + -
272B ALA* 4.3 4.9 - - + +
275B CYS* 4.6 4.8 - - - +
304B LEU* 4.0 40.8 - - + -
307B HIS* 3.9 25.6 - - + +
309B ASP 2.9 7.2 + - - +
311B LYS* 1.3 79.2 - - - +
313B VAL* 1.3 64.5 + - - +
315B PRO* 3.2 5.8 - - - +
316B ALA* 3.0 21.1 + - - +
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Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU 4.0 12.6 - - - +
305B LEU* 3.8 15.6 - - - +
307B HIS* 3.4 26.2 - - + +
308B ASN 5.3 0.2 - - - -
309B ASP 3.1 14.8 + - - +
310B TYR* 3.4 7.6 + - + +
312B VAL* 1.3 75.4 - - - +
314B SER* 1.3 56.3 - - - +
316B ALA* 3.8 1.2 - - - +
317B LEU* 2.8 31.2 + - + +
346B LEU* 4.0 29.4 - - + -
354B ILE* 3.3 30.7 - - + -
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Residues in contact with SER 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B TRP* 4.7 12.6 - - - -
310B TYR 3.0 16.9 + - - -
311B LYS* 5.4 0.4 - - - -
313B VAL* 1.3 78.2 - - - +
315B PRO* 1.3 69.3 - - - +
317B LEU* 4.7 0.4 - - - -
318B ARG* 3.1 19.9 + - - +
351B LYS* 3.1 26.1 + - - -
353B SER* 5.8 0.2 - - - -
354B ILE* 4.0 9.8 - - - +
357B GLU* 3.2 23.9 + - - +
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Residues in contact with PRO 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ALA 3.6 13.2 - - - +
275B CYS* 3.6 8.9 - - + +
276B TRP* 3.5 52.2 - - + +
279B SER* 4.0 0.2 - - - -
311B LYS 3.0 29.2 - - - +
312B VAL* 3.2 12.1 - - - +
314B SER* 1.3 93.4 - - - +
316B ALA* 1.3 60.8 + - - +
318B ARG* 3.2 8.7 + - + +
319B ALA* 3.1 22.2 + - - +
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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
----------------------------------------------------------
275B CYS* 3.7 22.5 - - - +
301B LEU* 3.9 20.0 - - + +
304B LEU* 4.1 16.6 - - + -
305B LEU* 4.0 3.8 - - + -
312B VAL 3.0 20.2 + - - +
313B VAL 3.8 3.1 - - - +
315B PRO* 1.3 76.4 - - - +
317B LEU* 1.3 56.7 + - - +
319B ALA* 3.4 6.4 + - - +
320B VAL* 3.1 32.7 + - - +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 3.6 17.2 - - + +
313B VAL* 2.8 18.9 + - + +
314B SER 3.8 3.8 - - - +
316B ALA* 1.3 73.5 - - - +
318B ARG* 1.3 59.4 + - - +
320B VAL* 4.4 2.2 - - + -
321B GLY* 2.9 25.8 + - - -
343B LEU* 3.5 32.5 - - + -
346B LEU* 4.0 16.4 - - + -
354B ILE* 3.6 25.4 - - + +
357B GLU* 3.5 35.9 - - + +
358B ALA* 3.7 3.1 - - - +
360B TRP* 4.2 1.4 - - - -
361B THR* 3.7 13.8 + - + +
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Residues in contact with ARG 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B TRP* 4.2 22.1 - - + -
279B SER* 3.8 20.2 + - - +
280B TYR* 6.2 1.4 - - - -
314B SER 3.1 11.5 + - - +
315B PRO* 3.3 13.2 - - + +
317B LEU* 1.3 74.3 - - - +
319B ALA* 1.3 65.5 + - - +
321B GLY* 3.4 1.4 + - - -
322B ASN* 3.0 29.3 + - - +
357B GLU* 3.9 28.8 + - - +
360B TRP* 3.9 12.1 - - + -
741D SER* 3.6 33.0 + - - +
748D GLN* 3.1 41.4 + - - +
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B CYS 4.3 3.8 - - - +
278B LEU* 4.3 3.6 - - + -
279B SER* 3.7 27.3 - - - +
282B SER* 4.0 4.0 + - - +
301B LEU* 3.8 27.8 - - + -
315B PRO 3.1 8.9 + - - +
316B ALA 3.4 7.8 + - - +
318B ARG* 1.3 78.5 - - - +
320B VAL* 1.3 64.0 + - - +
322B ASN* 3.0 4.2 + - - +
323B ILE* 3.0 29.9 + - + +
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Residues in contact with VAL 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LEU* 4.1 23.6 - - + +
302B VAL* 4.1 21.8 - - + -
305B LEU* 4.2 16.6 - - + -
316B ALA 3.1 18.0 + - - +
317B LEU* 3.8 7.4 - - + +
319B ALA* 1.3 74.3 - - - +
321B GLY* 1.3 62.7 + - - +
323B ILE* 3.3 11.7 + - - +
324B VAL* 3.2 22.5 + - - +
334B ILE* 4.0 26.9 - - + -
339B ALA* 5.0 2.7 - - + -
343B LEU* 5.2 0.7 - - + -
361B THR* 4.1 16.6 - - + -
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Residues in contact with GLY 321 (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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317B LEU 2.9 14.6 + - - -
320B VAL* 1.3 77.6 - - - +
322B ASN* 1.3 60.8 + - - +
324B VAL* 3.2 21.4 - - - +
325B THR* 3.3 14.2 - - - +
360B TRP* 3.6 14.3 - - - -
361B THR* 3.4 23.1 - - - -
364B ASN* 3.8 4.7 + - - -
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Residues in contact with ASN 322 (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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279B SER* 2.9 29.1 + - - +
282B SER* 3.6 20.1 - - - +
283B ASP* 3.6 17.3 - - - +
289B ILE* 3.3 7.6 - - - +
318B ARG* 3.0 22.4 + - - +
319B ALA 3.0 5.5 + - - +
321B GLY* 1.3 73.9 - - - +
323B ILE* 1.3 62.9 + - - +
325B THR* 2.7 27.7 + - - -
360B TRP* 3.4 8.8 - - - -
740D ASP* 3.6 16.2 - - + +
741D SER* 3.4 22.6 + - - -
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Residues in contact with ILE 323 (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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282B SER* 4.2 13.7 - - - -
289B ILE* 3.9 24.8 - - + +
292B VAL* 4.4 14.1 - - + -
293B ILE* 4.2 5.6 - - + -
298B CYS* 3.5 28.7 - - - -
301B LEU* 4.0 22.0 - - + -
319B ALA* 3.0 19.6 + - + +
320B VAL* 3.3 6.9 + - - +
322B ASN* 1.3 77.3 - - - +
324B VAL* 1.3 55.6 + - - +
326B GLY* 2.8 23.2 + - - -
330B GLN* 4.1 16.2 - - - +
331B THR* 4.6 0.5 - - - +
334B ILE* 3.6 26.0 - - + -
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Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B VAL* 3.2 15.0 + - + +
321B GLY* 3.2 21.1 - - - +
323B ILE* 1.3 73.2 - - - +
325B THR* 1.3 53.6 + - - +
326B GLY 3.1 4.5 - - - -
331B THR* 3.9 22.4 - - - +
334B ILE* 3.8 34.1 - - + -
361B THR* 3.6 27.6 - - + +
364B ASN* 3.4 13.8 - - + +
365B ILE* 4.0 15.3 - - + -
738D LYS* 3.0 22.5 + - - -
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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
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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