Contacts of the helix formed by residues 310 - 324 (chain B) in PDB entry 2JJD
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 PRO 310 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308B PHE 4.8 0.9 - - - +
309B THR* 1.3 86.9 - - - +
311B ILE* 1.3 66.5 + - - +
312B GLY 3.4 1.3 - - - -
313B MET* 3.3 6.2 + - - +
314B LEU* 3.0 23.4 + - + +
386B PHE* 4.3 16.8 - - + -
389B GLN* 4.0 20.4 - - + +
390B ALA* 3.6 36.8 - - + +
393B GLU* 4.1 23.6 - - + +
667B LEU* 6.2 0.2 - - + -
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Residues in contact with ILE 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B THR* 3.5 8.9 - - - -
310B PRO* 1.3 76.5 - - - +
312B GLY* 1.3 51.6 + - - +
314B LEU* 2.7 15.6 + - - +
315B LYS* 2.6 38.1 + - + +
393B GLU* 4.5 9.0 - - + +
660B GLN* 4.2 25.8 - - + +
664B SER* 6.1 4.7 - - - -
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Residues in contact with GLY 312 (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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271B ASP* 4.9 14.4 - - - -
272B TYR* 5.4 2.3 - - - -
298B PHE* 4.3 7.8 - - - -
309B THR* 5.0 3.0 + - - -
310B PRO 3.4 0.6 - - - -
311B ILE* 1.3 77.2 - - - +
313B MET* 1.3 58.0 + - - +
315B LYS* 3.1 6.8 + - - +
316B PHE* 2.8 30.8 + - - +
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Residues in contact with MET 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LEU* 3.9 7.6 - - + -
298B PHE* 4.1 32.3 - - + -
301B TRP* 3.7 27.1 - - + -
307B PRO* 4.8 3.6 - - + +
309B THR 5.3 1.0 + - - -
310B PRO* 3.3 9.5 + - + +
312B GLY* 1.3 74.3 - - - +
314B LEU* 1.3 57.9 + - + +
316B PHE* 3.6 12.8 - - - +
317B LEU* 3.0 29.5 + - + +
344B THR* 4.8 2.0 - - - +
345B PHE* 3.4 44.4 - - + +
348B ILE* 4.6 11.0 - - + -
386B PHE* 4.1 29.8 - - + -
390B ALA* 6.0 0.7 - - + -
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Residues in contact with LEU 314 (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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310B PRO 3.0 16.5 + - - +
311B ILE* 2.7 16.7 + - - +
313B MET* 1.3 71.7 - - - +
315B LYS* 1.3 62.5 + - - +
317B LEU* 3.3 5.4 + - - +
318B LYS* 3.1 22.3 + - - +
348B ILE* 4.3 12.8 - - + -
352B MET* 3.6 36.7 - - + +
390B ALA* 3.5 29.6 - - + +
393B GLU* 3.9 20.6 - - + -
394B TYR* 3.9 26.7 - - + +
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Residues in contact with LYS 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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272B TYR* 5.1 8.7 + - + +
311B ILE* 2.6 16.9 + - + +
312B GLY* 3.6 10.3 - - - +
314B LEU* 1.3 69.9 - - - +
316B PHE* 1.3 64.9 + - - +
318B LYS* 3.1 8.8 + - - +
319B LYS* 3.0 21.5 + - - +
649B ARG* 5.3 12.6 - - - +
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Residues in contact with PHE 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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231B VAL* 3.7 24.9 - - + -
233B LEU* 4.1 9.9 - - + -
272B TYR* 3.5 48.4 - + + -
296B LEU* 3.7 40.4 - - + -
298B PHE* 3.6 33.7 - + + -
312B GLY 2.8 20.0 + - - +
313B MET* 3.6 10.5 - - - +
315B LYS* 1.3 72.5 - - - +
317B LEU* 1.3 63.6 + - - +
319B LYS* 3.2 5.6 + - - +
320B VAL* 3.1 24.0 + - + +
345B PHE* 3.8 17.3 - + - -
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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
----------------------------------------------------------
313B MET* 3.0 20.5 + - + +
314B LEU* 3.7 6.1 - - - +
315B LYS 3.2 0.4 - - - -
316B PHE* 1.3 76.3 - - - +
318B LYS* 1.3 61.7 + - - +
320B VAL* 3.7 4.5 + - - +
321B LYS* 3.5 18.7 + - + +
345B PHE* 3.8 39.9 - - + +
348B ILE* 3.7 27.6 - - + -
349B ASP* 3.8 27.4 - - + +
352B MET* 3.6 29.6 - - + -
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Residues in contact with LYS 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LEU 3.1 12.0 + - - +
315B LYS* 3.1 11.4 + - - +
317B LEU* 1.3 79.3 - - + +
319B LYS* 1.3 63.8 + - - +
320B VAL 3.2 0.2 - - - -
321B LYS* 3.2 8.8 + - - +
322B THR* 3.0 24.7 + - - -
352B MET* 6.2 2.9 - - + -
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Residues in contact with LYS 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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272B TYR* 3.9 19.7 - - + +
274B ILE* 4.1 13.7 - - + -
296B LEU* 4.0 20.0 - - + -
315B LYS 3.0 12.0 + - - +
316B PHE* 3.2 10.7 + - - +
318B LYS* 1.3 75.2 - - - +
320B VAL* 1.3 62.2 + - - +
322B THR* 3.2 17.4 + - + +
323B LEU* 3.0 31.9 + - + +
653B GLU* 3.9 22.4 - - - +
655B LEU* 6.1 1.8 - - + -
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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
----------------------------------------------------------
229B THR* 4.4 7.5 + - + -
231B VAL* 3.8 25.1 - - + -
296B LEU* 3.7 31.2 - - + -
316B PHE* 3.1 18.9 + - + +
317B LEU 3.9 7.9 - - - +
318B LYS 3.2 0.2 - - - -
319B LYS* 1.3 74.9 - - - +
321B LYS* 1.3 66.4 + - - +
322B THR 3.1 0.9 + - - -
323B LEU* 3.2 1.6 + - - +
324B ASN* 3.2 22.5 + - - +
331B ILE* 3.9 26.7 - - + -
345B PHE* 4.3 17.7 - - + -
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Residues in contact with LYS 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* 3.5 12.1 + - + +
318B LYS* 3.2 12.6 + - - +
320B VAL* 1.3 79.9 - - - +
322B THR* 1.3 63.1 + - - +
324B ASN* 3.8 14.6 + - - +
331B ILE* 6.3 0.4 - - - -
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Residues in contact with THR 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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318B LYS 3.0 14.4 + - - -
319B LYS* 3.4 18.1 - - + +
320B VAL 3.1 0.2 - - - -
321B LYS* 1.3 79.4 - - - +
323B LEU* 1.3 80.3 + - + +
324B ASN 3.6 3.6 + - - +
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Residues in contact with LEU 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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229B THR* 4.1 3.1 + - - +
274B ILE* 3.4 36.6 - - + -
276B LYS* 4.1 24.0 + - - +
294B SER* 3.9 22.0 + - - +
296B LEU* 4.1 19.7 - - + -
319B LYS* 3.0 22.6 + - + +
320B VAL 3.2 1.8 + - - +
322B THR* 1.3 90.5 - - + +
324B ASN* 1.3 59.5 + - - +
325B PRO* 3.3 11.7 - - - +
581C GLY* 4.6 16.6 - - - +
582C GLU* 4.8 6.1 - - + +
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Residues in contact with ASN 324 (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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228B ALA* 3.9 8.3 + - - +
229B THR* 2.9 27.7 + - - +
320B VAL 3.2 16.6 + - - +
321B LYS* 3.8 12.6 - - - +
322B THR 3.4 3.0 - - - +
323B LEU* 1.3 75.9 - - - +
325B PRO* 1.3 78.4 + - - +
326B VAL 3.7 1.0 + - - -
328B ALA* 4.0 4.8 - - - +
329B GLY 4.6 8.2 + - - +
331B ILE* 3.7 32.8 - - + +
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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