Contacts of the strand formed by residues 272 - 279 (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 TYR 272 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B LEU* 3.0 61.8 + - + +
270B VAL 3.5 1.0 - - - -
271B ASP* 1.3 90.4 - - + +
273B THR* 1.3 73.8 + - - +
274B ILE* 4.4 13.2 - - + -
296B LEU* 4.8 4.0 - - + -
297B HIS 3.4 14.4 - - - +
298B PHE* 3.9 2.7 - + + -
299B THR* 4.0 3.8 - - - +
312B GLY 5.4 0.7 - - - -
315B LYS* 5.1 8.1 + - + +
316B PHE* 3.5 48.5 - + + -
319B LYS* 3.9 36.4 - - + +
653B GLU* 3.9 8.5 + - - -
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Residues in contact with THR 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B CYS* 5.9 0.9 - - - +
267B VAL 3.2 13.5 - - - -
268B VAL* 3.6 34.0 - - + +
269B LEU 4.3 2.2 - - - +
272B TYR* 1.3 81.5 - - - +
274B ILE* 1.3 62.5 + - - +
275B ARG* 3.7 29.1 + - - +
296B LEU* 3.8 1.2 - - - -
297B HIS* 2.8 35.6 + - + +
299B THR* 3.6 17.7 - - + +
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASP* 4.0 1.4 - - + +
266B CYS* 3.3 2.4 - - - -
267B VAL* 2.7 58.4 + - + +
269B LEU* 6.2 1.6 - - + -
272B TYR* 4.4 10.8 - - + -
273B THR* 1.3 74.7 - - - +
275B ARG* 1.3 63.9 + - - +
276B LYS* 5.6 5.2 - - + +
294B SER* 5.9 1.6 - - - -
295B GLN 3.5 2.5 - - - +
296B LEU* 3.6 29.8 - - + -
319B LYS* 4.1 14.4 - - + -
323B LEU* 3.4 29.6 - - + -
581C GLY* 5.2 15.5 - - - +
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Residues in contact with ARG 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B TRP* 3.6 39.3 - - - +
263B VAL* 5.4 4.0 - - + -
265B ASP 3.3 3.4 - - - +
266B CYS* 3.8 24.9 - - + +
268B VAL* 6.1 1.8 - - - +
273B THR* 3.7 19.3 + - - +
274B ILE* 1.3 77.0 - - - +
276B LYS* 1.3 63.4 + - - +
277B PHE* 3.9 21.1 + - + -
294B SER* 3.4 3.6 - - - -
295B GLN* 2.7 66.9 + - - +
297B HIS* 2.9 34.2 + - - +
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Residues in contact with LYS 276 (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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263B VAL* 3.8 2.3 - - - -
264B GLU* 2.8 31.2 + - + +
265B ASP* 2.8 29.8 + - + +
274B ILE* 4.4 5.3 + - + +
275B ARG* 1.3 74.8 - - - +
277B PHE* 1.3 61.8 + - - +
292B LEU* 4.1 13.9 - - + -
293B VAL 3.9 1.3 - - - +
294B SER* 3.3 33.4 + - - +
323B LEU* 4.1 19.4 + - + +
581C GLY* 3.2 34.5 + - - +
584C VAL* 3.5 33.0 - - + -
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Residues in contact with PHE 277 (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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219B TRP* 4.2 15.3 - + - -
230B ILE* 5.5 1.1 - - + -
247B TYR* 5.6 1.6 - + - -
248B TRP* 3.3 40.6 - + + -
249B PRO* 4.5 0.9 - - + -
261B VAL* 3.8 20.2 - - + -
262B CYS 3.3 12.1 - - - +
263B VAL* 3.7 26.2 - - + -
264B GLU* 4.6 0.2 - - - -
275B ARG* 3.9 20.2 - - + -
276B LYS* 1.3 76.6 - - - +
278B CYS* 1.3 61.4 + - - +
279B ILE* 3.9 9.2 - - + -
292B LEU* 3.1 12.9 - - - +
293B VAL* 2.7 46.3 + - + +
295B GLN* 3.7 32.8 - - + -
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Residues in contact with CYS 278 (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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260B ARG 3.5 4.7 - - - +
262B CYS* 2.9 32.2 + - + +
264B GLU* 3.7 24.7 - - + +
277B PHE* 1.3 74.0 - - - +
279B ILE* 1.3 61.0 + - - +
280B GLN* 5.2 1.3 - - - +
290B PRO* 4.4 20.4 - - - -
291B ARG 3.4 9.4 - - - -
292B LEU* 4.4 0.9 - - + -
556C LYS* 5.6 3.8 - - - -
570C LEU* 3.7 33.2 - - + -
586C VAL* 4.7 4.3 - - - -
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Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B TRP* 3.5 30.1 - - + -
222B VAL* 4.0 17.7 - - + +
223B TRP* 3.6 35.6 - - + +
259B ILE* 4.1 8.7 - - + -
260B ARG 3.3 5.8 - - - +
261B VAL* 3.8 16.2 - - + -
277B PHE* 4.3 8.3 - - + -
278B CYS* 1.3 76.2 - - - +
280B GLN* 1.3 63.1 + - - +
290B PRO* 3.7 0.5 - - - +
291B ARG* 2.9 42.2 + - + +
293B VAL* 3.7 24.5 - - + -
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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