Contacts of the strand formed by residues 319 - 329 (chain B) in PDB entry 3L73
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 SER 319 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B TYR* 3.2 16.9 + - - -
172B LEU* 4.4 2.9 - - - -
237B ALA* 4.1 11.0 - - - -
260B GLU* 2.8 29.0 + - - -
261B GLY 5.3 1.6 - - - -
262B ALA 3.7 5.2 - - - -
263B ALA* 3.3 10.4 - - - +
316B TYR* 2.5 46.9 + - - +
318B ASP* 1.3 87.7 + - - +
320B GLY* 1.3 61.7 + - - +
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Residues in contact with GLY 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B TYR* 3.5 6.9 + - - -
260B GLU* 3.6 5.5 - - - +
261B GLY 3.2 20.8 + - - -
262B ALA 3.0 19.8 + - - -
314B VAL 3.2 7.9 - - - -
316B TYR* 4.2 5.4 - - - -
319B SER* 1.3 83.0 + - - +
321B LEU* 1.3 72.8 + - - +
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Residues in contact with LEU 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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163B LEU* 4.3 11.2 - - + -
164B HIS* 4.3 26.5 - - + +
167B ALA* 3.8 22.7 - - + -
168B TYR* 3.7 23.6 - - + +
239B TYR* 4.5 5.8 - - + -
258B VAL* 3.6 25.8 - - + -
259B THR 3.6 10.8 - - - +
261B GLY* 4.0 2.6 - - - +
312B PHE* 4.2 7.6 - - + -
313B ASN* 3.4 4.2 - - - +
314B VAL* 2.8 47.1 + - + +
316B TYR* 5.2 2.5 - - + -
320B GLY* 1.3 81.6 - - - +
322B PHE* 1.3 60.6 + - - +
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Residues in contact with PHE 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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258B VAL* 3.0 7.5 - - - +
259B THR* 2.7 38.6 + - - +
261B GLY* 4.4 7.0 - - - -
272B PHE* 3.4 51.1 - + + -
275B LEU* 3.5 37.2 - - + -
276B GLN* 4.3 9.4 - - + -
279B LEU* 4.1 13.7 - - + -
311B ALA* 5.1 2.0 - - + -
312B PHE 3.4 14.8 - - - -
313B ASN* 3.4 23.1 - - + +
321B LEU* 1.3 76.8 - - - +
323B GLY* 1.3 82.3 + - - +
344B LEU* 4.6 7.6 - - + -
417B PHE* 3.4 17.6 - + + -
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Residues in contact with GLY 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B VAL 3.3 12.6 - - - -
258B VAL* 3.9 2.1 - - - +
279B LEU* 5.9 1.0 - - - +
311B ALA* 3.5 5.4 - - - +
312B PHE* 2.5 40.2 + - - +
322B PHE* 1.3 87.4 - - - +
324B PHE* 1.3 56.2 + - - -
344B LEU* 5.2 2.0 - - - -
417B PHE* 3.5 13.7 - - - -
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Residues in contact with PHE 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ALA* 5.3 2.7 - - + -
256B ALA* 3.4 3.1 - - - +
257B VAL* 3.2 50.6 + - + +
258B VAL* 4.9 0.5 - - - +
279B LEU* 6.5 0.2 - - + -
295B LEU* 3.7 17.7 - - + -
310B SER 3.1 13.9 - - - +
312B PHE* 4.0 4.7 - - - +
323B GLY* 1.3 74.8 - - - -
325B TYR* 1.3 60.9 + - - +
326B THR* 3.5 23.6 - - + -
337B ILE* 4.0 23.8 - - + -
340B ALA* 3.5 26.7 - - + -
341B MET* 3.6 34.1 - - + -
344B LEU* 3.3 21.1 - - + -
417B PHE* 4.1 7.4 - + - -
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Residues in contact with TYR 325 (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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156B GLN* 3.5 13.4 - - - -
159B VAL* 3.2 34.5 - - + +
160B LEU* 4.1 4.9 - - + -
254B HIS* 2.4 45.2 + + + -
255B ALA 3.2 9.6 - - - -
256B ALA* 4.2 11.9 - - + -
309B ALA* 3.3 0.7 - - - -
310B SER 3.0 30.8 + - - +
312B PHE* 4.4 4.9 - + + +
324B PHE* 1.3 74.1 - - - +
326B THR* 1.3 67.6 + - - +
327B ILE* 3.9 11.4 - - + -
58I ARG 4.7 0.2 - - - -
59I SER* 3.1 18.6 + - - -
60I ALA* 3.0 53.6 - - + +
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Residues in contact with THR 326 (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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253B VAL 3.3 4.9 - - - +
254B HIS* 3.4 0.5 - - - -
255B ALA* 2.7 47.9 + - - +
308B ASP 3.3 7.4 - - - -
309B ALA* 4.0 14.8 - - + -
324B PHE* 3.5 28.7 - - + -
325B TYR* 1.3 82.7 - - - +
327B ILE* 1.3 63.3 + - - +
328B SER* 5.2 2.1 + - - -
336B VAL* 4.3 17.4 - - + +
337B ILE* 3.7 14.0 - - + +
340B ALA* 4.3 7.9 - - + -
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Residues in contact with ILE 327 (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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252B LEU* 4.3 8.7 - - + -
253B VAL 3.4 4.0 - - - +
254B HIS* 3.5 36.3 - - + +
307B PHE* 3.2 3.3 - - - +
308B ASP* 2.8 38.9 + - + +
325B TYR* 3.9 5.4 - - + -
326B THR* 1.3 74.3 - - - +
328B SER* 1.3 67.6 + - - +
336B VAL* 5.2 0.3 - - - +
49I LEU* 6.3 0.2 - - + -
55I MET* 3.2 28.0 - - + +
58I ARG* 3.3 50.0 - - + +
59I SER* 3.6 12.3 - - - +
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Residues in contact with SER 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU* 3.6 7.3 - - - -
253B VAL* 2.9 30.6 + - - -
306B PRO 4.3 2.2 - - - -
307B PHE* 4.1 10.5 - - - +
326B THR* 5.2 3.0 + - - -
327B ILE* 1.3 80.8 - - - +
329B GLN* 1.3 68.0 + - - +
332B HIS* 4.7 1.3 - - - -
333B ALA* 3.2 30.3 - - - +
336B VAL* 4.1 27.1 - - - +
55I MET* 4.6 2.0 - - - -
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Residues in contact with GLN 329 (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 SER 3.8 7.6 - - - +
252B LEU* 4.0 11.6 - - + +
305B GLN* 3.4 39.6 + - + +
306B PRO* 3.9 25.6 + - + +
328B SER* 1.3 75.4 - - - +
330B ALA* 1.3 67.2 + - - +
331B ALA* 3.3 3.7 - - + +
332B HIS* 2.8 30.8 + - + +
333B ALA 3.2 6.9 + - - -
50I LEU 5.0 2.9 - - - +
55I MET* 6.5 0.2 - - - -
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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