Contacts of the strand formed by residues 396 - 411 (chain B) in PDB entry 3C0M
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 VAL 396 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 3.8 18.2 - - + +
93B ILE* 3.5 31.0 - - + -
105B LEU* 4.1 26.2 - - + -
311B ASP* 3.7 4.0 - - - +
312B VAL* 2.8 52.5 + - + +
314B TYR* 4.6 11.7 - - + +
345B ILE* 6.4 0.4 - - + -
394B ARG* 3.4 15.9 + - + +
395B PRO* 1.3 73.9 - - - +
397B ARG* 1.3 64.7 + - - +
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Residues in contact with ARG 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA* 3.8 24.5 - - + +
91B LEU 3.3 8.8 + - - +
92B ASP* 3.4 37.3 + - - +
93B ILE* 3.0 25.2 + - - +
180B ASP* 5.2 5.5 + - - -
183B SER* 4.6 7.1 - - - -
309B LYS* 3.9 35.1 - - + +
310B ALA 3.2 6.1 - - - +
311B ASP* 3.1 26.0 - - - +
312B VAL* 4.3 1.6 - - - -
395B PRO* 4.2 3.7 + - + -
396B VAL* 1.3 80.3 - - - +
398B ALA* 1.3 60.8 + - - +
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Residues in contact with ALA 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 3.6 9.0 - - + +
94B PRO 5.5 0.4 - - - +
101B VAL* 4.3 12.3 - - + -
177B TYR* 5.4 0.4 - - + -
235B LEU* 3.8 28.3 - - + -
309B LYS* 3.3 5.4 - - - -
310B ALA* 2.6 44.3 + - + +
312B VAL* 3.8 20.3 - - + +
397B ARG* 1.3 74.9 - - - +
399B GLY* 1.3 59.8 + - - +
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Residues in contact with GLY 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE 3.1 14.9 + - - -
94B PRO* 5.3 0.7 - - - -
95B ASP* 2.9 35.5 - - - +
307B GLU* 4.6 7.4 - - - -
308B PHE 3.7 9.6 - - - -
309B LYS* 4.1 11.4 - - - +
397B ARG 4.2 0.2 + - - -
398B ALA* 1.3 74.5 - - - +
400B ILE* 1.3 64.2 + - - +
401B THR* 5.0 2.0 - - - -
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Residues in contact with ILE 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ASP* 4.0 9.9 - - - +
179B LEU* 4.5 17.5 - - + -
235B LEU* 4.1 23.1 - - + -
236B SER* 4.4 12.6 - - - +
239B VAL* 4.3 16.6 - - + -
265B TRP* 3.9 34.5 - - + +
306B TYR* 4.1 5.5 - - + +
307B GLU* 3.1 5.9 - - - -
308B PHE* 2.9 35.3 + - + +
309B LYS 4.8 0.7 - - - -
310B ALA* 4.1 24.0 - - + +
398B ALA 4.5 0.9 - - - +
399B GLY* 1.3 80.0 - - - +
401B THR* 1.3 66.0 + - - +
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Residues in contact with THR 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ASP* 2.9 30.4 + - + +
231B ASN* 3.8 2.3 + - - -
232B THR* 3.2 30.9 + - - +
233B TYR* 4.7 1.4 - - - -
236B SER* 5.4 1.0 + - - -
306B TYR* 3.6 18.0 + - - +
307B GLU* 3.6 32.8 - - + +
399B GLY 5.0 0.4 - - - -
400B ILE* 1.3 84.1 - - - +
402B GLY* 1.3 59.5 + - - +
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Residues in contact with GLY 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B THR* 3.2 14.8 - - - -
232B THR* 3.9 12.1 + - - -
305B PRO* 3.3 7.1 - - - +
306B TYR* 2.8 36.7 + - - +
401B THR* 1.3 79.3 - - - +
403B ASP* 1.3 63.4 + - - +
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Residues in contact with ASP 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LYS* 3.0 9.1 - - - +
230B THR* 2.9 46.5 + - + +
304B TYR 4.0 2.9 - - - +
305B PRO* 3.6 23.4 - - - +
306B TYR* 3.5 3.5 - - - -
402B GLY* 1.3 76.1 - - - +
404B PHE* 1.3 61.8 + - - +
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Residues in contact with PHE 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B TRP* 3.8 28.3 - + + -
228B SER 3.6 9.2 - - - -
229B LYS* 4.4 2.7 - - + -
247B TRP* 3.6 41.3 - + + -
255B LEU* 4.0 5.2 - - + -
257B ILE* 3.9 14.1 - - + -
302B ILE* 4.1 7.9 - - + -
303B SER* 3.3 3.5 - - - -
304B TYR* 3.1 76.2 + + + +
306B TYR* 4.0 12.6 - - + -
403B ASP* 1.3 77.6 - - - +
405B SER* 1.3 65.6 + - - +
406B ALA* 3.6 28.0 - - + -
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Residues in contact with SER 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLN* 5.7 0.2 - - - -
226B ASN 4.1 0.3 - - - +
227B TRP* 3.3 4.2 - - - +
228B SER* 2.9 42.4 + - - +
302B ILE 3.2 6.5 - - - -
303B SER* 3.2 22.4 - - - -
404B PHE* 1.3 79.3 - - - +
406B ALA* 1.3 60.4 + - - +
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Residues in contact with ALA 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B THR* 5.0 1.6 - - + -
226B ASN 3.5 5.2 - - - -
227B TRP* 4.1 9.0 - - + -
253B THR* 5.4 0.2 + - - -
255B LEU* 3.7 28.7 - - + -
257B ILE* 4.5 0.9 - - + -
301B ASP* 3.1 5.6 - - - +
302B ILE* 2.9 36.8 + - + +
404B PHE* 3.6 24.9 - - + -
405B SER* 1.3 75.0 - - - +
407B GLU* 1.3 60.5 + - - +
408B SER 4.3 0.2 - - - -
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Residues in contact with GLU 407 (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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224B ALA 4.2 0.9 - - - +
225B THR* 3.4 2.2 - - - +
226B ASN* 2.8 64.4 + - + +
299B LYS* 4.9 17.0 + - + -
300B ALA 3.4 10.3 - - - +
301B ASP* 4.0 18.8 - - + +
406B ALA* 1.3 74.9 - - - +
408B SER* 1.3 65.6 + - - +
409B GLN* 6.4 0.4 - - + -
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Residues in contact with SER 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ALA 3.8 6.7 - - - -
225B THR* 3.5 21.8 - - - -
253B THR* 4.5 1.6 + - - -
254B GLU 3.1 22.7 + - - -
255B LEU* 3.5 16.8 - - - +
299B LYS* 3.4 1.9 - - - +
300B ALA 3.0 30.7 + - - +
406B ALA 4.3 0.2 - - - -
407B GLU* 1.3 77.0 - - - +
409B GLN* 1.3 74.1 + - - +
410B PHE* 4.0 8.8 - - - -
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Residues in contact with GLN 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 5.4 0.9 - - - +
223B THR* 3.0 45.9 + - - +
224B ALA 3.8 7.8 + - - +
275B THR* 5.0 4.0 + - - +
277B LEU* 4.4 0.3 - - - +
298B TYR 3.4 17.0 - - - +
299B LYS* 3.7 22.6 - - + +
407B GLU* 6.4 0.4 - - + -
408B SER* 1.3 84.7 - - - +
410B PHE* 1.3 69.2 + - - +
455B LEU 3.3 20.2 + - - +
456B GLY* 3.5 8.9 + - - -
457B PHE* 3.4 24.3 - - + -
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Residues in contact with PHE 410 (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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194B ARG* 3.6 20.6 - - - -
252B GLU 5.0 0.9 - - - -
253B THR* 4.4 9.0 - - - -
254B GLU* 3.8 58.1 - - + +
277B LEU* 3.6 14.6 - - + -
297B LEU* 3.6 2.8 - - - +
298B TYR* 2.8 66.2 + + + +
300B ALA* 4.5 10.8 - - + -
408B SER* 4.0 8.1 - - - -
409B GLN* 1.3 83.5 - - - +
411B ALA* 1.3 73.3 + - - +
412B GLY* 5.6 0.4 - - - -
457B PHE* 4.5 4.6 - - - -
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Residues in contact with ALA 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 4.0 20.9 - - + -
254B GLU* 4.6 4.5 - - - +
277B LEU* 3.5 17.8 - - + +
279B GLN* 4.5 12.8 + - - +
295B ILE* 4.1 1.3 - - + -
296B GLU 3.5 5.8 - - - +
297B LEU* 3.8 20.9 - - + -
410B PHE* 1.3 88.5 - - - +
412B GLY* 1.3 70.2 + - - +
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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
------------------------------------------------------------
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