Contacts of the strand formed by residues 330 - 340 (chain B) in PDB entry 3M9M
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 ILE 330 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251B MET* 3.0 16.7 - - + +
254B ASN* 2.9 8.2 - - - -
255B SER 2.9 39.1 + - - +
261B ILE* 4.0 11.9 - - + -
288B ALA* 3.5 23.3 - - + -
289B VAL 4.5 3.8 - - - +
290B THR* 4.5 6.1 - - + +
319B LEU* 5.0 6.1 - - + -
322B ILE* 4.3 14.6 - - + -
323B LEU* 4.1 24.5 - - + -
328B ARG 4.4 4.5 - - - +
329B LYS* 1.3 76.6 - - - +
331B ARG* 1.3 59.6 + - - +
332B ARG 3.1 28.5 - - - +
333B ILE* 4.5 6.3 - - + -
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Residues in contact with ARG 331 (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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36B ARG* 2.9 54.8 + - - +
37B PHE* 6.1 1.8 - - - -
250B THR* 3.7 3.7 + - - +
251B MET* 2.7 45.8 + - - +
254B ASN* 3.4 26.3 + - - +
289B VAL* 3.2 18.3 + - - +
290B THR 4.1 10.3 - - - +
291B GLU* 4.3 12.8 + - - +
293B LEU* 4.2 22.8 - - - +
329B LYS 4.2 0.6 + - - -
330B ILE* 1.3 73.0 - - - +
332B ARG* 1.3 76.5 + - + +
3T G 5.5 4.8 + - - -
4T G 4.3 16.8 + - - -
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Residues in contact with ARG 332 (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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248B ILE* 2.9 35.8 + - + +
249B VAL 3.5 6.0 - - - +
250B THR* 3.2 23.5 + - - +
251B MET* 4.6 0.2 - - - -
287B VAL 4.5 0.2 - - - -
288B ALA* 3.1 14.0 - - - -
289B VAL* 3.1 37.8 + - + +
293B LEU* 5.9 1.6 - - - -
330B ILE* 3.1 19.3 - - - +
331B ARG* 1.3 100.6 - - + +
333B ILE* 1.3 61.7 + - - +
4T G 4.1 19.3 + - - +
5T C 2.3 53.0 + - - -
6T T 5.1 3.2 - - - +
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Residues in contact with ILE 333 (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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248B ILE* 3.8 2.5 - - - -
249B VAL* 2.7 47.1 + - + +
251B MET* 4.3 11.4 - - - -
261B ILE* 3.8 26.2 - - + +
264B TYR* 3.4 33.4 - - + -
265B LEU* 3.9 22.2 - - + +
268B ALA* 4.5 0.5 - - - +
286B VAL* 4.3 16.2 - - + -
287B VAL 3.5 8.3 - - - +
288B ALA* 3.6 24.7 - - + -
319B LEU* 4.4 9.2 - - + -
330B ILE* 4.5 3.1 - - + -
331B ARG 4.3 0.2 + - - -
332B ARG* 1.3 74.0 - - - +
334B GLY* 1.3 56.7 + - - +
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Residues in contact with GLY 334 (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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247B ARG 3.3 7.9 - - - -
248B ILE* 3.3 16.4 - - - +
265B LEU* 3.8 6.5 - - - +
268B ALA* 4.2 7.2 - - - -
286B VAL* 3.5 11.8 - - - +
287B VAL 2.7 32.0 + - - +
333B ILE* 1.3 77.4 - - - +
335B VAL* 1.3 62.0 + - - +
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Residues in contact with VAL 335 (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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246B GLY* 3.5 0.7 - - - -
247B ARG 3.1 26.1 + - - +
248B ILE* 4.4 2.0 - - - +
265B LEU* 5.3 3.4 - - + -
268B ALA* 5.1 0.2 - - + -
269B ILE* 4.1 23.3 - - + +
272B SER* 3.1 28.3 - - - +
284B ILE* 3.5 37.7 - - + -
285B HIS 3.2 10.3 - - - +
286B VAL* 5.0 3.1 - - + -
287B VAL* 4.5 3.7 - - - +
315B SER* 5.4 0.7 - - - -
334B GLY* 1.3 76.7 - - - +
336B ARG* 1.3 78.2 + - - +
337B PHE* 3.8 16.8 - - + -
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Residues in contact with ARG 336 (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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244B SER* 3.3 26.9 + - - -
245B ILE 3.8 7.2 - - - +
246B GLY* 3.5 17.9 - - - +
247B ARG 4.5 0.6 - - - +
248B ILE* 6.3 1.0 - - - +
283B ALA 3.6 0.7 - - - +
284B ILE* 3.3 5.4 - - - +
285B HIS* 2.8 47.4 + - + +
287B VAL* 4.8 10.3 - - + +
335B VAL* 1.3 87.2 + - - +
337B PHE* 1.3 68.8 + - - +
338B SER* 4.1 4.9 + - - +
6T T 3.4 15.0 + - - +
7T T 2.2 63.6 + - - +
8T T 4.7 11.6 - - - +
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Residues in contact with PHE 337 (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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244B SER* 3.1 6.1 - - - -
245B ILE 2.9 42.4 + - - +
269B ILE* 4.5 4.5 - - + -
272B SER* 3.4 31.9 - - - -
273B TYR* 3.6 31.9 - + - -
276B LEU* 4.1 16.6 - - + -
281B PRO* 3.5 32.5 - - + -
283B ALA 3.3 9.4 - - - -
284B ILE* 3.8 27.4 - - + -
306B ILE* 4.5 3.6 - - + -
311B ALA* 4.2 7.6 - - + -
335B VAL* 3.8 23.1 - - + -
336B ARG* 1.3 73.5 - - - +
338B SER* 1.3 62.1 + - - +
340B PHE* 3.4 5.8 - - - -
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Residues in contact with SER 338 (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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243B LYS 3.7 12.8 - - - -
244B SER* 4.5 7.1 - - - -
281B PRO* 3.4 5.2 - - - +
282B LYS 3.2 15.2 + - - -
283B ALA* 2.7 13.8 + - - -
285B HIS* 3.9 19.6 + - - -
336B ARG* 4.6 5.2 + - - +
337B PHE* 1.3 75.8 + - - +
339B LYS* 1.3 92.5 + - - +
340B PHE* 3.3 3.9 + - - -
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Residues in contact with LYS 339 (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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243B LYS 3.9 5.1 + - - -
282B LYS* 3.0 40.3 + - + +
283B ALA* 3.2 23.2 - - + +
285B HIS* 5.1 6.9 + - - -
301B THR* 3.2 30.6 + - + +
338B SER* 1.3 85.2 - - - +
340B PHE* 1.3 70.4 + - - +
6P A 3.5 16.6 + - - -
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Residues in contact with PHE 340 (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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241B VAL* 6.0 1.1 - - + -
242B ARG* 3.3 28.9 - - + -
243B LYS* 3.5 14.3 + - - -
244B SER* 3.5 17.5 - - - -
245B ILE* 3.7 13.9 - - + -
276B LEU* 3.4 24.5 - - + -
279B ARG* 3.6 30.7 - - + -
280B ILE 3.0 10.3 - - - +
281B PRO* 3.8 14.6 - - + -
282B LYS* 3.8 10.2 + - - -
337B PHE 3.4 28.9 - - - -
338B SER* 4.0 0.9 - - - -
339B LYS* 1.3 79.8 - - - +
341B ILE* 1.3 65.7 + - - +
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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