Contacts of the strand formed by residues 317 - 330 (chain B) in PDB entry 3MA2
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 LEU 317 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315B SER* 3.7 0.2 - - - -
316B ASP* 1.3 86.1 - - + +
318B VAL* 1.3 66.4 + - - +
319B ILE* 4.3 9.2 - - + -
345B MET* 4.9 2.9 - - - -
347B LYS 3.4 4.0 - - - +
348B GLY* 3.7 24.7 - - - +
358B ILE* 3.5 33.9 - - + -
385B ILE 3.8 1.4 - - - +
386B ALA* 3.5 0.3 - - - -
387B GLY 3.0 30.1 + - - +
389B LEU* 3.7 33.9 - - + -
394B LEU* 3.5 32.9 - - + +
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Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B PHE* 4.1 18.8 - - + -
315B SER* 3.9 17.5 - - - -
317B LEU* 1.3 79.3 - - - +
319B ILE* 1.3 60.7 + - - +
346B TYR* 2.7 39.8 + - + -
347B LYS* 3.0 32.1 + - + +
384B LEU* 3.8 29.2 - - + -
385B ILE 3.5 3.4 - - - +
386B ALA* 4.1 7.6 - - + -
416B PHE* 3.9 19.3 - - + -
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Residues in contact with ILE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU* 4.6 8.7 - - + -
318B VAL* 1.3 84.0 - - - +
320B ARG* 1.3 61.3 + - - +
321B ALA* 4.3 4.3 - - + -
340B ILE* 3.7 30.1 - - + -
342B MET* 3.9 28.5 - - + -
344B LYS 3.2 15.9 - - - +
345B MET* 4.1 15.5 - - + +
346B TYR* 4.3 2.2 - - - +
358B ILE* 4.7 7.0 - - + -
384B LEU* 3.4 10.7 - - - +
385B ILE* 2.8 47.4 + - + +
394B LEU* 3.9 18.2 - - + -
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Residues in contact with ARG 320 (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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319B ILE* 1.3 74.6 - - - +
321B ALA* 1.3 66.4 + - - +
342B MET* 3.5 3.3 - - - +
343B THR* 2.8 37.6 + - - +
344B LYS* 2.9 42.8 + - + +
346B TYR* 3.1 26.5 + - + +
382B GLU* 2.4 65.0 + - + +
383B PHE 3.1 10.3 - - - +
384B LEU* 4.4 1.3 - - - +
405B TRP* 3.7 40.5 - - - +
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Residues in contact with ALA 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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319B ILE* 4.3 2.9 - - + -
320B ARG* 1.3 80.9 - - - +
322B LYS* 1.3 64.2 + - - +
340B ILE* 4.0 16.8 - - + -
341B LYS 3.3 12.8 - - - +
342B MET* 4.0 7.2 - - - -
343B THR* 4.2 2.2 - - - +
382B GLU* 3.6 3.2 - - - -
383B PHE* 2.8 37.0 + - - +
385B ILE* 3.7 24.7 - - + -
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Residues in contact with LYS 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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321B ALA* 1.3 76.0 - - - +
323B PHE* 1.3 66.4 + - - +
324B VAL* 3.9 3.2 - - + +
340B ILE* 3.3 6.8 - - - +
341B LYS* 2.9 60.4 + - + +
343B THR* 4.1 10.3 - - - +
379B ARG* 3.3 27.8 - - + +
380B SER* 3.6 17.0 + - - +
381B GLU 3.7 13.7 - - - +
382B GLU* 3.7 22.7 + - - +
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Residues in contact with PHE 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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322B LYS* 1.3 76.7 - - - +
324B VAL* 1.3 62.8 + - - +
325B GLY 3.8 6.5 + - - +
338B TYR* 3.8 43.1 - + + -
339B GLU 3.8 2.2 - - - -
340B ILE* 4.0 4.5 - - + -
361B VAL* 4.1 11.9 - - + -
372B TYR* 4.1 18.4 - + - -
374B HIS* 3.3 47.1 - + + +
378B ASN 5.1 1.3 + - - +
379B ARG* 4.0 21.5 + - - +
381B GLU 4.5 3.0 + - - -
383B PHE* 3.9 20.4 - + + -
385B ILE* 3.9 31.6 - - + -
396B ILE* 4.7 2.7 - - + -
402B VAL* 4.7 3.6 - - + -
251D SER* 4.9 1.0 + - - -
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Residues in contact with VAL 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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322B LYS* 3.9 10.8 - - + +
323B PHE* 1.3 74.6 - - - +
325B GLY* 1.3 64.1 + - - +
326B THR 4.5 1.9 - - - +
339B GLU* 2.8 57.8 + - + +
340B ILE 4.2 2.5 - - - -
341B LYS* 4.1 21.5 - - + +
379B ARG* 3.9 32.5 - - + +
277D ARG* 5.5 1.6 + - - -
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Residues in contact with GLY 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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323B PHE* 3.8 5.9 + - - +
324B VAL* 1.3 76.2 + - - +
326B THR* 1.3 66.9 + - - -
327B PRO* 3.8 2.1 - - - +
338B TYR* 4.4 10.6 - - - -
339B GLU 5.2 1.4 + - - +
379B ARG* 3.2 18.9 - - - +
251D SER* 3.7 10.2 + - - -
274D ASP* 3.3 14.8 - - - -
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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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324B VAL 4.5 1.2 - - - +
325B GLY* 1.3 75.8 - - - -
327B PRO* 1.3 71.7 - - + +
338B TYR* 5.6 0.3 - - - -
339B GLU 5.6 0.7 + - - -
247D LEU* 6.2 0.2 - - + -
250D SER* 6.2 1.6 - - - -
274D ASP* 2.7 46.2 + - - +
277D ARG* 3.1 28.9 + - - +
278D GLY* 3.8 23.6 - - - -
281D GLN* 5.7 2.9 - - - +
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Residues in contact with PRO 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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326B THR* 1.3 92.7 - - + +
328B GLU* 1.3 65.9 + - - +
329B VAL* 3.9 3.6 + - + +
336B GLN* 3.2 33.0 - - + +
337B ARG 3.3 19.7 - - - +
338B TYR* 3.4 37.5 - - + -
277D ARG* 3.4 23.7 - - - +
281D GLN* 3.5 19.1 - - + +
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Residues in contact with GLU 328 (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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327B PRO* 1.3 73.3 - - - +
329B VAL* 1.3 63.0 + - - +
330B ASN 4.1 1.0 + - - +
335B TYR 4.2 0.3 - - - +
336B GLN* 3.2 2.4 - - - -
337B ARG* 2.9 57.4 + - + +
360B PHE* 6.3 0.2 - - + -
276D ARG* 5.6 3.4 - - - +
277D ARG* 3.3 39.6 - - + +
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Residues in contact with VAL 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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327B PRO 3.9 5.8 + - - +
328B GLU* 1.3 78.3 - - - +
330B ASN* 1.3 67.3 + - - +
331B GLN* 3.6 31.5 + - - +
335B TYR 3.7 5.6 - - - +
336B GLN* 3.7 22.4 - - + +
365B ALA* 3.7 29.8 - - + +
277D ARG* 5.5 0.8 - - - +
280D GLN* 5.1 2.7 - - + +
281D GLN* 4.2 27.6 - - + +
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Residues in contact with ASN 330 (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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328B GLU* 4.1 1.2 + - - +
329B VAL* 1.3 73.2 - - - +
331B GLN* 1.3 53.0 + - - +
332B THR* 2.7 39.0 + - - +
333B THR* 3.3 28.8 + - - +
334B LEU* 2.8 34.8 + - - -
335B TYR* 2.8 17.3 + - + +
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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