Contacts of the helix formed by residues 321 - 333 (chain B) in PDB entry 5A86
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 GLU 321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207B CYS 3.4 6.6 - - - +
208B SER* 3.0 47.8 + - - +
317B GLN 4.2 0.6 + - - +
318B LEU* 2.9 12.8 + - - +
319B LEU 4.3 0.4 - - - -
320B LEU* 1.3 76.6 - - - +
322B PRO* 1.4 80.3 - - - +
323B MET* 4.4 8.5 + - + +
324B LEU* 3.0 19.4 + - + +
325B LYS* 2.9 21.5 + - - +
410B ARG* 2.7 37.9 + - - -
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Residues in contact with PRO 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU 5.3 0.2 - - - +
320B LEU 3.2 10.3 - - - +
321B GLU* 1.4 95.3 - - - +
323B MET* 1.3 56.1 + - - +
325B LYS* 3.3 10.6 + - + +
326B PHE* 2.8 29.8 + - - +
399B GLU* 4.3 8.5 - - - +
403B ILE* 3.7 26.4 - - + +
406B GLN* 4.5 22.4 - - - +
410B ARG* 4.8 3.6 - - - +
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Residues in contact with MET 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PHE* 4.0 18.2 - - + -
285B GLN* 3.6 16.8 - - + +
321B GLU* 3.3 9.1 + - + +
322B PRO* 1.3 78.8 - - - +
324B LEU* 1.3 62.0 + - + +
326B PHE* 3.3 33.7 - - + +
327B HIS* 3.1 57.2 + - + +
400B LEU* 4.2 4.5 - - + -
403B ILE* 3.5 29.4 - - + +
1432B D7E 3.6 32.8 - - - +
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Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B SER* 4.7 6.7 - - - +
292B PHE* 5.7 0.2 - - + -
299B TRP* 3.7 32.8 - - + -
308B LEU* 3.7 27.8 - - + -
318B LEU* 3.5 52.5 - - + +
319B LEU* 5.4 0.2 - - - -
321B GLU* 3.0 22.0 + - + +
323B MET* 1.3 77.6 - - - +
325B LYS* 1.3 63.9 + - - +
327B HIS* 3.2 5.1 + - + +
328B TYR* 3.2 38.4 + - + -
1432B D7E 4.6 8.3 - - - +
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Residues in contact with LYS 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU 4.5 0.6 + - - -
319B LEU* 3.5 50.7 - - + +
321B GLU 2.9 7.0 + - - +
322B PRO* 3.6 11.9 - - + +
324B LEU* 1.3 72.6 - - - +
326B PHE* 1.3 60.1 + - - +
328B TYR* 3.4 3.2 + - - +
329B MET* 2.9 61.5 + - + +
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Residues in contact with PHE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLN* 5.2 6.1 - - + -
286B LEU* 4.4 5.6 - - + -
322B PRO 2.8 14.6 + - - +
323B MET* 3.3 35.9 - - + +
325B LYS* 1.3 76.1 - - - +
327B HIS* 1.3 62.9 + + - +
329B MET* 3.8 1.6 - - - +
330B LEU* 2.8 63.5 + - + +
343B MET* 5.1 1.6 - - + -
396B MET* 3.3 55.5 - - + +
399B GLU* 4.6 5.2 - - + -
400B LEU* 3.8 31.0 - - + -
403B ILE* 4.0 17.3 - - + -
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Residues in contact with HIS 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLN* 2.9 50.0 + - - -
288B PHE* 4.0 1.8 - - + -
289B ASN* 2.9 50.9 + - + +
292B PHE* 4.0 19.8 - - + +
299B TRP* 3.8 23.2 + + + -
323B MET* 3.1 32.6 + - + +
324B LEU* 3.2 7.6 + - - +
326B PHE* 1.3 80.8 - + - +
328B TYR* 1.3 58.6 + - - +
331B LYS* 3.0 19.6 + - - +
1432B D7E 3.1 19.6 + - - -
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Residues in contact with TYR 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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292B PHE* 3.7 26.0 - + - -
294B ALA* 3.5 32.1 + - + +
297B GLY* 3.5 21.5 + - - -
308B LEU* 4.2 5.2 - - + +
315B PHE* 3.8 36.5 - + + -
318B LEU* 4.4 10.0 - - + +
319B LEU* 4.3 22.2 - - + -
324B LEU* 3.2 45.2 + - + -
325B LYS* 3.9 6.3 - - - +
327B HIS* 1.3 75.9 - - - +
329B MET* 1.3 62.7 + - + +
331B LYS* 3.5 3.9 + - - +
332B LYS* 3.1 26.2 + - - +
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Residues in contact with MET 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 5.6 3.8 - - + -
325B LYS* 2.9 53.0 + - + +
326B PHE* 3.8 3.1 - - - +
328B TYR* 1.3 78.7 - - + +
330B LEU* 1.3 61.6 + - - +
332B LYS* 3.3 26.4 + - - +
333B LEU* 3.6 13.0 + - - +
396B MET* 3.9 28.7 - - + +
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 3.9 21.5 - - + -
289B ASN* 3.4 26.8 - - + +
326B PHE* 2.8 46.7 + - + +
329B MET* 1.3 69.5 - - - +
331B LYS* 1.3 66.5 + - - +
333B LEU* 3.1 31.1 + - + +
334B GLN 4.0 2.1 + - - -
335B LEU* 3.7 26.6 - - + +
340B TYR* 3.9 13.2 + - + -
343B MET* 4.0 11.7 - - + -
393B ILE* 5.7 0.4 - - + -
396B MET* 4.1 14.3 - - + -
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Residues in contact with LYS 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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289B ASN* 3.3 30.2 + - - +
290B THR* 3.6 18.0 + - - +
291B VAL 4.9 0.2 - - - -
292B PHE* 3.0 29.4 + - + +
293B ASN* 5.3 0.2 - - - +
294B ALA* 4.0 27.8 - - + +
327B HIS 3.0 19.9 + - - +
328B TYR 3.8 4.5 - - - +
330B LEU* 1.3 76.2 - - - +
332B LYS* 1.3 57.7 + - - +
334B GLN* 3.0 26.0 + - - +
340B TYR* 4.5 7.0 + - - +
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Residues in contact with LYS 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B TYR 3.1 18.2 + - - +
329B MET* 3.5 16.4 - - - +
330B LEU 3.2 0.2 - - - -
331B LYS* 1.3 75.7 - - - +
333B LEU* 1.3 63.8 + - + +
334B GLN* 3.2 12.6 + - - +
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B MET 3.6 12.6 - - - +
330B LEU* 3.1 27.8 + - + +
331B LYS 3.1 1.0 - - - -
332B LYS* 1.3 79.1 - - + +
334B GLN* 1.4 68.4 + - - +
335B LEU* 3.4 16.2 + - + +
381B ARG* 4.3 4.0 + - - -
386B HIS* 5.2 7.8 + - - -
389B LEU* 4.2 22.9 - - + +
392B LYS* 4.2 36.3 - - + +
393B ILE* 4.4 12.1 - - + -
396B MET* 4.3 15.7 - - + -
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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
------------------------------------------------------------
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