Contacts of the helix formed by residues 317 - 331 (chain B) in PDB entry 5C16
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 CYS 317 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B LYS* 4.1 13.9 - - - -
282B PHE* 3.4 45.2 - - + -
316B ARG* 1.3 75.9 - - - +
318B LYS* 1.3 67.9 + - - +
319B GLU* 3.9 14.6 - - - -
320B ASP* 3.3 21.4 + - + +
321B GLU* 3.1 28.1 + - - +
364B TYR* 4.7 0.4 + - - -
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Residues in contact with LYS 318 (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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316B ARG* 4.2 1.4 - - - +
317B CYS* 1.3 72.6 - - - +
319B GLU* 1.3 68.4 + - - +
321B GLU* 3.2 14.2 + - - +
322B LYS* 2.9 70.1 + - + +
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Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ASP* 3.7 46.0 - - + +
278B LYS* 3.4 41.8 + - + +
279B VAL* 3.9 3.6 - - + +
317B CYS* 3.3 8.7 - - - -
318B LYS* 1.3 89.1 + - - +
320B ASP* 1.3 52.9 + - - +
322B LYS* 3.6 7.4 - - - +
323B TYR* 2.7 35.5 + - - +
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Residues in contact with ASP 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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279B VAL* 3.1 29.0 - - + +
282B PHE* 3.5 24.8 - - + -
283B ARG* 2.8 39.4 + - - +
317B CYS* 3.3 16.9 + - - +
319B GLU* 1.3 75.3 - - - +
321B GLU* 1.3 65.4 + - - +
323B TYR* 3.4 1.7 + - - +
324B LEU* 3.1 26.4 + - - +
364B TYR* 2.5 24.4 + - - +
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Residues in contact with GLU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ARG* 2.9 52.7 + - - +
317B CYS 3.1 16.9 + - - +
318B LYS* 3.5 14.6 - - - +
320B ASP* 1.3 72.8 - - - +
322B LYS* 1.3 70.6 + - + +
324B LEU* 3.3 4.5 + - - +
325B GLN* 3.1 21.9 + - - +
363B ALA* 3.4 30.5 - - - +
364B TYR* 3.6 26.0 + - + -
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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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318B LYS* 2.9 59.8 + - + +
319B GLU* 3.7 7.4 - - - +
321B GLU* 1.3 82.8 + - + +
323B TYR* 1.3 52.1 + - - +
325B GLN* 3.1 10.1 + - + +
326B THR* 2.7 41.2 + - - +
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Residues in contact with TYR 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TRP* 5.5 0.2 - - - -
267B VAL* 3.2 22.3 - - - +
268B PRO* 3.5 27.3 - - + +
271B VAL* 3.8 29.2 - - + -
276B LEU* 3.9 21.3 - - + +
279B VAL* 4.0 17.0 - - + -
289B PRO* 2.7 61.1 + - + -
319B GLU 2.7 23.0 + - - +
320B ASP* 3.6 5.2 - - - +
321B GLU 3.2 0.2 - - - -
322B LYS* 1.3 73.8 - - - +
324B LEU* 1.3 65.3 + - + +
326B THR* 3.1 9.5 + - - -
327B ILE* 3.0 29.6 + - + +
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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
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283B ARG* 3.9 16.6 - - - +
289B PRO* 4.0 23.3 - - + -
320B ASP* 3.1 23.1 + - - +
321B GLU 3.3 4.0 + - - +
323B TYR* 1.3 79.7 - - + +
325B GLN* 1.3 62.0 + - - +
327B ILE* 3.3 7.3 + - + +
328B MET* 3.1 17.7 + - - +
337B LEU* 3.2 30.6 - - + +
339B ILE* 3.9 25.1 - - + -
359B GLU* 4.1 7.2 - - + +
364B TYR* 3.6 29.4 - - + -
367B ALA* 5.4 2.2 - - + -
435B VAL* 4.5 10.1 - - + -
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Residues in contact with GLN 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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321B GLU 3.1 13.2 + - - +
322B LYS* 3.3 14.4 - - + +
324B LEU* 1.3 75.3 - - - +
326B THR* 1.3 59.4 + - - +
328B MET* 3.2 29.4 + - - +
329B ASP* 2.9 51.2 + - - +
365B PRO* 5.8 2.8 - - - +
366B ASN* 2.8 39.8 + - - +
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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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268B PRO* 3.4 22.9 - - + -
270B SER* 3.1 28.4 + - - +
271B VAL* 5.1 4.4 - - + +
322B LYS* 2.7 22.2 + - - +
323B TYR* 3.1 15.5 + - + -
325B GLN* 1.3 71.9 - - - +
327B ILE* 1.3 63.4 + - - +
329B ASP* 3.2 11.0 + - + +
330B ALA* 3.1 21.7 + - - +
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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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246B TRP* 4.0 21.1 - - + -
268B PRO* 4.0 22.0 - - + -
289B PRO* 3.8 30.1 - - + +
301B THR* 4.0 12.3 - - - +
303B THR* 4.2 20.6 - - + +
323B TYR* 3.0 27.3 + - + +
324B LEU* 3.3 14.3 + - - +
326B THR* 1.3 74.7 - - - +
328B MET* 1.3 66.1 + - - +
330B ALA* 3.2 16.3 + - - +
331B ASN 3.7 2.4 + - - -
337B LEU* 4.3 15.5 - - + -
433B SER* 4.6 5.6 + - - -
434B VAL 6.4 0.2 - - - -
435B VAL* 4.7 6.1 - - + -
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Residues in contact with MET 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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324B LEU 3.1 12.7 + - - +
325B GLN* 3.2 36.8 - - - +
326B THR 3.3 0.2 - - - -
327B ILE* 1.3 76.7 - - - +
329B ASP* 1.3 66.3 + - - +
331B ASN* 2.9 30.7 + - - +
334B SER* 3.3 25.7 + - - +
335B HIS* 3.7 13.7 - - - +
336B LYS* 3.6 21.5 - - - +
337B LEU* 3.5 37.0 - - + +
366B ASN* 3.7 20.9 - - + +
433B SER* 5.2 1.3 - - - -
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Residues in contact with ASP 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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325B GLN* 2.9 44.5 + - - +
326B THR* 3.2 10.0 + - + +
328B MET* 1.3 83.0 - - - +
330B ALA* 1.3 62.3 + - - +
331B ASN 3.2 1.6 + - - -
332B ALA* 3.3 20.3 + - - +
334B SER 6.1 0.4 - - - -
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Residues in contact with ALA 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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245B SER* 3.6 40.5 + - - +
246B TRP* 3.6 25.0 + - + +
268B PRO* 5.4 2.7 - - + -
299B GLN* 4.5 13.9 - - - +
326B THR 3.1 11.6 + - - +
327B ILE* 3.5 11.2 - - - +
328B MET 3.2 0.4 - - - -
329B ASP* 1.3 76.9 - - - +
331B ASN* 1.3 57.1 + - - +
332B ALA* 3.4 5.2 + - - +
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Residues in contact with ASN 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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298B SER 3.6 2.5 - - - +
299B GLN* 4.0 14.3 + - - +
300B ALA* 3.5 12.7 - - - +
327B ILE 3.7 1.8 + - - -
328B MET 2.9 14.4 + - - +
330B ALA* 1.3 74.5 - - - +
332B ALA* 1.3 53.3 + - - +
333B GLN* 3.1 27.0 - - - +
334B SER* 2.7 48.9 + - - +
431B LYS 3.2 22.2 + - - -
433B SER* 3.3 34.9 + - - +
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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