Contacts of the helix formed by residues 317 - 329 (chain B) in PDB entry 3CX5
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 ALA 317 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255B VAL* 4.3 8.3 - - + +
259B TYR* 3.8 34.3 - - + +
264B LEU* 3.6 20.6 - - + -
314B LEU* 2.9 13.3 + - - +
316B PRO* 1.3 77.4 - - - +
318B ILE* 1.3 58.2 + - - +
319B ASN 3.5 1.8 - - - -
320B TYR* 3.4 8.1 + - + +
321B THR* 2.9 36.1 + - - +
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B VAL* 4.0 7.6 - - + -
314B LEU 3.7 2.7 + - - -
315B SER* 3.1 24.2 + - - +
316B PRO 3.3 1.3 - - - -
317B ALA* 1.3 77.6 - - - +
319B ASN* 1.3 87.8 + - - +
321B THR* 3.3 3.3 + - - -
322B LYS* 3.1 42.3 + - - +
340B PHE* 3.1 48.7 - - + +
341B ASP* 4.7 4.5 - - - +
343B VAL* 3.5 17.5 - - + +
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Residues in contact with ASN 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA 5.1 0.2 - - - +
88A LYS 4.2 13.1 + - - +
89A GLU* 4.5 4.8 + - - +
90A GLY* 3.6 25.5 - - - +
109A LEU* 4.3 4.0 - - + +
316B PRO 4.7 3.1 + - - +
317B ALA 3.5 0.2 - - - -
318B ILE* 1.3 94.0 - - - +
320B TYR* 1.3 61.3 + - - +
322B LYS* 3.5 24.2 + - - +
323B LEU* 3.3 18.2 + - - +
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Residues in contact with TYR 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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87A ALA* 3.8 30.4 + - + +
90A GLY* 3.7 8.1 - - - -
91A LEU 3.6 29.6 - - - -
92A ALA* 4.6 3.3 - - + +
258B ASN* 3.9 24.0 - - + -
261B THR 5.4 0.7 + - - -
262B SER* 3.4 36.5 - - - -
263B ALA 5.5 0.2 + - - -
264B LEU* 4.7 2.7 - - + -
316B PRO 5.1 0.2 + - - -
317B ALA* 3.4 15.2 + - + +
318B ILE 3.2 0.4 - - - -
319B ASN* 1.3 78.7 - - - +
321B THR* 1.3 58.6 + - - +
323B LEU* 3.2 5.5 + - + +
324B LYS* 2.9 63.3 + - + +
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Residues in contact with THR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B GLU* 4.0 5.4 - - - +
255B VAL* 3.2 33.2 + - + +
258B ASN* 3.5 28.1 - - - +
317B ALA 2.9 18.0 + - - -
318B ILE 3.7 4.5 - - - -
320B TYR* 1.3 74.8 - - - +
322B LYS* 1.3 57.2 + - - +
324B LYS* 4.3 5.2 - - - +
325B ASN* 2.7 38.1 + - - +
340B PHE* 3.6 31.4 - - + -
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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
----------------------------------------------------------
109A LEU* 4.3 15.5 - - + +
318B ILE* 3.1 32.4 + - - +
319B ASN* 3.7 23.9 + - - +
320B TYR 3.3 0.2 - - - -
321B THR* 1.3 76.2 - - - +
323B LEU* 1.3 61.4 + - - +
325B ASN* 4.2 4.2 - - - +
326B ALA* 3.1 24.8 + - - +
338B LEU* 6.2 2.0 - - - -
340B PHE* 4.3 27.6 - - + -
341B ASP* 3.2 27.5 + - - -
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Residues in contact with LEU 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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48A THR* 4.1 15.9 - - + -
90A GLY 3.7 23.6 - - - +
91A LEU 4.9 1.1 - - - -
92A ALA* 3.7 31.0 - - + +
107A SER* 4.0 4.9 - - - +
108A SER* 3.5 36.3 - - - +
109A LEU* 3.8 9.4 - - + +
319B ASN 3.3 5.4 + - - +
320B TYR* 3.2 8.7 + - + +
321B THR 3.1 0.4 - - - -
322B LYS* 1.3 77.7 - - - +
324B LYS* 1.3 77.3 + - + +
326B ALA* 3.2 3.8 + - - +
327B VAL* 3.1 37.0 + - + +
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Residues in contact with LYS 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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92A ALA* 4.0 18.0 - - - +
258B ASN* 3.1 32.5 - - - +
320B TYR* 2.9 50.9 + - + +
321B THR 3.9 1.6 - - - +
323B LEU* 1.3 86.5 - - + +
325B ASN* 1.3 63.7 + - - +
327B VAL* 3.0 34.0 - - + +
328B GLN* 3.1 10.6 + - - +
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Residues in contact with ASN 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B GLU* 3.3 28.6 + - - +
278B LYS* 4.2 11.7 - - - +
321B THR 2.7 23.4 + - - +
322B LYS 4.2 2.0 - - - +
324B LYS* 1.3 72.3 - - - +
326B ALA* 1.3 62.8 + - - +
328B GLN* 3.4 11.5 + - - +
329B ASN* 3.2 43.3 + - - +
336B ILE 5.6 2.8 + - - +
337B GLU* 5.6 6.1 - - - +
340B PHE* 3.8 31.3 - - + -
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Residues in contact with ALA 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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47A HIS* 4.6 16.8 - - + +
48A THR* 4.0 17.9 - - + +
109A LEU* 4.3 11.9 - - + -
322B LYS 3.1 20.4 + - - +
323B LEU 3.5 5.2 - - - +
324B LYS 3.2 0.2 - - - -
325B ASN* 1.3 79.5 + - - +
327B VAL* 1.3 61.0 + - - +
329B ASN* 3.3 24.6 + - - +
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Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A THR* 3.6 25.4 - - + +
107A SER* 5.9 3.6 - - - -
383A PRO* 6.3 1.1 - - + -
323B LEU* 3.1 23.3 + - + +
324B LYS* 3.0 38.8 - - + +
326B ALA* 1.3 72.9 - - - +
328B GLN* 1.3 65.7 + - + +
329B ASN 3.3 7.6 + - - +
330B GLU* 5.3 1.6 - - - +
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Residues in contact with GLN 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B GLU* 4.6 4.9 + - - +
278B LYS* 3.3 32.8 + - - +
324B LYS 3.1 13.1 + - - +
325B ASN* 3.6 13.4 + - - +
326B ALA 3.3 0.2 - - - -
327B VAL* 1.3 83.1 - - + +
329B ASN* 1.3 66.6 + - - +
330B GLU* 3.7 4.2 + - - +
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Residues in contact with ASN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ASN* 3.2 38.8 + - - +
326B ALA* 3.3 17.9 - - - +
327B VAL 3.2 6.8 - - - +
328B GLN* 1.3 83.7 - - - +
330B GLU* 1.3 70.3 + - - +
331B SER 5.5 0.4 - - - +
334B SER* 3.8 32.7 + - - +
335B PRO* 5.1 3.7 - - - +
337B GLU* 6.0 4.6 - - - +
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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