Contacts of the helix formed by residues 338 - 349 (chain B) in PDB entry 3DFX
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 338 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B ZN 2.4 34.5 - - - -
317B CYS* 3.2 10.0 - - + +
320B CYS* 4.1 0.9 - - - -
322B THR* 3.7 22.9 - - + -
324B THR 4.6 0.4 - - - +
325B THR* 3.6 19.7 - - - +
327B LEU 3.9 0.7 - - - -
328B TRP* 3.9 5.1 - - + -
329B ARG* 4.2 1.1 - - - -
337B VAL* 1.3 76.4 - - - +
339B ASN* 1.3 67.6 + - - +
340B ALA* 3.7 10.3 - - - -
341B CYS* 3.3 16.8 + - - -
342B GLY* 3.0 20.4 + - - -
352B ARG* 4.9 1.3 - - - -
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Residues in contact with ASN 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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325B THR* 2.9 17.7 + - - +
326B THR* 3.4 12.9 + - - +
327B LEU* 3.1 18.5 + - - +
329B ARG* 2.5 43.8 + - - +
338B CYS* 1.3 71.0 - - - +
340B ALA* 1.3 62.2 + - - +
343B LEU* 3.0 31.8 + - - +
6Y T 3.5 3.0 + - - +
7Y A 2.8 49.3 + - - +
8Y T 3.7 4.8 - - - +
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Residues in contact with ALA 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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325B THR* 4.7 0.2 + - - -
338B CYS* 3.3 9.9 - - - -
339B ASN* 1.3 78.8 - - - +
341B CYS* 1.3 58.1 + - - +
343B LEU* 3.9 0.9 - - - +
344B TYR* 2.9 30.8 + - - +
352B ARG* 3.7 31.0 - - - +
6Y T 3.9 34.9 + - + +
7Y A 4.3 4.8 + - - +
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Residues in contact with CYS 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ZN 2.5 33.9 - - - -
317B CYS* 4.0 7.0 - - - -
319B ASN* 3.3 35.0 - - + +
320B CYS* 3.8 8.5 - - - -
337B VAL* 4.4 4.9 - - + -
338B CYS* 3.3 7.3 + - - +
340B ALA* 1.3 76.2 - - - +
342B GLY* 1.3 66.8 + - - +
344B TYR* 3.4 1.2 + - - +
345B TYR* 3.0 25.1 + - - +
352B ARG* 3.9 24.0 + - - +
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Residues in contact with GLY 342 (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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329B ARG* 4.2 12.1 - - - -
330B ARG 5.7 1.3 - - - -
337B VAL* 3.9 17.1 - - - +
338B CYS 3.0 15.8 + - - -
339B ASN 3.8 0.7 - - - -
341B CYS* 1.3 77.7 - - - +
343B LEU* 1.3 63.9 + - - +
345B TYR* 3.5 5.5 + - - +
346B LYS* 3.2 22.7 + - - +
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Residues in contact with LEU 343 (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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329B ARG* 3.9 22.4 - - - +
339B ASN* 3.0 44.0 + - - +
340B ALA 4.0 2.2 - - - +
342B GLY* 1.3 73.7 - - - +
344B TYR* 1.3 65.2 + - - +
346B LYS* 3.3 11.2 + - + +
347B LEU* 3.1 23.9 + - - +
14X G 5.2 2.7 - - + +
15X A 4.2 11.9 - - - +
6Y T 3.7 28.7 - - + +
7Y A 3.6 27.8 - - - +
8Y T 4.3 1.8 - - - +
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Residues in contact with TYR 344 (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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340B ALA 2.9 18.4 + - - +
341B CYS 3.8 3.6 - - - +
342B GLY 3.3 0.2 - - - -
343B LEU* 1.3 76.7 - - - +
345B TYR* 1.3 63.2 + - - +
347B LEU* 3.3 1.3 + - - -
348B HIS* 2.9 61.6 + + + +
350B ILE* 3.5 28.9 - - + +
351B ASN 3.7 4.5 - - - -
352B ARG* 3.4 35.7 - - + -
353B PRO* 3.8 15.4 - - + +
356B MET* 3.5 34.2 - - + -
5Y T 4.1 12.9 + - + -
6Y T 4.3 13.4 - - + +
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Residues in contact with TYR 345 (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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331B ASN* 6.6 0.4 - - + -
332B ALA* 5.7 11.9 - - + +
341B CYS 3.0 15.9 + - - +
342B GLY* 3.9 5.6 - - - +
344B TYR* 1.3 78.1 - - - +
346B LYS* 1.3 70.6 + - - +
349B ASN* 2.7 64.8 + - - +
350B ILE* 3.5 28.3 - - - +
351B ASN* 3.5 23.8 - - - +
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Residues in contact with LYS 346 (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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342B GLY 3.2 12.8 + - - +
343B LEU* 3.6 15.7 - - + +
344B TYR 3.3 0.2 - - - -
345B TYR* 1.3 89.6 - - - +
347B LEU* 1.3 60.5 + - + +
349B ASN* 4.4 12.8 + - - +
14X G 3.9 20.6 + - - +
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Residues in contact with LEU 347 (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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343B LEU 3.1 15.1 + - - +
344B TYR* 3.8 3.4 - - + +
346B LYS* 1.3 80.1 - - + +
348B HIS* 1.3 87.0 + - + +
349B ASN* 4.5 3.9 - - - +
4Y G 5.1 1.6 - - + -
5Y T 4.0 32.3 - - + +
6Y T 4.1 14.4 - - + +
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Residues in contact with HIS 348 (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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344B TYR* 2.9 53.6 + + + +
347B LEU* 1.3 98.1 - - + +
349B ASN* 1.3 70.4 + - - +
350B ILE* 3.1 27.5 + - + +
4Y G 5.3 1.8 - - - -
5Y T 3.0 30.2 + - - -
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Residues in contact with ASN 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B TYR* 2.7 52.4 + - + +
346B LYS* 4.4 13.3 + - - +
347B LEU 4.5 3.3 - - - +
348B HIS* 1.3 76.3 - - - +
350B ILE* 1.3 62.9 + - - +
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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