Contacts of the helix formed by residues 339 - 349 (chain D) in PDB entry 3DFV
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 ASN 339 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325D THR* 2.8 15.3 + - - +
326D THR* 4.5 1.1 - - - +
327D LEU* 3.1 29.9 + - - +
329D ARG* 2.8 36.9 + - - +
337D VAL 3.5 0.6 + - - -
338D CYS* 1.3 67.7 - - - +
340D ALA* 1.3 67.6 + - - +
342D GLY 3.5 0.2 + - - -
343D LEU* 3.1 20.1 + - - +
14Y T 3.7 5.3 - - - +
15Y A 2.6 42.2 + - - +
16Y T 3.0 20.5 - - - +
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Residues in contact with ALA 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D THR* 4.3 1.0 + - - -
338D CYS* 2.9 9.0 + - - +
339D ASN* 1.3 87.6 - - - +
341D CYS* 1.3 64.3 + - - +
343D LEU* 2.9 2.8 + - - +
344D TYR* 2.9 23.8 + - - +
352D ARG* 3.4 33.4 - - - +
14Y T 3.9 28.1 + - + +
15Y A 4.0 5.0 + - - +
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Residues in contact with CYS 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ZN 2.3 33.7 - - - -
317D CYS* 3.9 4.9 - - - -
319D ASN* 3.2 35.9 - - - -
320D CYS 3.6 2.0 - - - -
337D VAL* 4.2 8.3 - - + -
338D CYS* 2.8 10.3 + - - +
340D ALA* 1.3 74.2 - - - +
342D GLY* 1.3 65.5 + - - +
343D LEU 2.8 1.7 + - - -
344D TYR* 2.9 2.8 + - - +
345D TYR* 2.9 24.9 + - - +
352D ARG* 3.3 24.9 - - - +
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Residues in contact with GLY 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D ARG* 3.5 29.6 - - - -
330D ARG 5.6 1.8 - - - -
331D ASN* 6.2 1.1 - - - -
337D VAL* 4.1 13.0 - - - +
338D CYS 3.1 7.3 + - - -
341D CYS* 1.3 79.2 - - - +
343D LEU* 1.3 59.2 - - - +
345D TYR* 3.8 5.0 + - - +
346D LYS* 3.3 26.4 + - - +
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Residues in contact with LEU 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D ARG* 3.7 22.8 - - - +
339D ASN* 3.1 12.8 + - - +
340D ALA 2.9 8.8 + - - +
341D CYS 2.8 3.2 + - - -
342D GLY* 1.3 70.8 - - - +
344D TYR* 1.3 59.2 + - - +
345D TYR 3.0 1.6 - - - -
346D LYS* 2.8 39.4 + - + +
347D LEU* 3.1 12.3 + - - +
14Y T 3.5 36.1 - - + +
15Y A 3.2 40.6 - - - +
6Z G 6.2 1.6 - - + +
7Z A 5.1 6.5 - - - +
8Z T 5.1 4.3 - - - +
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Residues in contact with TYR 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C THR* 5.0 1.0 + - - -
340D ALA 2.9 15.5 + - - +
341D CYS 3.6 6.3 - - - +
343D LEU* 1.3 73.3 - - - +
345D TYR* 1.3 58.2 + - - +
347D LEU* 3.4 0.8 + - - +
348D HIS* 2.9 60.7 + + + +
350D ILE* 4.1 4.5 - - + +
351D ASN 3.8 12.1 - - - -
352D ARG* 3.6 23.8 - - + -
353D PRO* 3.1 33.2 - - + +
356D MET* 3.4 34.8 - - + +
13Y T 3.6 23.7 + - + -
14Y T 4.2 17.9 - - + +
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Residues in contact with TYR 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D ASN* 6.3 3.6 - - + -
332D ALA* 5.0 21.7 - - + +
341D CYS 2.9 14.8 + - - +
342D GLY* 4.1 5.2 - - - +
344D TYR* 1.3 79.9 - - - +
346D LYS* 1.3 65.5 + - + +
349D ASN* 2.7 68.3 + - - +
350D ILE* 3.4 31.4 - - - +
351D ASN* 3.7 18.2 - - - -
352D ARG* 5.5 0.8 - - - +
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Residues in contact with LYS 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D ARG* 5.6 6.3 - - - +
342D GLY 3.3 16.1 + - - +
343D LEU* 2.8 29.2 + - + +
345D TYR* 1.3 81.8 - - + +
347D LEU* 1.3 58.2 + - - +
349D ASN* 4.2 11.9 + - - +
5Z A 3.7 5.5 - - + +
6Z G 2.6 62.2 + - - +
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Residues in contact with LEU 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D LEU 3.1 11.0 + - - +
344D TYR* 4.1 1.8 - - - +
345D TYR 3.1 0.4 - - - -
346D LYS* 1.3 79.8 - - - +
348D HIS* 1.3 84.4 + - + +
349D ASN* 3.4 6.8 + - - +
12Y C 5.7 0.4 - - + -
13Y T 3.8 29.8 - - + +
14Y T 4.9 9.0 - - + +
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Residues in contact with HIS 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D TYR* 2.9 51.8 + + + +
347D LEU* 1.3 97.9 - - + +
349D ASN* 1.3 60.1 + - - +
350D ILE* 2.6 43.6 + - + +
12Y C 4.8 0.8 + - - -
13Y T 3.0 39.8 + - - -
14Y T 6.4 0.4 - - + -
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Residues in contact with ASN 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345D TYR* 2.7 54.5 + - - +
346D LYS* 4.2 10.9 + - - +
347D LEU 4.1 7.6 - - - +
348D HIS* 1.3 74.3 - - - +
350D ILE* 1.3 59.2 + - + +
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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