Contacts of the helix formed by residues 294 - 301 (chain D) in PDB entry 2VM8
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 294 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292D SER* 3.2 13.1 + - - +
293D LYS* 1.3 76.9 - - - +
295D TRP* 1.3 62.8 + - - +
296D ALA* 3.0 18.0 + - - +
297D LYS* 3.2 10.1 + - + +
298D ALA* 3.2 22.5 + - - +
431D TYR* 2.4 37.5 + - - -
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Residues in contact with TRP 295 (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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218D THR 5.4 0.4 + - - -
219D GLY* 5.0 2.2 - - - -
220D PRO* 3.5 29.9 - - + +
292D SER 5.1 0.9 - - - -
293D LYS 3.5 6.0 + - - +
294D ASN* 1.3 73.3 + - - +
296D ALA* 1.3 69.6 + - + +
298D ALA* 3.6 5.4 + - - +
299D ALA* 2.9 44.8 + - + +
338D THR* 4.4 13.0 - - + -
341D LYS* 3.4 25.6 - - + -
342D ALA* 3.5 20.6 - - + -
344D GLY 4.7 1.2 + - - -
345D LYS* 3.7 41.2 + - + +
351D ILE* 4.0 9.4 - - + +
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Residues in contact with ALA 296 (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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294D ASN* 3.0 11.5 + - - +
295D TRP* 1.3 90.7 - - + +
297D LYS* 1.3 60.0 + - - +
299D ALA* 3.9 1.6 - - - +
300D ALA* 3.0 27.4 + - - +
338D THR* 4.0 22.6 + - + +
341D LYS* 5.8 1.0 - - - +
431D TYR* 3.6 27.4 - - + +
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Residues in contact with LYS 297 (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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289D HIS* 3.0 39.9 + - - -
292D SER* 3.8 19.9 + - - +
294D ASN* 3.2 20.0 + - + +
296D ALA* 1.3 75.3 - - - +
298D ALA* 1.3 68.4 + - - +
300D ALA* 3.0 18.6 - - + +
301D PHE* 3.1 27.4 - - + -
431D TYR* 3.7 29.1 - - + -
432D ASN 6.2 0.2 - - - -
435D GLU* 6.0 5.8 - - - -
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Residues in contact with ALA 298 (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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220D PRO* 4.1 19.7 - - + -
289D HIS 3.5 25.5 + - - +
290D TYR* 3.8 21.2 - - - +
292D SER* 4.2 8.3 - - - +
294D ASN 3.2 13.6 + - - +
295D TRP* 3.7 5.6 - - - +
297D LYS* 1.3 81.0 - - - +
299D ALA* 1.3 61.5 + - - +
301D PHE* 3.1 19.4 + - - +
302D VAL* 3.8 1.6 + - - +
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Residues in contact with ALA 299 (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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220D PRO* 4.0 2.8 - - + +
295D TRP* 2.9 56.6 + - + +
296D ALA 3.9 2.0 - - - +
298D ALA* 1.3 72.9 - - - +
300D ALA* 1.3 62.9 + - - +
302D VAL* 3.1 23.8 + - - +
341D LYS* 3.2 23.4 + - + +
351D ILE* 3.9 11.2 - - + -
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Residues in contact with ALA 300 (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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296D ALA 3.0 15.1 + - - +
297D LYS* 3.0 16.1 + - + +
299D ALA* 1.3 78.0 - - - +
301D PHE* 1.3 60.2 + - + +
302D VAL 3.3 0.2 - - - -
336D PHE 6.0 0.2 - - - -
341D LYS* 4.2 10.9 - - - +
354D GLY 3.6 9.7 - - - +
355D THR* 3.1 18.7 + - - -
429D LEU* 6.3 2.9 - - + -
431D TYR* 3.9 25.6 - - + -
433D ILE* 3.7 10.5 - - + +
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Residues in contact with PHE 301 (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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285D THR* 3.8 16.6 - - + -
286D ASP 3.6 15.9 - - - -
287D GLY* 5.3 1.1 - - - -
289D HIS* 3.1 51.8 - + + -
290D TYR* 2.6 41.1 + - + -
297D LYS* 3.1 39.5 - - + -
298D ALA* 3.1 6.5 + - - +
300D ALA* 1.3 78.4 - - + +
302D VAL* 1.3 55.6 + - - +
303D THR* 3.1 7.1 + - - +
307D LEU* 3.4 24.5 - - + +
355D THR* 3.9 7.4 - - - -
432D ASN 5.3 1.3 - - - -
433D ILE* 3.4 34.3 - - + -
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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