Contacts of the helix formed by residues 271 - 277 (chain C) in PDB entry 1VI9
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 271 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253C GLU* 4.1 3.6 - - + +
254C ILE* 4.0 24.5 - - + +
257C THR* 3.6 22.2 - - - +
267C GLN 3.1 17.7 + - - +
268C VAL 3.9 1.8 - - - +
269C VAL 3.2 0.2 - - - -
270C ALA* 1.3 74.7 - - - +
272C GLN* 1.3 61.7 + - - +
273C ASP 3.4 2.5 - - - -
274C ARG* 2.9 30.3 + - + +
275C ILE* 3.2 10.2 + - - +
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Residues in contact with GLN 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C PHE* 3.6 21.6 - - + -
28C ARG* 2.7 36.2 + - - +
268C VAL 3.3 6.5 + - - -
269C VAL* 3.2 21.0 + - - +
270C ALA 3.4 2.8 + - - +
271C ALA* 1.3 75.9 - - - +
273C ASP* 1.3 75.7 + - - +
275C ILE* 2.9 19.9 + - - +
276C ALA 3.3 8.5 + - - -
27D ARG 2.9 25.5 + - - -
28D ARG* 3.3 29.4 + - - -
30D GLY* 3.9 10.7 - - - +
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Residues in contact with ASP 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ARG* 2.7 32.1 + - - +
270C ALA 5.1 0.4 + - - -
271C ALA 3.4 0.8 - - - -
272C GLN* 1.3 86.6 - - - +
274C ARG* 1.3 69.1 + - + +
275C ILE 3.2 0.2 - - - -
276C ALA* 3.5 3.8 + - - +
277C LYS* 2.9 29.5 + - - +
28D ARG* 4.3 4.0 + - - -
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Residues in contact with ARG 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C ALA* 4.0 1.0 - - - -
253C GLU* 3.4 43.5 + - + +
256C VAL* 5.9 0.6 - - - +
257C THR* 2.6 32.5 + - - +
270C ALA 4.0 12.3 + - - -
271C ALA* 2.9 27.4 + - - +
273C ASP* 1.3 83.1 - - + +
275C ILE* 1.3 63.7 + - - +
277C LYS 3.4 14.6 - - - +
278C PRO* 3.3 21.0 - - - +
279C GLU* 3.8 30.7 - - + +
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Residues in contact with ILE 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C PHE* 4.9 2.9 - - + -
25C PRO* 3.9 38.8 - - + +
28C ARG* 4.9 4.7 - - + -
29C LEU* 3.8 6.9 - - + +
229C LEU* 4.2 24.0 - - + -
246C HIS* 2.7 34.0 + - - -
250C ALA* 3.7 7.2 - - + +
254C ILE* 3.4 39.3 - - + -
268C VAL 3.7 22.4 - - - +
271C ALA* 3.2 7.3 + - + +
272C GLN* 2.9 12.0 + - - +
274C ARG* 1.3 79.5 - - - +
276C ALA* 1.3 55.3 + - - +
278C PRO* 3.8 0.2 - - - +
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Residues in contact with ALA 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ARG* 3.6 38.5 - - + +
29C LEU* 3.9 12.3 - - + +
246C HIS* 3.5 15.9 + - - -
272C GLN 3.3 3.6 + - - +
273C ASP 3.9 6.3 - - - +
275C ILE* 1.3 82.6 - - - +
277C LYS* 1.3 69.0 + - + +
278C PRO* 3.7 0.7 - - - +
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Residues in contact with LYS 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C ASP 2.9 12.1 + - - +
274C ARG* 3.4 16.3 - - - +
276C ALA* 1.3 86.7 - - + +
278C PRO* 1.3 70.9 - - - +
279C GLU* 3.6 3.8 + - - +
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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