Contacts of the helix formed by residues 2273 - 2281 (chain A) in PDB entry 5DZZ
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 GLY2273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2261A ALA 4.8 0.4 - - - -
2262A GLY* 4.6 0.7 - - - -
2272A LEU* 1.3 79.3 - - - +
2274A ILE* 1.3 61.1 + - - -
2275A TYR 3.3 2.5 - - - -
2276A GLU* 3.3 13.3 + - - +
2277A ALA* 3.0 25.6 + - - +
2302A VAL 5.2 1.8 - - - -
2303A ASP* 4.6 7.6 + - - -
2304A PRO* 3.6 24.1 - - - +
2305A VAL* 5.6 1.2 - - - +
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Residues in contact with ILE2274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2260A ILE* 3.6 10.8 - - + +
2261A ALA 4.3 1.9 + - - +
2262A GLY* 3.8 20.8 - - - -
2263A ILE* 4.7 8.3 - - + -
2272A LEU 3.9 0.2 + - - -
2273A GLY* 1.3 71.4 - - - -
2275A TYR* 1.3 64.3 + - - +
2277A ALA* 3.1 17.6 + - - +
2278A MET* 3.2 12.8 + - - +
2283A VAL* 4.1 7.1 - - + +
2288A ALA* 3.8 34.8 - - + +
2291A LEU* 3.6 36.3 - - + +
2292A LEU* 4.2 9.8 - - + +
2295A GLN* 3.4 29.6 - - - +
2302A VAL 5.7 0.4 + - - -
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Residues in contact with TYR2275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2273A GLY* 3.3 0.6 - - - -
2274A ILE* 1.3 81.0 - - - +
2276A GLU* 1.3 65.1 + - + +
2278A MET* 3.4 37.4 + - + +
2279A LYS* 3.4 49.6 + - + +
2292A LEU* 4.5 12.3 - - + +
2319A GLY 3.7 16.4 - - - -
2320A LEU* 3.2 28.5 - - - +
2321A VAL* 4.2 0.4 - - - -
2322A GLY* 3.2 36.5 - - - -
2325A PHE* 4.7 13.5 - + - -
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Residues in contact with GLU2276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2272A LEU* 4.1 10.5 - - + -
2273A GLY* 3.3 19.8 + - - +
2274A ILE 3.2 0.6 - - - -
2275A TYR* 1.3 78.9 - - + +
2277A ALA* 1.3 64.9 + - - +
2279A LYS* 3.3 43.9 + - - +
2280A ILE* 3.3 21.4 + - + +
2303A ASP* 6.0 1.3 - - - +
2319A GLY 4.2 11.5 - - - +
2320A LEU* 6.5 0.9 - - - -
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Residues in contact with ALA2277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2263A ILE* 3.6 28.0 - - + -
2272A LEU* 3.6 20.9 - - + -
2273A GLY 3.0 13.5 + - - +
2274A ILE 3.1 9.6 + - - +
2276A GLU* 1.3 75.8 - - - +
2278A MET* 1.3 58.1 + - - +
2280A ILE* 3.4 2.7 + - - +
2281A GLY 3.1 6.8 + - - -
2282A LEU* 2.9 40.1 + - + +
2283A VAL* 4.1 2.2 - - + -
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Residues in contact with MET2278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2274A ILE 3.2 8.6 + - - +
2275A TYR* 3.4 41.1 - - + +
2276A GLU 3.2 0.4 - - - -
2277A ALA* 1.3 74.0 - - - +
2279A LYS* 1.3 63.4 + - + +
2280A ILE 3.1 1.8 - - - -
2281A GLY* 3.0 18.0 + - - -
2283A VAL* 3.6 25.8 - - + +
2285A PRO* 3.6 39.9 - - + -
2288A ALA* 3.7 10.3 - - + -
2292A LEU* 5.4 0.2 - - + -
2325A PHE* 3.5 22.9 - - + -
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Residues in contact with LYS2279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2275A TYR* 3.4 47.5 + - + +
2276A GLU* 3.3 41.3 + - - +
2277A ALA 3.3 0.2 - - - -
2278A MET* 1.3 79.7 - - + +
2280A ILE* 1.3 60.6 + - + +
2319A GLY 4.8 2.4 + - - -
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Residues in contact with ILE2280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2265A ASN* 6.3 0.2 - - - +
2270A GLN* 6.2 0.2 - - - +
2272A LEU* 3.7 29.6 - - + -
2276A GLU* 3.3 12.3 - - + +
2277A ALA 3.7 5.6 - - - +
2278A MET 3.1 0.4 - - - -
2279A LYS* 1.3 80.1 - - + +
2281A GLY* 1.3 60.4 + - - +
2282A LEU* 4.5 16.8 - - + +
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Residues in contact with GLY2281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2277A ALA 3.1 0.2 + - - -
2278A MET 3.0 16.0 + - - -
2280A ILE* 1.3 79.9 - - - +
2282A LEU* 1.3 65.7 + - - +
2283A VAL* 3.3 7.8 + - - +
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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