Contacts of the helix formed by residues 2219 - 2225 (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 VAL2219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2206A ARG* 5.6 4.0 - - + -
2208A MET* 2.9 29.9 + - + +
2209A SER* 4.1 1.3 - - - +
2210A PHE* 4.8 8.1 - - + -
2217A VAL 3.6 0.4 + - - -
2218A THR* 1.3 72.4 - - - +
2220A THR* 1.3 72.9 + - + +
2222A LEU* 3.5 11.4 + - + +
2223A VAL* 3.3 23.4 + - - +
2228A LEU* 3.9 15.5 - - + -
2233A VAL* 3.7 36.0 - - + +
2236A LEU* 5.5 6.3 - - + -
2237A GLU* 3.8 21.5 - - - +
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Residues in contact with THR2220 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2206A ARG* 4.2 34.5 - - + +
2218A THR* 3.1 15.6 + - - -
2219A VAL* 1.3 88.2 - - + +
2221A GLU* 1.3 64.1 + - - +
2223A VAL* 3.2 11.8 - - - +
2224A ASP* 2.8 28.9 - - - +
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Residues in contact with GLU2221 (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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2217A VAL* 3.8 8.3 - - + -
2218A THR* 3.1 20.9 + - - +
2220A THR* 1.3 81.9 + - - +
2222A LEU* 1.3 59.7 + - - +
2224A ASP* 3.1 9.2 + - - +
2225A SER* 2.7 55.8 + - - -
2382A GLU* 3.6 33.0 - - - +
2384A HIS* 3.4 18.3 - - + -
2394A ARG* 3.0 24.8 + - - -
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Residues in contact with LEU2222 (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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2210A PHE* 3.8 24.2 - - + -
2217A VAL* 3.7 24.0 - - + +
2218A THR 3.3 13.8 + - - +
2219A VAL* 3.7 11.0 - - - +
2220A THR 3.3 0.2 - - - -
2221A GLU* 1.3 78.2 - - - +
2223A VAL* 1.3 54.8 + - - +
2225A SER* 4.6 0.2 - - - -
2226A GLY 3.2 4.3 + - - -
2227A ILE* 2.6 55.9 + - + +
2228A LEU* 3.2 33.8 + - + -
2250A ILE* 3.9 7.6 - - + -
2253A PHE* 6.0 0.2 - - + -
2254A LEU* 4.0 19.1 - - + -
2384A HIS* 4.8 8.1 - - + -
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Residues in contact with VAL2223 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2219A VAL 3.3 14.6 + - - +
2220A THR* 3.2 20.9 - - - +
2222A LEU* 1.3 75.7 - - - +
2224A ASP* 1.3 69.1 + - - +
2226A GLY* 3.6 10.0 + - - +
2228A LEU* 3.4 27.3 - - + +
2230A PRO* 4.7 17.3 - - + +
2233A VAL* 3.5 26.5 - - + -
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Residues in contact with ASP2224 (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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2220A THR* 2.8 20.6 - - - +
2221A GLU* 3.1 16.0 + - - +
2223A VAL* 1.3 89.2 - - - +
2225A SER* 1.3 57.9 + - - +
2226A GLY 3.2 3.2 + - - -
2390A ILE* 4.3 10.4 - - - +
2394A ARG* 3.9 15.6 + - - +
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Residues in contact with SER2225 (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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2221A GLU* 2.7 36.5 + - - -
2222A LEU 3.5 0.2 + - - -
2224A ASP* 1.3 76.0 - - - +
2226A GLY* 1.3 62.3 + - - +
2227A ILE* 3.2 12.6 - - - -
2384A HIS* 3.0 23.8 + - - -
2386A LEU* 3.9 9.4 - - - -
2387A PRO* 3.2 11.6 - - - +
2390A ILE* 3.2 27.1 - - - +
2394A ARG* 3.2 9.6 + - - +
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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