Contacts of the helix formed by residues 2024 - 2029 (chain K) in PDB entry 2BT4
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 GLN2024 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2023K ARG* 1.3 116.1 + - + +
2025K PRO* 1.3 67.8 - - - +
2026K GLU* 3.1 19.5 - - - +
2027K ILE* 3.0 30.2 + - + +
2028K TYR* 2.9 50.3 + - + -
2113K ARG* 4.5 7.3 + - - +
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Residues in contact with PRO2025 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2021K GLY 5.8 2.9 - - - +
2023K ARG* 3.3 6.3 - - - +
2024K GLN 1.3 87.1 - - - +
2026K GLU* 1.3 78.2 + - + +
2029K GLY* 2.8 42.7 + - - +
2030K SER* 3.8 17.5 - - - +
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Residues in contact with GLU2026 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2024K GLN* 3.3 19.3 + - - +
2025K PRO* 1.3 107.1 - - + +
2027K ILE* 1.3 69.3 + - + +
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Residues in contact with ILE2027 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2024K GLN* 3.0 38.4 + - + +
2026K GLU* 1.3 93.7 - - + +
2028K TYR* 1.3 86.5 + - + +
2029K GLY 3.7 0.7 - - - -
2107K ILE* 4.4 6.9 - - - +
2108K SER* 4.0 22.6 - - - -
2113K ARG* 4.5 15.3 - - - +
2134K GLY* 6.0 0.3 - - - -
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Residues in contact with TYR2028 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2017K LEU* 6.0 0.2 - - + -
2020K LEU* 3.9 24.1 - - + +
2024K GLN* 2.9 39.4 + - + +
2027K ILE* 1.3 90.3 - - + +
2029K GLY* 1.3 64.0 + - - +
2031K ASP 5.2 0.5 - - - +
2107K ILE* 3.8 33.8 - - + +
2108K SER* 4.0 4.5 - - - -
2113K ARG* 2.6 34.6 + - - -
2117K ARG* 5.5 0.2 + - - -
2134K GLY* 6.2 0.4 - - - -
2135K VAL* 4.6 9.0 + - - +
2160K CA2 3.3 78.2 - + + +
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Residues in contact with GLY2029 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2021K GLY* 4.0 13.9 + - - -
2023K ARG 4.7 1.4 - - - +
2025K PRO* 2.8 31.7 + - - +
2027K ILE 3.7 0.6 - - - -
2028K TYR* 1.3 84.0 - - - +
2030K SER* 1.3 63.1 + - - -
2031K ASP* 3.5 4.5 - - - -
2135K VAL* 6.2 0.2 - - - -
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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