Contacts of the helix formed by residues 2082 - 2087 (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 ALA2082 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2015K PRO* 4.2 4.7 - - + +
2081K ALA* 1.3 79.0 - - - +
2083K TYR* 1.3 62.0 + - + +
2085K HIS* 3.0 26.4 + - - +
2086K THR* 3.7 9.3 + - - +
2160K CA2 3.4 11.6 + - - -
2288L VAL* 3.6 6.5 - - + +
2289L ALA* 3.3 40.8 - - + +
2292L ASP* 3.4 17.6 + - + +
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Residues in contact with TYR2083 (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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2015K PRO* 3.4 30.7 - - + -
2057K ASN 2.7 21.5 + - - -
2058K HIS* 4.0 2.4 - - - -
2059K GLU* 3.5 35.2 + - + -
2062K LEU* 3.7 15.9 - - + -
2080K PRO* 3.1 10.5 + - + +
2081K ALA 3.1 1.0 + - - -
2082K ALA* 1.3 74.5 - - + +
2084K SER* 1.3 66.3 + - - +
2085K HIS 3.1 0.4 - - - -
2086K THR* 3.6 15.5 - - - -
2087K SER* 2.8 37.6 + - - +
2090K ILE* 3.9 11.7 - - + -
2122K VAL* 5.0 2.1 - - - +
2259L GLU* 3.6 42.5 + - - +
2260L GLY* 4.6 0.2 - - - -
2263L VAL* 5.2 0.2 - - - +
2289L ALA* 4.0 12.2 - - + +
2408L TRS 4.0 6.5 - - - -
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Residues in contact with SER2084 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2080K PRO* 3.1 25.8 - - - +
2081K ALA 2.5 21.4 + - - -
2083K TYR* 1.3 78.9 - - - +
2085K HIS* 1.3 67.9 + - - +
2086K THR 3.6 0.2 + - - -
2106K HIS* 3.0 31.1 - - - -
2120K SER* 3.3 13.6 - - - -
2121K TYR* 2.9 32.7 + - - +
2122K VAL* 4.1 3.9 + - - -
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Residues in contact with HIS2085 (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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2081K ALA 4.1 1.3 + - - -
2082K ALA* 3.0 26.3 + - - +
2084K SER* 1.3 88.6 - - - +
2086K THR* 1.3 65.7 + - + +
2106K HIS* 5.0 0.2 - + - -
2110K ILE* 4.5 10.1 - - + -
2116K PHE* 3.8 15.3 - + + +
2117K ARG* 3.0 36.3 + - + +
2119K HIS* 2.9 30.3 + - - +
2120K SER* 4.7 0.2 - - - +
2121K TYR* 3.6 15.4 - - - -
2160K CA2 2.6 33.5 + - - -
2288L VAL* 4.3 17.3 - - + -
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Residues in contact with THR2086 (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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1886J THR* 3.4 13.2 - - - +
2082K ALA 3.8 5.1 + - - +
2083K TYR* 3.2 19.5 + - - -
2085K HIS* 1.3 83.1 - - + +
2087K SER* 1.3 61.1 + - - +
2088K VAL 3.3 6.1 + - - -
2121K TYR* 3.9 8.5 - - - -
2286L THR 3.6 18.6 - - - +
2288L VAL* 3.6 29.2 - - + +
2289L ALA 5.8 0.5 + - - -
2321L TYR* 5.4 3.8 - - + +
2408L TRS 3.0 40.9 + - - -
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Residues in contact with SER2087 (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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2059K GLU* 2.6 24.0 + - - -
2083K TYR* 2.8 32.9 + - - +
2085K HIS 3.9 0.2 - - - -
2086K THR* 1.3 73.8 + - - +
2088K VAL* 1.3 62.4 + - - +
2089K ALA 3.5 0.2 + - - -
2090K ILE* 2.9 33.3 + - - +
2091K LEU 3.4 13.3 + - - -
2121K TYR* 3.8 14.4 - - - +
2122K VAL* 5.1 1.4 - - - +
2408L TRS 3.5 7.9 - - - -
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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