Contacts of the helix formed by residues 2148 - 2152 (chain B) in PDB entry 2H7C
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 ALA2148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2086B MET* 3.6 17.0 - - + -
2098B SER* 6.1 0.9 - - - -
2110B LEU* 3.6 31.2 - - + -
2140B HIS* 3.6 15.4 + - - +
2147B GLY* 1.3 75.9 - - - +
2149B ALA* 1.3 64.4 + - - +
2150B SER 4.3 0.7 - - - +
2151B THR* 3.6 14.6 + - - +
2152B TYR* 3.4 22.4 - - - -
2169B GLN* 3.8 7.6 - - - +
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Residues in contact with ALA2149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2084B PRO* 6.1 0.2 - - + -
2118B TYR 5.2 0.9 - - - +
2119B LEU* 5.7 0.2 - - - -
2120B ASN* 4.3 5.8 - - - +
2138B TRP* 5.7 0.9 - - - -
2140B HIS* 3.7 3.9 - - - -
2148B ALA* 1.3 67.8 - - - +
2150B SER* 1.3 58.3 + - - +
2151B THR 3.1 4.7 - - - -
2152B TYR* 3.0 33.8 + - - +
2167B THR* 3.7 31.9 + - - +
2168B ILE 3.5 18.4 - - - +
2169B GLN* 3.1 31.3 + - + +
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Residues in contact with SER2150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2083B TYR* 3.4 26.5 - - - +
2084B PRO* 3.6 17.3 + - - +
2104B ARG* 2.9 32.3 + - - +
2108B ILE* 4.8 4.6 - - - +
2110B LEU* 4.0 26.2 - - - +
2120B ASN* 3.4 20.7 + - - +
2122B TYR* 5.5 0.2 - - - -
2148B ALA 3.4 0.6 - - - -
2149B ALA* 1.3 72.0 - - - +
2151B THR* 1.3 60.4 + - - +
2152B TYR* 3.0 3.4 - - - -
2169B GLN* 4.1 2.4 + - - -
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Residues in contact with THR2151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2098B SER* 2.7 53.6 + - - +
2101B PHE* 4.0 6.3 - - + -
2102B THR* 2.8 43.0 + - - +
2103B ASN* 3.6 2.8 - - - +
2104B ARG* 4.1 1.4 + - - +
2107B ASN* 5.1 1.3 - - - -
2108B ILE* 6.1 1.6 - - - -
2110B LEU* 4.8 2.1 - - - +
2148B ALA* 3.6 26.8 + - - +
2149B ALA 3.0 1.0 + - - -
2150B SER* 1.3 77.8 - - - +
2152B TYR* 1.3 73.8 + - + +
2153B ASP 3.9 0.5 + - - -
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Residues in contact with TYR2152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2097B LEU* 5.6 1.4 - - - +
2101B PHE* 3.6 32.4 - - + +
2103B ASN* 3.6 4.5 - - - -
2104B ARG* 4.0 3.8 + - - -
2122B TYR* 3.5 11.8 + - - -
2138B TRP* 3.5 34.7 - + - -
2140B HIS* 3.5 20.4 - - + +
2141B GLY 4.3 8.7 + - - -
2148B ALA 3.4 19.5 - - - -
2149B ALA 3.0 21.7 + - - +
2150B SER 4.2 0.3 - - - +
2151B THR* 1.3 94.2 - - + +
2153B ASP* 1.3 62.1 + - - +
2154B GLY 3.6 1.6 + - - -
2167B THR* 3.8 13.5 - - + +
2220B GLU* 5.4 0.5 + - - -
2472B LEU* 4.3 17.4 - - + +
2476B PHE* 4.1 33.0 - + + -
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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
------------------------------------------------------------
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