Contacts of the strand formed by residues 2150 - 2156 (chain D) in PDB entry 2C5L
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 ARG2150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B SER* 2.9 57.2 + - - +
41B ARG* 4.2 19.6 - - - +
54B ASP* 4.4 13.3 + - - -
56B LEU* 5.5 2.8 - - - +
2140D GLN* 4.4 15.7 - - - +
2141D VAL 3.3 6.7 - - - +
2142D HIS* 3.5 38.5 - - + +
2144D VAL* 4.8 0.9 - - - -
2148D GLN* 3.2 16.0 + - - -
2149D PRO* 1.3 95.1 + - - +
2151D THR* 1.3 61.2 + - - +
2152D VAL* 6.2 0.4 - - + -
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Residues in contact with THR2151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B GLU 3.8 2.7 - - - -
38B ASP* 2.6 25.3 + - - -
2139D VAL 3.6 0.9 - - - +
2140D GLN* 3.3 4.2 - - - +
2141D VAL* 3.0 34.7 + - + +
2144D VAL* 4.0 22.2 - - + -
2148D GLN* 3.7 9.4 - - - -
2150D ARG* 1.3 75.7 - - - +
2152D VAL* 1.3 63.9 + - - +
2153D ILE* 3.7 21.3 + - + -
2168D THR* 4.1 8.7 - - + -
2171D LYS* 3.6 26.6 - - + +
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Residues in contact with VAL2152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 3.7 39.3 + - + +
37B GLU* 3.0 37.5 + - + +
38B ASP* 4.6 0.5 - - - +
67B MET* 4.7 10.8 - - + -
2138D PHE* 4.3 19.7 - - + -
2139D VAL 3.4 8.1 - - - +
2140D GLN* 3.6 31.2 - - + +
2150D ARG* 6.2 0.9 - - + -
2151D THR* 1.3 74.0 + - - +
2153D ILE* 1.3 63.7 + - - +
2171D LYS* 3.7 16.8 + - - -
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Residues in contact with ILE2153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 4.2 3.6 - - - -
2137D PHE 3.6 0.7 - - - +
2138D PHE* 3.2 7.7 - - - -
2139D VAL* 2.8 47.4 + - + +
2141D VAL* 4.2 8.3 - - + -
2151D THR* 3.7 24.2 - - + +
2152D VAL* 1.3 75.8 - - - +
2154D LYS* 1.3 62.9 + - - +
2155D ALA* 4.1 5.8 - - + -
2164D VAL* 4.6 5.2 - - + +
2167D GLN* 3.5 40.6 - - + +
2168D THR* 3.3 38.4 - - - +
2171D LYS* 3.7 21.5 - - + +
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Residues in contact with LYS2154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 3.7 21.6 - - + +
63B GLU* 2.9 28.9 + - - -
64B TYR* 3.6 13.1 + - - +
2136D SER* 4.2 26.9 - - - +
2137D PHE 3.5 7.0 - - - +
2138D PHE* 3.8 21.4 - - + -
2153D ILE* 1.3 71.8 - - - +
2155D ALA* 1.3 59.3 + - - +
2156D PRO* 4.5 2.3 - - - +
2167D GLN* 3.0 17.0 + - - +
2171D LYS* 5.3 1.6 - - - +
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Residues in contact with ALA2155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2136D SER* 3.4 4.2 - - - -
2137D PHE* 2.7 58.5 + - + +
2139D VAL* 4.2 7.0 - - + -
2153D ILE* 3.8 7.6 + - + -
2154D LYS* 1.3 74.4 - - - +
2156D PRO* 1.4 67.7 - - + +
2159D SER* 4.0 10.1 - - - +
2164D VAL* 4.6 2.9 - - + -
2167D GLN* 3.4 22.2 - - - +
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Residues in contact with PRO2156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2135D GLU* 3.3 15.0 - - + +
2136D SER* 4.0 7.3 - - - +
2137D PHE* 4.1 0.5 - - - -
2154D LYS 4.5 2.7 - - - +
2155D ALA* 1.4 82.2 - - + +
2157D ARG* 1.3 53.2 + - - +
2158D VAL* 3.1 17.5 - - + -
2159D SER* 2.8 51.1 + - - +
2167D GLN* 4.7 5.6 - - - +
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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