Contacts of the helix formed by residues 2151 - 2157 (chain A) in PDB entry 3CMT
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 PRO2151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2123A GLU* 3.5 16.8 - - - +
2149A LEU 3.3 9.6 - - - +
2150A THR* 1.3 87.8 - - - +
2152A LYS* 1.3 66.7 + - - +
2153A ALA 3.3 0.2 - - - -
2154A GLU* 3.1 35.4 + - + +
2155A ILE* 3.2 10.7 + - - +
2166A LEU* 3.8 28.9 - - + -
2167A ALA* 3.8 35.9 - - + +
2170A MET* 4.4 6.3 - - - -
3176A ARG* 5.0 1.3 - - - +
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Residues in contact with LYS2152 (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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2121A THR* 3.8 29.8 - - + +
2123A GLU* 2.7 28.1 + - + +
2150A THR 3.6 0.2 + - - -
2151A PRO* 1.3 72.2 - - - +
2153A ALA* 1.3 61.8 + - - +
2155A ILE* 3.3 3.9 + - + +
2156A GLU* 3.1 59.0 + - + +
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Residues in contact with ALA2153 (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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2123A GLU* 5.3 0.4 + - - -
2151A PRO* 3.3 1.0 - - - +
2152A LYS* 1.3 78.4 - - - +
2154A GLU* 1.3 57.8 + - - +
2156A GLU* 3.8 7.5 - - - +
2157A GLY* 2.9 25.8 + - - -
2163A HIS* 3.7 11.6 - - + +
2166A LEU* 3.8 22.4 - - + -
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Residues in contact with GLU2154 (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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2150A THR* 3.6 13.5 - - + +
2151A PRO* 3.1 34.2 + - + +
2153A ALA* 1.3 76.7 - - - +
2155A ILE* 1.3 64.1 + - - +
2157A GLY 3.3 17.0 + - - +
2158A GLU 4.7 0.5 - - - +
2163A HIS* 3.4 33.5 + - + +
2166A LEU* 4.7 0.2 - - - +
3173A GLN* 3.3 27.8 - - + +
3176A ARG* 2.7 42.1 + - - -
3177A LYS* 3.5 12.2 - - + +
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Residues in contact with ILE2155 (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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2120A ASP* 3.2 28.7 - - + +
2121A THR* 3.9 14.8 - - + -
2150A THR* 3.7 38.4 - - + +
2151A PRO 3.2 3.6 + - - +
2152A LYS* 3.3 7.6 + - - +
2154A GLU* 1.3 78.0 - - - +
2156A GLU* 1.3 69.4 + - + +
2157A GLY 3.4 0.9 - - - +
3130A ASP* 5.3 0.5 - - - +
3134A ARG* 5.9 0.5 + - - -
3176A ARG 5.4 1.6 - - - +
3177A LYS* 3.4 33.7 + - - +
3181A ASN* 6.0 4.0 - - - +
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Residues in contact with GLU2156 (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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2152A LYS* 3.1 55.5 + - - +
2153A ALA* 4.2 6.1 + - - +
2155A ILE* 1.3 78.8 - - + +
2157A GLY* 1.3 64.9 + - - +
2158A GLU* 5.7 0.3 - - - +
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Residues in contact with GLY2157 (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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2153A ALA 2.9 19.0 + - - -
2154A GLU 3.3 7.2 + - - +
2155A ILE 3.4 0.3 - - - +
2156A GLU* 1.3 81.7 - - - +
2158A GLU* 1.3 59.1 + - - -
2161A ASP* 3.5 10.3 - - - -
2163A HIS* 4.7 4.3 - - - -
3177A LYS* 2.8 28.2 + - - -
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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