Contacts of the helix formed by residues 110 - 116 (chain A) in PDB entry 4CYM
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 ARG 110 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLU* 5.1 0.8 - - - +
34A LEU* 2.9 37.6 + - - +
35A GLY* 3.3 18.2 + - - -
107A ASP* 2.7 43.6 + - + +
108A ILE 3.4 1.8 - - - -
109A SER* 1.3 83.8 - - - +
111A SER* 1.3 62.2 + - - +
112A SER* 3.3 12.2 + - - +
113A THR* 2.6 56.2 + - + +
114A PHE 3.8 0.5 + - - -
144A LYS* 4.5 1.6 - - - +
150A ASP* 3.4 6.3 - - - +
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Residues in contact with SER 111 (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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107A ASP 5.1 0.2 - - - -
110A ARG* 1.3 69.6 - - - +
112A SER* 1.3 58.2 + - - +
114A PHE* 2.7 32.1 + - - +
115A GLU* 3.1 23.1 + - - +
150A ASP* 2.9 21.1 + - - +
151A SER* 3.5 28.0 + - - -
153A GLN* 5.9 1.6 - - - +
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Residues in contact with SER 112 (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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33A GLU* 5.6 0.4 - - - -
110A ARG* 3.9 21.1 + - - +
111A SER* 1.3 74.1 + - - +
113A THR* 1.3 66.8 + - - +
115A GLU* 3.3 20.8 + - - +
116A ALA* 3.2 21.5 + - - +
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Residues in contact with THR 113 (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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33A GLU* 4.2 19.2 + - + +
36A VAL* 3.8 22.0 - - + -
105A VAL 4.9 1.2 - - - +
106A PHE* 3.5 3.9 - - - +
107A ASP* 3.0 21.9 + - + -
110A ARG* 2.6 60.2 + - + +
111A SER 3.1 0.2 - - - -
112A SER* 1.3 77.4 - - - +
114A PHE* 1.3 61.0 + - - +
116A ALA* 3.5 4.4 + - - +
117A VAL* 3.4 20.6 + - - +
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Residues in contact with PHE 114 (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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106A PHE* 3.6 45.5 - + + -
111A SER* 2.7 21.7 + - - +
113A THR* 1.3 72.5 + - - +
115A GLU* 1.3 71.4 + - + +
116A ALA 3.0 1.3 - - - -
117A VAL* 3.1 23.9 + - + +
118A LEU* 4.4 1.7 + - + +
140A LEU* 4.5 5.2 - - + -
153A GLN* 3.8 30.5 - - - +
158A VAL* 5.0 5.2 - - + -
161A PHE* 3.7 53.9 - + + -
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Residues in contact with GLU 115 (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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111A SER* 3.1 30.9 + - - +
112A SER* 3.5 15.7 + - - +
114A PHE* 1.3 81.6 - - + +
116A ALA* 1.3 61.4 + - - +
117A VAL 3.4 0.5 + - - -
118A LEU* 3.7 19.3 + - - +
119A LYS* 4.6 5.7 + - - +
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Residues in contact with ALA 116 (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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33A GLU* 3.3 43.3 - - + +
87A ARG* 4.3 5.6 - - - +
112A SER 3.2 8.5 + - - +
113A THR 3.6 6.3 - - - +
114A PHE 3.0 0.8 - - - -
115A GLU* 1.3 75.7 - - - +
117A VAL* 1.3 63.6 + - - +
118A LEU 3.1 3.1 - - - -
119A LYS* 3.0 23.2 + - + +
120A TRP* 3.4 16.0 + - + -
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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
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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