Contacts of the helix formed by residues 99 - 105 (chain E) in PDB entry 6I3N
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 ASP 99 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94E THR* 4.5 17.3 + - - +
97E GLY* 2.9 19.1 + - - +
98E ARG* 1.3 73.6 - - - +
100E ASP* 1.3 63.4 + - - +
101E VAL 3.3 1.1 - - - -
102E LEU* 4.0 17.2 - - + +
103E LEU* 3.7 23.8 + - + +
81I ARG 5.1 4.1 + - - +
82I PRO* 4.5 21.8 - - + +
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Residues in contact with ASP 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E PHE* 3.3 33.0 - - + -
98E ARG* 3.2 19.3 + - + +
99E ASP* 1.3 80.0 - - - +
101E VAL* 1.3 61.6 + - - +
103E LEU* 3.9 2.8 + - - +
104E GLU* 3.9 17.0 + - - +
21I PRO* 3.3 30.3 - - - +
79I GLN* 3.7 38.2 + - - +
80I GLY* 4.4 2.0 - - - -
81I ARG 5.4 2.6 + - - +
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Residues in contact with VAL 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU* 4.5 12.6 - - + -
36E PHE* 3.6 42.8 - - + -
37E LEU* 3.8 8.7 - - + -
93E LEU* 3.8 20.6 - - + -
98E ARG* 3.4 36.8 - - + +
100E ASP* 1.3 74.4 - - - +
102E LEU* 1.3 71.3 + - + +
103E LEU 3.2 2.7 - - - -
104E GLU 4.8 0.2 - - - +
105E LEU* 2.8 37.2 + - + +
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E LEU* 3.8 26.0 - - + +
93E LEU* 3.7 32.1 - - + +
94E THR* 3.4 20.6 - - + +
98E ARG 3.5 20.4 - - - +
99E ASP* 3.8 16.2 + - + +
100E ASP 3.5 0.4 - - - -
101E VAL* 1.3 80.8 - - + +
103E LEU* 1.3 57.4 + - - +
105E LEU 4.8 1.3 - - - -
106E GLY* 3.3 24.5 + - - +
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E ASP* 3.7 17.2 + - + +
100E ASP* 4.4 3.6 - - - +
101E VAL 3.2 0.8 - - - -
102E LEU* 1.3 81.3 - - - +
104E GLU* 1.3 61.4 + - + +
106E GLY* 4.2 2.0 + - - -
107E PRO* 4.6 6.6 - - - +
19I SER 4.6 19.1 - - - +
20I LEU* 5.8 0.7 - - - -
21I PRO* 5.2 11.9 - - + -
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Residues in contact with GLU 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E ARG* 5.4 5.2 + - - +
32E ARG* 3.7 30.6 + - + -
36E PHE* 3.2 30.0 - - + -
100E ASP 3.9 11.2 + - - +
101E VAL 3.4 2.5 + - - +
103E LEU* 1.3 81.9 - - + +
105E LEU* 1.3 60.0 + - + +
106E GLY 3.2 7.1 + - - -
107E PRO* 4.0 9.7 - - - +
108E SER* 4.4 6.4 + - - -
21I PRO* 4.7 6.2 - - + +
116I TYR* 2.8 29.1 + - - -
120I GLN* 4.1 20.3 + - + +
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Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E ARG* 4.3 6.3 - - - +
29E VAL* 4.2 16.4 - - + +
32E ARG* 3.6 31.9 - - + +
33E LEU* 3.7 49.1 - - + +
36E PHE* 5.1 2.5 - - + -
90E LEU* 5.3 2.1 - - - +
101E VAL* 2.8 27.1 + - + +
102E LEU* 4.2 2.7 - - - -
104E GLU* 1.3 74.1 - - + +
106E GLY* 1.3 64.9 + - - +
107E PRO 3.7 0.4 - - - -
108E SER* 4.1 23.1 - - - -
109E ILE* 3.3 32.8 + - + +
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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