Contacts of the helix formed by residues 93 - 103 (chain E) in PDB entry 4DVQ
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 LEU 93 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77E PRO* 4.0 20.0 - - + -
92E MET* 1.3 88.6 - - + +
94E PRO* 1.3 73.5 - - + +
95E GLU* 3.6 24.2 - - + +
96E ASP* 2.9 28.8 + - - +
97E VAL* 3.4 6.8 + - - +
393E GLN* 3.2 35.4 - - - +
405E VAL* 5.2 0.9 - - - +
410E LEU* 4.1 3.4 - - - -
413E ASN* 3.3 30.3 - - - +
416E LEU* 4.6 8.7 - - + -
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Residues in contact with PRO 94 (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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93E LEU* 1.3 80.4 - - + +
95E GLU* 1.3 58.1 + - + +
97E VAL* 2.4 37.0 + - + -
98E GLU* 3.0 9.5 + - - -
410E LEU* 3.9 19.2 - - + -
416E LEU* 3.5 26.0 - - + -
438E PHE* 3.5 36.1 - - + +
439E HIS* 3.6 27.1 - - + +
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Residues in contact with GLU 95 (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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93E LEU* 3.6 26.8 - - + +
94E PRO* 1.3 81.7 - - + +
96E ASP* 1.3 60.9 + - - +
98E GLU* 3.4 8.9 + - - +
99E LYS* 3.0 49.7 + - + +
393E GLN* 3.9 14.6 + - - -
416E LEU* 5.5 4.9 - - - +
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Residues in contact with ASP 96 (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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91E VAL* 3.5 38.4 - - + +
92E MET 4.0 0.3 + - - -
93E LEU* 2.9 26.5 + - - +
94E PRO 2.5 5.3 + - - -
95E GLU* 1.3 78.5 - - - +
97E VAL* 1.3 57.3 + - - +
99E LYS* 3.6 0.9 + - - +
100E LEU* 3.0 30.2 + - - +
392E LEU* 3.6 32.4 - - + +
393E GLN* 2.7 36.7 + - - +
405E VAL* 5.7 0.2 - - - -
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Residues in contact with VAL 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E LEU 3.9 9.6 - - - +
94E PRO* 2.4 29.4 + - + +
96E ASP* 1.3 65.8 - - - +
98E GLU* 1.3 55.3 + - - +
100E LEU* 2.9 9.9 + - - +
101E GLN* 2.8 32.9 + - - +
382E LEU* 4.5 2.0 - - + -
405E VAL* 3.9 26.5 - - + -
410E LEU* 4.4 7.4 - - + -
438E PHE* 3.9 19.3 - - + -
441E VAL* 4.5 17.5 - - + -
445E PHE* 3.3 37.2 - - + -
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Residues in contact with GLU 98 (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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94E PRO 3.0 7.8 + - - +
95E GLU* 3.4 13.7 - - - +
97E VAL* 1.3 78.3 - - - +
99E LYS* 1.3 78.5 + - - +
101E GLN* 3.3 3.6 + - - +
102E GLN* 3.2 35.9 + - + +
438E PHE* 3.7 45.0 - - + -
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Residues in contact with LYS 99 (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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95E GLU* 3.0 42.9 + - + +
96E ASP* 5.7 0.7 - - - +
97E VAL 3.2 0.2 - - - -
98E GLU* 1.3 91.8 + - - +
100E LEU* 1.3 63.7 + - - +
102E GLN* 3.0 45.9 + - - +
103E VAL* 3.3 13.3 + - + +
390E LEU* 4.8 4.7 - - + -
391E VAL 3.8 20.0 - - - +
392E LEU* 3.6 22.2 - - + -
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Residues in contact with LEU 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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91E VAL* 5.2 0.4 - - + -
96E ASP 3.0 19.2 + - - +
97E VAL* 2.9 9.6 + - - +
99E LYS* 1.3 77.1 - - - +
101E GLN* 1.3 58.6 + - - +
103E VAL* 3.3 14.7 + - + +
104E ASP* 3.5 13.9 + - - +
382E LEU 6.3 0.2 - - - -
383E GLU 6.1 0.4 - - - -
384E ARG* 4.7 10.0 - - + +
386E VAL* 3.6 31.6 - - + -
390E LEU* 4.4 13.7 - - + -
392E LEU* 4.7 2.7 - - + +
403E VAL* 3.7 33.7 - - + +
405E VAL* 3.7 24.5 - - + -
445E PHE* 4.2 20.4 - - + -
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Residues in contact with GLN 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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97E VAL 2.8 14.9 + - - +
98E GLU 3.6 8.5 - - - +
100E LEU* 1.3 71.5 - - - +
102E GLN* 1.3 65.8 + - - +
104E ASP* 3.1 22.4 + - - +
438E PHE* 3.0 31.3 - - + -
445E PHE* 3.9 27.0 - - + +
446E GLY* 3.9 25.4 - - - +
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Residues in contact with GLN 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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98E GLU* 3.2 27.5 + - + +
99E LYS* 3.0 38.0 + - - +
101E GLN* 1.3 76.1 - - - +
103E VAL* 1.3 62.1 + - + +
104E ASP 3.2 9.4 + - - +
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Residues in contact with VAL 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 LYS* 3.3 13.7 + - + +
100E LEU* 3.3 9.2 + - - +
101E GLN 3.2 0.6 - - - -
102E GLN* 1.3 77.1 - - + +
104E ASP* 1.3 63.7 + - - +
105E SER* 3.2 4.0 + - - -
386E VAL* 3.5 34.5 - - + -
387E SER* 4.3 9.4 + - - +
388E SER* 4.0 21.5 - - - +
389E ASP 5.0 1.3 - - - +
390E LEU* 3.8 31.0 - - + -
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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