Contacts of the helix formed by residues 93 - 103 (chain E) in PDB entry 5VOT
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 THR 93 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92E ASP* 1.3 79.3 - - - +
94E ALA* 1.3 59.0 + - - +
96E TYR* 3.0 12.3 + - - +
97E PHE* 2.9 38.4 + - - +
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Residues in contact with ALA 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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513A GLY* 5.9 7.9 - - - +
514A VAL* 6.2 1.6 - - + +
92E ASP* 3.3 1.7 - - + +
93E THR* 1.3 78.8 - - - +
95E GLU* 1.3 57.8 + - - +
97E PHE* 3.8 11.6 - - - +
98E LEU* 2.9 27.4 + - - +
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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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92E ASP 2.8 29.6 + - - +
94E ALA* 1.3 76.6 - - - +
96E TYR* 1.3 60.2 + - + +
98E LEU* 3.3 6.5 - - - +
99E ARG* 2.9 33.1 + - - +
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Residues in contact with TYR 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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92E ASP* 2.9 39.3 + - - -
93E THR* 3.6 8.5 - - - +
95E GLU* 1.3 74.0 - - + +
97E PHE* 1.3 57.7 + - + +
99E ARG* 4.6 2.1 - - - +
100E ALA* 2.7 38.7 + - - +
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Residues in contact with PHE 97 (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 THR* 2.9 23.8 + - - +
94E ALA* 3.9 10.5 - - - +
96E TYR* 1.3 78.8 - - + +
98E LEU* 1.3 58.2 + - - +
100E ALA* 3.3 6.2 - - + +
101E VAL* 2.9 39.0 + - + +
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Residues in contact with LEU 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 ALA 2.9 20.1 + - - +
95E GLU* 3.1 10.0 + - - +
97E PHE* 1.3 78.2 - - - +
99E ARG* 1.3 57.6 + - - +
101E VAL* 3.2 3.5 + - - +
102E ARG* 2.9 27.0 + - - +
155E VAL* 5.6 1.4 - - - +
159E ALA* 4.7 11.4 - - + +
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Residues in contact with ARG 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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83E PHE* 4.5 27.6 - - + +
95E GLU 2.9 16.4 + - - +
96E TYR* 4.6 1.8 - - - +
98E LEU* 1.3 74.0 - - - +
100E ALA* 1.3 63.3 + - - +
102E ARG* 3.3 11.0 + - - +
103E ALA* 3.3 19.9 + - - +
159E ALA* 5.6 0.7 - - - -
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Residues in contact with ALA 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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83E PHE* 6.0 1.1 - - - -
96E TYR 2.7 24.2 + - - +
97E PHE* 3.3 13.0 - - + +
98E LEU 3.1 0.2 - - - -
99E ARG* 1.3 79.5 - - - +
101E VAL* 1.3 61.2 + - + +
103E ALA* 3.0 22.6 + - - +
104E SER* 5.0 1.4 - - - -
106E ILE* 5.1 2.8 - - - +
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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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97E PHE* 2.9 20.9 + - + +
98E LEU* 4.0 2.7 - - - +
100E ALA* 1.3 76.9 - - + +
102E ARG* 1.3 63.0 + - - +
103E ALA 2.8 14.7 - - - +
105E SER* 3.8 9.4 + - - -
106E ILE* 4.2 32.9 + - + +
107E PHE* 5.1 7.4 - - + +
108E PRO* 6.5 0.2 - - + -
155E VAL* 4.1 26.2 - - + +
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Residues in contact with ARG 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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63E LEU 5.5 2.6 - - - +
81E ASP* 5.8 2.3 - - - +
98E LEU 2.9 14.0 + - - +
99E ARG* 3.4 16.8 - - - +
100E ALA 3.2 0.4 - - - -
101E VAL* 1.3 77.2 - - - +
103E ALA* 1.3 58.4 + - - +
104E SER 4.2 0.2 + - - -
105E SER* 4.2 7.4 + - - -
155E VAL* 5.1 5.5 - - - +
156E TYR* 5.9 3.9 - - - +
159E ALA* 3.9 23.3 - - + +
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Residues in contact with ALA 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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81E ASP* 4.6 17.5 - - + +
83E PHE* 4.5 17.7 - - + -
99E ARG 3.3 8.1 + - - +
100E ALA* 3.0 15.4 - - - +
101E VAL* 2.8 16.0 - - - +
102E ARG* 1.3 75.8 - - - +
104E SER* 1.3 67.9 + - - +
105E SER 2.9 8.2 + - - -
106E ILE* 4.4 1.2 + - - +
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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