Contacts of the helix formed by residues 94 - 103 (chain H) 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 ALA 94 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91H ALA* 5.4 5.8 - - + +
92H ASP 2.8 13.8 + - - +
93H THR* 1.3 76.9 - - - +
95H GLU* 1.3 66.9 + - - +
98H LEU* 3.2 32.5 + - + +
99H ARG 3.7 0.3 + - - -
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Residues in contact with GLU 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90H GLU* 3.9 33.5 - - + +
94H ALA* 1.3 77.3 - - - +
96H TYR* 1.3 63.6 + - + +
99H ARG* 2.6 39.4 + - + +
100H ALA 3.7 0.2 + - - -
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Residues in contact with TYR 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90H GLU* 4.0 32.2 - - + +
93H THR* 4.7 19.3 - - - -
94H ALA 3.4 0.6 - - - +
95H GLU* 1.3 76.6 - - + +
97H PHE* 1.3 58.6 + - + +
100H ALA* 2.8 36.3 + - - +
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Residues in contact with PHE 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797D TYR* 5.4 14.4 - + - -
93H THR* 3.2 28.3 + - - +
95H GLU 3.5 0.2 - - - -
96H TYR* 1.3 79.1 - - + +
98H LEU* 1.3 64.1 + - + +
100H ALA* 3.8 2.8 - - - +
101H VAL* 2.9 35.7 + - + +
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Residues in contact with LEU 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797D TYR* 3.5 41.1 - - + +
93H THR 5.1 0.4 - - - +
94H ALA* 3.2 18.4 + - + +
97H PHE* 1.3 82.0 - - + +
99H ARG* 1.3 66.8 + - - +
101H VAL* 2.9 11.5 + - + +
102H ARG* 2.9 23.3 + - + +
155H VAL* 6.2 3.4 - - + -
158H SER* 4.9 15.9 - - - +
159H ALA* 5.4 13.2 - - + -
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Residues in contact with ARG 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H PHE* 4.2 23.8 - - + +
94H ALA 3.7 0.6 + - - -
95H GLU* 2.6 28.5 + - + +
98H LEU* 1.3 79.7 - - - +
100H ALA* 1.3 56.7 + - - +
102H ARG* 3.4 7.3 + - - +
103H ALA* 2.9 27.4 + - - +
159H ALA* 5.5 4.3 - - - -
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Residues in contact with ALA 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H PHE* 5.5 1.1 - - - -
96H TYR* 2.8 23.6 + - - +
97H PHE* 3.9 2.5 - - - +
99H ARG* 1.3 74.9 - - - +
101H VAL* 1.3 66.4 + - - +
103H ALA* 3.0 28.0 + - - +
104H SER* 4.4 2.3 + - - -
106H ILE* 4.6 3.5 - - - +
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Residues in contact with VAL 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797D TYR* 6.5 0.4 - - + -
97H PHE* 2.9 24.3 + - + +
98H LEU* 2.9 16.8 + - + +
100H ALA* 1.3 75.4 - - - +
102H ARG* 1.3 61.3 + - - +
103H ALA 3.0 9.7 - - - +
105H SER* 4.9 0.3 - - - -
106H ILE* 4.2 23.3 + - - +
107H PHE* 5.5 7.0 + - + -
155H VAL* 5.8 5.5 - - + +
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Residues in contact with ARG 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63H LEU* 4.3 21.0 - - + +
98H LEU* 2.9 11.1 + - + +
99H ARG* 3.8 7.0 - - - +
101H VAL* 1.3 76.5 - - - +
103H ALA* 1.3 61.0 + - - +
104H SER 3.7 0.2 + - - -
105H SER* 3.4 13.0 + - - -
155H VAL* 4.5 19.2 - - + +
156H TYR* 5.5 2.7 - - - -
159H ALA* 3.5 31.0 - - + -
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Residues in contact with ALA 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63H LEU* 6.0 1.1 - - - -
81H ASP* 5.7 4.7 - - + +
83H PHE* 3.8 21.8 - - + -
99H ARG 2.9 14.9 + - - +
100H ALA* 3.0 19.1 + - - +
101H VAL 3.0 10.9 - - - +
102H ARG* 1.3 71.1 - - - +
104H SER* 1.3 72.2 + - - +
105H SER 2.8 12.5 + - - -
106H ILE* 4.0 1.0 - - - +
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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