Contacts of the helix formed by residues 98 - 104 (chain B) in PDB entry 5T0I
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 LYS 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A LEU* 5.0 15.6 + - - -
80A LEU* 4.5 14.1 + - - +
81A ALA* 4.5 12.8 - - - +
94B GLU* 3.1 16.1 + - + +
95B GLU* 4.0 13.7 - - - +
96B ARG 3.3 0.4 - - - -
97B SER* 1.3 76.0 - - - +
99B VAL* 1.3 90.5 + - - +
100B ASP* 3.1 7.7 + - - +
101B ASP* 3.4 5.9 + - - +
102B LEU* 3.4 28.1 - - + +
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU* 4.0 39.3 - - + +
83A ASP* 5.4 0.2 - - - +
95B GLU* 3.2 19.5 + - + +
96B ARG* 4.7 1.6 - - - +
98B LYS* 1.3 96.4 - - - +
100B ASP* 1.3 60.7 + - - +
101B ASP 3.2 0.2 - - - -
102B LEU* 2.8 34.2 + - + +
103B ARG* 2.8 40.2 + - + +
160B ILE* 5.0 4.7 - - + -
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Residues in contact with ASP 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ARG* 3.4 18.9 + - - +
97B SER* 2.9 32.6 - - - +
98B LYS 3.1 1.9 - - - +
99B VAL* 1.3 77.2 - - - +
101B ASP* 1.3 78.1 + - - +
103B ARG* 3.9 15.7 - - - +
104B GLY* 2.8 33.6 + - - -
105B THR 3.9 0.7 + - - -
98C ASP* 3.9 15.7 - - - +
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B SER 4.4 5.9 - - - +
98B LYS 4.1 5.0 - - - +
99B VAL 3.2 0.4 - - - -
100B ASP* 1.3 101.5 + - - +
102B LEU* 1.3 67.3 + - + +
103B ARG 3.7 0.2 + - - -
104B GLY 3.8 11.6 - - - +
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU 4.2 8.3 - - - +
81A ALA* 5.8 1.3 - - - -
83A ASP* 3.5 44.7 - - + +
84A LYS 5.6 0.4 - - - +
87A LEU* 5.7 6.5 - - + -
98B LYS* 3.4 28.9 - - + +
99B VAL* 2.8 22.9 + - + +
101B ASP* 1.3 85.5 - - + +
103B ARG* 1.3 55.9 + - + +
153B ASN* 4.3 5.5 + - - -
155B LYS 5.0 6.2 - - - +
160B ILE* 5.6 1.5 - - + +
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ARG* 3.0 39.9 + - - +
99B VAL* 2.8 32.1 + - - +
100B ASP* 3.9 14.9 - - - +
102B LEU* 1.3 79.2 - - - +
104B GLY* 1.3 70.1 + - - +
106B PRO 3.8 8.5 - - - +
107B MET* 3.4 8.1 - - + +
153B ASN* 3.6 37.5 - - - +
154B HIS 5.0 0.5 + - - -
155B LYS* 5.0 5.2 + - - +
160B ILE* 3.6 38.4 - - + -
82C LYS* 5.8 1.1 - - - -
84C LYS* 3.4 15.2 - - - +
98C ASP* 2.6 40.8 + - - -
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Residues in contact with GLY 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ASP 2.8 21.8 + - - +
101B ASP* 3.8 12.1 - - - +
103B ARG* 1.3 82.5 - - - +
105B THR* 1.3 69.2 + - - -
106B PRO* 3.5 8.5 - - - +
107B MET* 3.6 9.0 - - - -
98C ASP* 4.4 1.1 - - - -
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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