Contacts of the helix formed by residues 97 - 106 (chain B) in PDB entry 5DPT
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 97 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B SER 3.5 14.6 + - - +
61B ASP* 4.3 15.7 - - + +
62B LEU 3.4 6.7 - - - -
63B THR* 4.1 6.7 - - + +
64B VAL* 4.6 0.4 - - - -
95B SER 4.5 6.3 - - - +
96B ALA* 1.3 77.0 - - - +
98B MET* 1.3 59.6 + - - +
99B GLY* 4.1 0.2 - - - -
100B GLN* 3.0 27.6 + - + +
101B LEU* 2.8 30.0 + - - +
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Residues in contact with MET 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 3.8 6.9 - - + +
38B VAL* 3.7 30.7 - - + -
58B VAL* 3.9 18.8 - - + -
59B PRO 3.8 12.6 - - - +
60B SER 3.7 0.2 + - - -
62B LEU* 2.7 29.5 + - + +
63B THR 4.3 2.2 - - - +
64B VAL* 3.9 30.7 - - - -
67B PHE* 4.0 29.6 - - + -
97B THR* 1.3 72.1 - - - +
99B GLY* 1.3 56.8 + - - +
101B LEU* 3.7 8.3 - - + +
102B TYR* 2.8 30.7 + - - +
112B LEU* 3.9 16.9 - - + +
114B VAL* 4.9 3.4 - - + -
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Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ARG* 6.0 0.8 + - - -
36B VAL* 3.9 14.1 - - - -
60B SER* 2.8 29.5 + - - +
97B THR* 4.1 0.2 - - - -
98B MET* 1.3 76.7 - - - +
100B GLN* 1.3 57.4 + - - +
102B TYR* 3.3 3.5 + - - +
103B GLU* 2.9 31.9 + - - +
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Residues in contact with GLN 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA* 5.4 5.6 - - + -
97B THR* 3.0 26.4 + - - +
99B GLY* 1.3 74.2 - - - +
101B LEU* 1.3 62.5 + - - +
103B GLU* 3.6 16.4 + - - +
104B ASP* 2.8 62.3 + - - +
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Residues in contact with LEU 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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64B VAL* 3.6 24.9 - - + -
87B VAL* 3.8 25.6 - - + -
92B PRO* 3.8 23.6 - - + -
93B PRO* 5.2 2.7 - - + -
96B ALA* 4.8 9.6 - - + +
97B THR 2.8 17.3 + - - +
98B MET* 3.8 12.1 - - + +
100B GLN* 1.3 74.3 - - - +
102B TYR* 1.3 60.1 + - - +
104B ASP* 4.0 2.0 - - + -
105B ASN* 3.1 49.6 + - - +
112B LEU* 3.9 16.4 - - + +
114B VAL* 5.1 1.3 - - + -
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Residues in contact with TYR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ARG* 3.6 45.4 - - - -
36B VAL* 3.6 26.7 - - + -
37B PRO* 3.8 15.6 - - + +
98B MET 2.8 18.8 + - - +
99B GLY 3.6 6.1 - - - +
101B LEU* 1.3 73.2 - - - +
103B GLU* 1.3 62.0 + - + +
104B ASP 3.0 4.5 - - - -
106B HIS* 3.0 62.2 + + + +
110B TYR* 2.8 45.9 + + - +
112B LEU* 3.7 24.2 - - + +
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Residues in contact with GLU 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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99B GLY 2.9 18.7 + - - +
100B GLN* 4.0 19.5 + - - +
101B LEU 3.5 0.2 - - - -
102B TYR* 1.3 80.7 - - + +
104B ASP* 1.3 66.7 + - - +
106B HIS* 4.1 15.0 + - - +
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Residues in contact with ASP 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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88B ASN* 5.0 0.2 + - - -
100B GLN* 2.8 44.7 + - - +
101B LEU* 4.2 3.8 - - + +
102B TYR 3.0 0.8 - - - -
103B GLU* 1.3 86.1 - - - +
105B ASN* 1.3 74.2 + - - +
106B HIS* 3.8 1.8 - - - -
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Residues in contact with ASN 105 (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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87B VAL* 3.4 36.2 + - + +
88B ASN* 3.2 31.2 + - - +
101B LEU* 3.1 30.8 + - - +
102B TYR 3.9 0.2 - - - -
104B ASP* 1.3 94.3 - - - +
106B HIS* 1.3 63.4 + - - +
107B GLU* 3.5 8.3 + - - +
111B PHE 4.6 0.7 - - - +
112B LEU* 3.9 9.9 - - + +
113B TYR 5.1 1.6 + - - -
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Residues in contact with HIS 106 (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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102B TYR* 3.0 63.7 + + + +
103B GLU* 4.1 14.2 + - - -
104B ASP 3.8 1.0 - - - -
105B ASN* 1.3 77.9 - - - +
107B GLU* 1.3 71.9 + - - +
108B GLU* 5.8 0.9 - - - -
110B TYR* 4.2 27.1 - + - -
111B PHE 3.6 10.3 - - - +
112B LEU* 4.6 2.7 - - - +
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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