Contacts of the helix formed by residues 96 - 105 (chain C) in PDB entry 5DPS
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 96 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C SER 3.3 15.9 + - - -
60C ASP* 3.8 20.9 - - + +
61C LEU 3.2 6.1 - - - -
62C THR* 3.9 10.5 - - + +
63C VAL* 4.7 0.9 - - - -
94C SER 3.6 2.9 + - - +
95C ALA* 1.3 77.2 - - - +
97C MET* 1.3 64.4 + - - +
98C GLY* 4.1 0.5 - - - -
99C GLN* 3.0 37.7 + - - +
100C LEU* 3.0 20.8 + - - +
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Residues in contact with MET 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C VAL* 3.8 7.8 - - + +
37C VAL* 3.7 29.6 - - + -
57C VAL* 4.0 17.7 - - + -
58C PRO 3.9 11.9 - - - +
61C LEU* 2.6 34.2 + - + +
62C THR 4.3 1.3 - - - +
63C VAL* 4.1 19.5 - - - -
66C PHE* 3.8 38.6 - - + -
95C ALA 4.0 0.2 + - - -
96C THR* 1.3 72.7 - - - +
98C GLY* 1.3 56.1 + - - +
100C LEU* 3.6 7.8 - - - +
101C TYR* 2.8 31.0 + - - +
111C LEU* 4.2 8.8 - - + +
113C ILE* 4.1 11.7 - - + -
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Residues in contact with GLY 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C VAL* 3.8 14.1 - - - -
59C SER* 2.9 29.1 + - - +
96C THR* 4.1 1.1 - - - -
97C MET* 1.3 77.8 - - - +
99C GLN* 1.3 53.8 + - - +
101C TYR* 3.4 4.0 + - - +
102C GLN* 3.0 31.0 + - - +
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Residues in contact with GLN 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C SER 4.5 1.4 - - - +
95C ALA* 3.4 14.7 - - + +
96C THR* 3.0 41.9 + - - +
98C GLY* 1.3 70.1 - - - +
100C LEU* 1.3 66.9 + - - +
102C GLN* 3.2 8.0 + - - +
103C GLU* 3.0 24.7 + - - +
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C VAL* 3.8 25.6 - - + -
84C PHE* 6.3 0.2 - - + -
86C VAL* 4.5 7.4 - - + -
91C PRO* 3.5 35.0 - - + -
92C PRO* 4.9 3.6 - - + -
95C ALA* 4.1 11.9 - - + -
96C THR 3.0 10.7 + - - +
97C MET* 3.6 12.8 - - - +
99C GLN* 1.3 74.0 - - - +
101C TYR* 1.3 64.4 + - - +
103C GLU* 3.2 1.9 + - - -
104C HIS* 2.9 47.6 + - + +
111C LEU* 4.3 18.6 - - + -
113C ILE* 4.5 15.3 - - + -
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Residues in contact with TYR 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ARG* 3.4 50.3 + - - +
35C VAL* 3.7 29.2 - - + -
36C PRO* 4.0 11.9 - - + -
97C MET 2.8 22.2 + - - +
98C GLY* 3.5 5.4 - - - +
100C LEU* 1.3 73.6 - - - +
102C GLN* 1.3 74.0 + - - +
105C HIS* 3.0 59.6 + + + +
109C PHE* 2.7 45.6 + + - +
111C LEU* 3.9 19.6 - - + +
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Residues in contact with GLN 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ASN* 5.3 0.5 + - - -
28C ARG* 4.1 11.0 + - - +
98C GLY 3.0 17.1 + - - +
99C GLN* 3.2 8.2 + - - +
101C TYR* 1.3 91.6 - - - +
103C GLU* 1.3 59.6 + - - +
105C HIS* 3.9 23.0 + - - -
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Residues in contact with GLU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ASN* 3.2 18.3 + - - +
99C GLN 3.0 16.0 + - - +
100C LEU* 4.6 0.4 - - - -
102C GLN* 1.3 79.7 - - - +
104C HIS* 1.3 88.9 + - + +
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Residues in contact with HIS 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ASN* 3.3 7.3 + - - +
86C VAL* 3.3 50.9 - - + +
87C ASN* 2.9 36.7 + - + +
89C VAL* 4.9 13.8 - - + +
91C PRO* 5.8 1.0 - - - +
100C LEU* 2.9 29.6 + - + +
103C GLU* 1.3 110.6 + - + +
105C HIS* 1.3 68.2 + - - +
106C GLU* 3.6 4.3 + - - +
111C LEU* 3.7 7.2 - - + +
112C TYR 5.5 0.9 + - - -
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Residues in contact with HIS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ASN* 3.0 23.7 + - - +
101C TYR* 3.0 64.9 + + + +
102C GLN* 3.9 23.8 + - - -
104C HIS* 1.3 76.2 - - - +
106C GLU* 1.3 81.5 + - - +
107C GLU* 5.4 2.0 - - - -
109C PHE* 4.2 25.3 - + - -
110C PHE 3.4 9.6 - - - +
111C LEU* 4.2 5.1 - - - +
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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