Contacts of the helix formed by residues 95 - 103 (chain C) in PDB entry 1TKP
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 SER 95 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C ALA* 1.3 78.6 - - - +
96C PRO* 1.3 64.9 - - - +
97C GLU* 4.4 2.6 + - - +
98C THR* 2.6 29.8 + - - -
99C LEU* 2.8 33.1 + - - +
46D HIS* 4.8 1.8 - - - -
100D GLN* 3.5 10.7 + - - -
107D VAL* 3.9 17.3 - - - -
108D GLU 4.6 5.6 - - - -
110D GLU* 3.0 13.7 + - - +
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Residues in contact with PRO 96 (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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95C SER* 1.3 86.9 - - - +
97C GLU* 1.3 55.4 + - - +
99C LEU* 3.4 8.7 + - + +
100C GLN* 2.9 25.8 + - - +
42D TYR 5.1 0.4 - - - -
43D VAL* 4.3 17.9 - - + +
46D HIS* 3.7 33.2 - - + -
96D PRO* 3.2 46.7 - - + +
99D LEU* 5.0 3.1 - - + -
100D GLN* 2.9 24.9 - - + +
107D VAL* 4.7 4.5 - - + -
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Residues in contact with GLU 97 (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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95C SER* 4.9 2.1 + - - -
96C PRO* 1.3 74.6 - - - +
98C THR* 1.3 65.8 + - - +
100C GLN* 3.3 1.9 + - - +
101C ALA* 2.9 31.0 + - + +
97D GLU* 4.7 14.1 - - + +
100D GLN* 2.7 44.6 + - + +
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Residues in contact with THR 98 (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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93C HIS* 3.8 27.4 - - + +
94C ALA 4.5 0.9 - - - -
95C SER* 2.6 27.6 + - - -
97C GLU* 1.3 82.9 + - - +
99C LEU* 1.3 63.2 + - - +
101C ALA* 3.8 4.6 - - - -
102C GLU* 3.0 33.6 + - + +
110D GLU* 3.2 33.5 - - + +
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Residues in contact with LEU 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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38C LEU* 3.9 6.7 - - + +
39C ALA* 3.3 34.8 - - - +
42C TYR* 3.8 30.7 - - + -
43C VAL* 4.4 3.4 - - + -
93C HIS* 3.7 28.5 - - + +
94C ALA 3.3 23.3 - - - +
95C SER 2.8 18.5 + - - +
96C PRO* 3.7 5.8 - - + +
98C THR* 1.3 73.6 - - - +
100C GLN* 1.3 61.9 + - - +
103C ALA* 3.2 19.6 + - - +
46D HIS* 3.6 26.7 - - + +
53D TRP* 5.7 0.2 - - + -
96D PRO* 5.1 5.6 - - + -
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Residues in contact with GLN 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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43C VAL* 3.9 10.7 - - + +
96C PRO 2.9 18.9 + - - +
97C GLU 4.1 2.2 - - - +
99C LEU* 1.3 71.1 - - - +
101C ALA* 1.3 68.3 + - - +
102C GLU 3.2 0.5 + - - -
103C ALA* 3.3 17.0 + - - +
107C VAL* 3.5 40.2 - - + +
95D SER* 3.6 4.1 + - - -
96D PRO* 3.1 16.0 - - + +
97D GLU* 2.7 64.9 + - + +
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Residues in contact with ALA 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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97C GLU* 2.9 22.8 + - + +
98C THR* 4.0 5.8 - - - +
100C GLN* 1.3 78.0 - - - +
102C GLU* 1.3 62.4 + - + +
103C ALA 3.5 4.0 + - - +
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Residues in contact with GLU 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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35C ASN 5.4 0.2 - - - +
36C ALA* 4.8 11.1 - - - +
39C ALA* 3.7 15.5 - - + +
93C HIS* 3.4 44.5 + - + +
98C THR* 3.0 31.0 + - + +
100C GLN 3.2 0.2 - - - -
101C ALA* 1.3 77.8 - - + +
103C ALA* 1.3 63.4 + - - +
104C SER* 3.7 1.4 + - - -
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Residues in contact with ALA 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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39C ALA* 3.8 8.5 - - - +
40C ASN* 3.1 17.3 - - - +
43C VAL* 3.7 21.1 - - + -
99C LEU 3.2 12.4 + - - +
100C GLN* 3.3 17.6 + - + +
101C ALA 4.0 3.6 - - - +
102C GLU* 1.3 80.6 - - - +
104C SER* 1.3 59.4 + - - +
105C VAL* 4.0 13.3 - - + +
107C VAL* 5.4 0.4 - - + -
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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