Contacts of the helix formed by residues 115 - 124 (chain B) in PDB entry 3TKR
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 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B ASP* 1.3 75.7 - - - +
116B GLN* 1.3 65.7 + - - +
117B PHE* 3.2 18.3 + - - +
118B GLU* 2.9 38.6 + - - +
119B HIS* 3.0 26.8 + - - -
141B SER* 3.4 7.2 - - - -
143B LEU* 3.7 21.6 - - - +
81G LEU* 4.1 10.8 - - - +
82G ASP 4.6 1.2 + - - -
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Residues in contact with GLN 116 (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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54B THR* 4.0 33.0 + - + +
56B VAL* 3.5 12.7 - - + +
61B PHE* 3.5 40.1 - - + -
115B SER* 1.3 77.6 - - - +
117B PHE* 1.3 82.7 + - + +
119B HIS* 3.3 11.3 + - + -
120B LEU 2.9 24.4 + - - -
141B SER* 3.7 17.2 + - - -
143B LEU* 4.4 7.8 - - - +
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Residues in contact with PHE 117 (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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61B PHE* 3.8 29.4 - + - -
115B SER* 3.2 11.8 - - - +
116B GLN* 1.3 103.4 - - + +
118B GLU* 1.3 58.5 + - - +
120B LEU* 3.6 4.1 + - - +
121B ALA* 3.0 27.5 + - - +
223C PRO* 4.6 6.7 - - + -
81G LEU* 3.8 18.2 - - + -
82G ASP 4.3 0.9 - - - +
83G PHE* 3.8 26.6 - - + +
84G THR* 3.5 27.4 - - + -
85G PHE* 3.8 30.7 - + - -
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Residues in contact with GLU 118 (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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82B ASP* 3.4 8.0 - - + +
83B PHE* 3.9 3.4 - - + -
114B ASP* 3.6 2.6 - - - +
115B SER* 2.9 38.2 + - - +
117B PHE* 1.3 75.0 - - - +
119B HIS* 1.3 66.2 + - - +
121B ALA* 3.3 6.3 + - - +
122B TRP* 2.9 25.8 + - - +
143B LEU* 5.1 0.9 - - - +
82G ASP* 3.7 7.2 - - - +
83G PHE* 3.9 19.3 - - + -
114G ASP* 2.4 35.0 - - - +
118G GLU* 2.9 47.6 - - + +
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Residues in contact with HIS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 3.6 11.0 - - + -
79B TYR* 3.1 24.2 + - - -
82B ASP* 2.7 27.5 + - - -
112B SER* 3.2 17.9 - - - -
114B ASP* 3.8 9.1 + - + -
115B SER 3.0 14.3 + - - -
116B GLN* 3.5 14.1 - - - +
118B GLU* 1.3 75.5 - - - +
120B LEU* 1.3 56.0 + - - +
122B TRP* 3.2 4.5 + - - +
123B ILE* 2.9 34.9 + - - +
139B LEU* 3.3 40.7 - - + +
140B LEU 2.9 25.0 + - - -
141B SER* 3.8 7.6 - - - -
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Residues in contact with LEU 120 (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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56B VAL* 4.1 7.5 - - + +
59B GLY* 3.7 36.3 - - - +
61B PHE* 4.2 12.1 - - + -
116B GLN 2.9 16.7 + - - +
117B PHE 3.9 4.0 - - - +
119B HIS* 1.3 77.6 - - - +
121B ALA* 1.3 56.2 + - - +
123B ILE* 3.3 10.7 + - + +
124B ASN* 3.0 54.8 + - - +
223C PRO* 3.6 38.8 - - + -
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Residues in contact with ALA 121 (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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83B PHE* 4.0 4.5 - - + -
117B PHE 3.0 19.1 + - - +
118B GLU* 3.7 5.2 - - - +
120B LEU* 1.3 77.2 - - - +
122B TRP* 1.3 54.0 + - - +
124B ASN* 3.4 9.4 + - - +
125B THR* 2.7 30.9 + - - -
83G PHE* 3.6 38.8 - - + -
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Residues in contact with TRP 122 (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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79B TYR* 3.6 5.2 - + - -
82B ASP* 3.2 37.5 - - - +
83B PHE* 3.2 52.9 - + + +
84B THR 4.3 0.2 - - - -
87B CYS* 4.1 6.3 - - + -
88B PRO* 3.5 46.9 - - + -
91B ILE* 3.4 26.9 - - + -
118B GLU 2.9 17.8 + - - +
119B HIS 3.5 3.6 - - - +
121B ALA* 1.3 74.1 - - - +
123B ILE* 1.3 66.6 + - - +
124B ASN 3.2 0.2 - - - -
125B THR* 3.1 13.1 + - - -
130B GLY 3.0 18.7 + - - -
131B GLY* 3.6 8.9 - - - -
132B LEU* 3.1 38.6 + - + -
139B LEU* 4.9 2.0 - - + -
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Residues in contact with ILE 123 (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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56B VAL* 3.6 31.9 - - + +
59B GLY* 5.4 5.8 - - - +
119B HIS 2.9 19.5 + - - +
120B LEU* 3.6 11.0 - - + +
122B TRP* 1.3 77.6 - - - +
124B ASN* 1.3 63.9 + - - +
125B THR 3.2 3.6 + - - -
132B LEU* 4.0 6.7 - - + -
133B GLY* 3.3 40.1 + - - +
134B PRO* 4.1 9.1 - - + +
135B ILE* 3.5 28.0 - - + +
139B LEU* 3.8 18.2 - - + -
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Residues in contact with ASN 124 (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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120B LEU* 3.0 43.3 + - - +
121B ALA* 3.6 9.7 - - - +
122B TRP 3.2 0.4 - - - -
123B ILE* 1.3 82.9 - - - +
125B THR* 1.3 57.6 - - - +
126B PRO* 4.0 5.2 - - - +
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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