Contacts of the helix formed by residues 115 - 124 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A LEU* 4.3 10.3 - - - +
82A ASP 4.7 2.1 + - - -
114H ASP* 1.3 76.1 - - - +
116H GLN* 1.3 62.0 + - - +
117H PHE* 3.1 18.6 + - - +
118H GLU* 3.0 40.1 + - - +
119H HIS* 3.0 27.0 + - - -
141H SER* 3.5 7.2 - - - -
143H LEU* 3.6 24.7 - - - +
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Residues in contact with GLN 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H THR* 4.1 32.5 + - + +
56H VAL* 3.6 7.9 - - + +
61H PHE* 3.5 45.8 - - + -
115H SER* 1.3 79.1 - - - +
117H PHE* 1.3 85.6 + - + +
119H HIS* 4.2 7.4 - - + -
120H LEU 3.1 18.9 + - - -
141H SER* 3.7 20.0 + - - -
143H LEU* 4.3 9.0 - - - +
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Residues in contact with PHE 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LEU* 4.0 16.4 - - + -
82A ASP 4.3 4.7 - - - +
83A PHE* 3.8 21.5 - - - +
84A THR* 3.5 26.5 - - + -
85A PHE* 3.7 31.2 - + - -
61H PHE* 3.8 28.0 - + - -
115H SER* 3.1 12.2 + - - +
116H GLN* 1.3 104.6 - - + +
118H GLU* 1.3 57.3 + - - +
120H LEU* 3.6 4.3 + - - +
121H ALA* 3.0 28.4 + - - +
221I PRO 5.6 0.2 - - - -
223I PRO* 4.4 8.7 - - + -
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Residues in contact with GLU 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ASP* 3.6 7.7 - - - +
83A PHE* 3.9 17.3 - - + -
114A ASP* 2.3 34.9 - - - +
118A GLU* 2.8 52.5 - - + +
82H ASP* 3.4 8.0 - - + +
83H PHE* 4.0 4.2 - - + -
114H ASP* 3.6 2.3 - - - +
115H SER* 3.0 35.5 + - - +
117H PHE* 1.3 73.4 - - - +
119H HIS* 1.3 66.0 + - - +
121H ALA* 3.2 6.4 + - - +
122H TRP* 2.9 25.1 + - - +
143H LEU* 5.1 0.5 - - - +
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Residues in contact with HIS 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H VAL* 3.7 11.0 - - + -
79H TYR* 3.1 16.0 + - - -
82H ASP* 2.6 27.2 + - - -
112H SER* 3.1 26.2 - - - -
114H ASP* 3.8 9.2 - - + -
115H SER 3.0 15.0 + - - -
116H GLN* 3.6 10.3 - - - +
118H GLU* 1.3 75.1 - - - +
120H LEU* 1.3 57.3 + - - +
122H TRP* 3.2 4.0 + - - +
123H ILE* 2.9 34.6 + - - +
139H LEU* 3.3 41.3 - - + +
140H LEU 2.9 25.6 + - - -
141H SER* 3.7 10.2 - - - -
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Residues in contact with LEU 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H VAL* 4.2 8.5 - - + +
59H GLY* 3.8 33.9 - - - +
61H PHE* 4.2 13.5 - - + -
116H GLN 3.1 17.2 + - - +
117H PHE 3.8 4.3 - - - +
118H GLU 3.2 0.2 - - - -
119H HIS* 1.3 74.9 - - - +
121H ALA* 1.3 60.9 + - - +
123H ILE* 3.2 12.0 + - + +
124H ASN* 2.9 55.0 + - - +
223I PRO* 3.7 37.5 - - + -
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Residues in contact with ALA 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 3.7 39.3 - - + -
83H PHE* 4.0 4.7 - - + -
117H PHE 3.0 17.8 + - - +
118H GLU 3.2 4.0 + - - +
120H LEU* 1.3 75.8 - - - +
122H TRP* 1.3 53.4 + - - +
124H ASN* 3.3 11.1 + - - +
125H THR* 2.7 31.4 + - - -
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Residues in contact with TRP 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H TYR* 3.6 3.6 - + - -
82H ASP* 3.3 36.6 - - - -
83H PHE* 3.2 52.5 - + + +
84H THR 4.3 0.2 - - - -
87H CYS* 4.1 6.5 - - + -
88H PRO* 3.5 47.3 - - + -
91H ILE* 3.4 26.5 - - + -
118H GLU 2.9 16.9 + - - +
119H HIS 3.4 4.0 - - - +
121H ALA* 1.3 75.6 - - - +
123H ILE* 1.3 64.7 + - - +
124H ASN 3.2 0.4 - - - -
125H THR* 3.1 12.8 + - - -
130H GLY 3.0 19.3 + - - -
131H GLY* 3.6 10.0 - - - -
132H LEU* 3.1 40.2 + - + -
139H LEU* 4.9 1.8 - - + -
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Residues in contact with ILE 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H VAL* 3.6 31.9 - - + +
59H GLY* 5.7 5.6 - - - +
119H HIS 2.9 21.2 + - - +
120H LEU* 3.5 12.1 - - + +
122H TRP* 1.3 76.9 - - - +
124H ASN* 1.3 67.6 + - - +
125H THR 3.2 3.6 + - - -
132H LEU* 4.1 12.3 - - + -
133H GLY* 3.4 32.3 + - - +
135H ILE* 3.9 28.3 - - + -
139H LEU* 3.9 23.6 - - + -
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Residues in contact with ASN 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120H LEU* 2.9 41.8 + - - +
121H ALA* 3.3 11.3 + - - +
122H TRP 3.2 0.6 - - - -
123H ILE* 1.3 82.7 - - - +
125H THR* 1.3 57.6 + - - +
126H PRO* 3.9 6.1 - - - +
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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