Contacts of the helix formed by residues 115 - 124 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ASP* 1.3 76.3 - - - +
116A GLN* 1.3 66.7 + - - +
117A PHE* 3.3 18.5 + - - +
118A GLU* 2.9 39.5 + - - +
119A HIS* 3.0 22.4 + - - -
141A SER* 3.4 7.2 - - - -
143A LEU* 3.7 24.6 - - - +
81H LEU* 4.2 9.4 - - - +
82H ASP 4.5 2.6 + - - -
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A THR* 3.9 32.3 + - + +
56A VAL* 3.4 18.5 - - + +
61A PHE* 3.4 40.7 - - + -
115A SER* 1.3 77.6 - - - +
117A PHE* 1.3 83.1 + - + +
119A HIS* 4.2 3.6 - - + -
120A LEU 3.0 23.4 + - - -
141A SER* 3.6 20.9 + - - -
143A LEU* 4.5 6.6 - - - +
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Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PHE* 3.6 30.5 - + - -
115A SER* 3.2 11.6 - - - +
116A GLN* 1.3 103.2 - - + +
118A GLU* 1.3 58.2 + - - +
120A LEU* 3.5 3.7 + - - +
121A ALA* 3.0 28.2 + - - +
221B PRO 5.6 0.2 - - - -
223B PRO* 4.7 5.4 - - + -
81H LEU* 3.9 16.6 - - + -
82H ASP 4.3 4.0 - - - +
83H PHE* 3.8 20.6 - - - +
84H THR* 3.5 28.5 - - + -
85H PHE* 3.7 32.5 - + - -
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Residues in contact with GLU 118 (chain A).
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* 3.4 8.6 - - + +
83A PHE* 3.9 3.5 - - + -
114A ASP* 3.6 2.1 - - - +
115A SER* 2.9 38.0 + - - +
117A PHE* 1.3 74.7 - - - +
119A HIS* 1.3 65.0 + - - +
121A ALA* 3.2 6.6 + - - +
122A TRP* 2.9 25.1 + - - +
143A LEU* 5.2 0.5 - - - +
82H ASP* 3.7 5.9 - - - +
83H PHE* 3.9 17.7 - - + -
114H ASP* 2.4 34.5 - - - +
118H GLU* 2.8 50.6 - - + +
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Residues in contact with HIS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A VAL* 3.7 10.8 - - + -
79A TYR* 3.2 15.1 + - - -
82A ASP* 2.6 26.7 + - - -
111A CYS* 5.4 0.2 - - - -
112A SER* 3.1 26.0 - - - -
114A ASP* 3.8 9.8 + - + -
115A SER 3.0 14.6 + - - -
116A GLN* 3.3 13.7 + - - +
118A GLU* 1.3 74.5 - - - +
120A LEU* 1.3 58.1 + - - +
122A TRP* 3.2 5.6 + - - +
123A ILE* 2.9 33.9 + - - +
139A LEU* 3.2 42.9 - - + +
140A LEU 2.9 25.4 + - - -
141A SER* 3.8 6.6 + - - -
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A VAL* 4.3 7.2 - - + -
59A GLY* 3.7 37.5 - - - +
61A PHE* 4.2 11.4 - - + -
116A GLN 3.0 16.8 + - - +
117A PHE* 3.9 4.0 - - - +
119A HIS* 1.3 73.6 - - - +
121A ALA* 1.3 61.2 + - - +
123A ILE* 3.3 12.7 + - + +
124A ASN* 2.9 49.8 + - - +
223B PRO* 3.5 39.3 - - + -
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Residues in contact with ALA 121 (chain A).
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* 3.9 4.4 - - + -
117A PHE 3.0 18.7 + - - +
118A GLU 3.6 4.3 - - - +
120A LEU* 1.3 75.8 - - - +
122A TRP* 1.3 60.4 - - - +
124A ASN* 3.3 10.5 + - - +
125A THR* 2.8 25.5 + - - -
83H PHE* 3.7 39.7 - - + -
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Residues in contact with TRP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TYR* 3.6 5.2 - + - -
82A ASP* 3.3 35.7 - - - +
83A PHE* 3.2 52.8 - + + +
87A CYS* 4.0 6.7 - - + -
88A PRO* 3.5 46.0 - - + -
91A ILE* 3.4 28.0 - - + -
118A GLU 2.9 17.7 + - - +
119A HIS 3.4 4.3 - - - +
121A ALA* 1.3 75.4 - - - +
123A ILE* 1.3 64.6 + - - +
125A THR* 3.0 14.9 + - - -
130A GLY 3.0 18.4 + - - -
131A GLY* 3.7 8.4 - - - -
132A LEU* 3.1 38.1 + - + -
139A LEU* 5.0 1.8 - - + -
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A VAL* 3.6 31.0 - - + +
59A GLY* 5.5 5.6 - - - +
119A HIS 2.9 19.6 + - - +
120A LEU* 3.5 13.5 - - + +
122A TRP* 1.3 76.3 - - - +
124A ASN* 1.3 65.9 + - - +
125A THR 3.2 2.3 + - - -
132A LEU* 4.1 6.5 - - + -
133A GLY* 3.1 44.8 + - - +
134A PRO* 4.3 9.4 - - + +
135A ILE* 3.7 27.8 - - + +
139A LEU* 3.8 17.5 - - + -
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Residues in contact with ASN 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 2.9 40.0 + - - +
121A ALA* 3.3 9.8 + - - +
122A TRP 3.2 0.4 - - - -
123A ILE* 1.3 82.9 - - - +
125A THR* 1.3 58.9 + - - +
126A PRO* 3.9 5.5 - - - +
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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