Contacts of the helix formed by residues 115 - 127 (chain C) in PDB entry 6T2C
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 TYR 115 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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659B ALA 3.9 15.1 + - - -
660B VAL* 3.6 14.1 - - + -
661B ALA* 3.8 25.6 + - + +
111C TYR* 3.3 50.8 + + - +
114C VAL* 1.3 96.1 - - + +
116C LYS* 1.3 63.6 + - - +
117C MET* 3.3 7.1 + - + -
118C TYR* 3.3 41.0 + + + +
119C PHE* 3.2 20.9 - - + -
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Residues in contact with LYS 116 (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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112C PRO 3.3 26.7 - - - +
113C ARG* 3.6 16.2 - - + +
114C VAL 3.4 3.2 + - - -
115C TYR* 1.3 75.8 - - - +
117C MET* 1.3 58.6 + - - +
119C PHE* 3.3 6.7 + - + +
120C ASP* 2.9 39.2 + - + +
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Residues in contact with MET 117 (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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658B ASP* 6.3 0.9 - - - -
115C TYR* 3.3 5.6 + - + -
116C LYS* 1.3 78.9 - - - +
118C TYR* 1.3 90.6 + - + +
120C ASP* 3.3 10.8 + - - +
121C ARG* 3.0 45.5 + - + +
124C ARG* 5.1 0.3 + - - -
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Residues in contact with TYR 118 (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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606B ILE* 4.5 2.9 - - - +
607B PRO* 4.0 9.2 - - + -
610B CYS* 3.5 23.7 - - - +
658B ASP* 3.2 39.7 - - + +
659B ALA 3.4 17.9 + - - -
660B VAL* 4.1 12.8 - - + -
115C TYR* 3.5 46.4 - + + +
116C LYS 3.2 0.8 - - - -
117C MET* 1.3 105.4 - - + +
119C PHE* 1.3 61.2 + - + +
121C ARG* 3.2 28.5 + - - +
122C LEU* 3.0 24.9 + - - +
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Residues in contact with PHE 119 (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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609B VAL* 5.0 1.3 - - + -
610B CYS* 4.0 27.1 - - + -
613B TRP* 3.5 61.2 - + + -
660B VAL* 6.1 3.4 - - + -
111C TYR* 3.3 29.8 - + + -
112C PRO* 4.4 14.4 - - + +
115C TYR* 3.2 31.4 - - + -
116C LYS* 3.3 6.2 + - + +
118C TYR* 1.3 74.7 - - + +
120C ASP* 1.3 60.2 + - - +
122C LEU* 3.3 15.4 + - + +
123C GLU* 2.9 30.8 + - - +
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Residues in contact with ASP 120 (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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116C LYS* 2.9 28.6 + - + +
117C MET* 3.4 14.7 - - - +
118C TYR 3.2 0.2 - - - -
119C PHE* 1.3 75.4 - - - +
121C ARG* 1.3 59.1 + - - +
123C GLU* 3.4 10.9 + - - +
124C ARG* 3.0 55.4 + - - +
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Residues in contact with ARG 121 (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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605B HIS* 2.8 49.0 + - + +
606B ILE* 4.3 13.3 - - + +
607B PRO* 4.2 5.5 - - - +
658B ASP* 4.3 20.6 + - - +
117C MET* 3.0 31.3 + - + +
118C TYR* 3.2 37.3 + - - +
120C ASP* 1.3 75.9 - - - +
122C LEU* 1.3 62.7 + - - +
124C ARG* 3.4 24.2 + - - +
125C LEU* 3.0 23.4 + - - +
230C GLU* 4.9 9.3 + - - +
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Residues in contact with LEU 122 (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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606B ILE* 4.0 21.3 - - + +
610B CYS* 3.3 23.1 - - + +
611B LEU* 4.1 28.5 - - + +
613B TRP* 5.6 2.7 - - + -
614B SER* 6.0 2.7 - - - +
118C TYR 3.0 13.3 + - - +
119C PHE* 3.6 21.1 - - + +
120C ASP 3.3 0.2 - - - -
121C ARG* 1.3 75.9 - - - +
123C GLU* 1.3 57.5 + - + +
125C LEU* 3.2 5.2 + - + +
126C THR* 2.6 55.4 + - + +
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Residues in contact with GLU 123 (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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119C PHE 2.9 18.0 + - - +
120C ASP* 4.1 12.7 - - - +
122C LEU* 1.3 78.3 - - + +
124C ARG* 1.3 65.6 + - - +
126C THR* 4.5 3.4 - - - +
127C HIS* 3.1 47.9 + - + +
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Residues in contact with ARG 124 (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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117C MET 5.1 0.6 + - - -
120C ASP* 3.0 38.7 + - - +
121C ARG* 4.0 25.0 + - - +
123C GLU* 1.3 79.1 - - - +
125C LEU* 1.3 62.2 + - - +
127C HIS 4.6 0.4 - - - -
128C GLY 3.9 1.0 + - - -
228C TYR* 6.1 4.9 - - - +
230C GLU* 2.5 45.3 + - - -
244C TYR* 3.5 11.7 + - - -
246C PRO* 4.5 8.2 - - + +
247C GLY* 3.8 27.8 + - - +
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Residues in contact with LEU 125 (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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602B ARG* 3.6 46.2 - - + +
603B ASN* 4.0 15.3 - - + +
605B HIS* 5.0 6.5 - - + +
606B ILE* 3.7 25.6 - - + -
611B LEU* 5.4 2.9 - - + -
121C ARG 3.0 15.1 + - - +
122C LEU* 3.2 8.7 + - + +
124C ARG* 1.3 78.6 - - - +
126C THR* 1.3 75.0 + - + +
127C HIS 3.4 0.2 - - - -
128C GLY* 3.2 18.9 + - - +
130C PHE* 4.9 8.2 - - + -
231C VAL* 5.6 1.6 - - + -
234C LEU* 5.3 2.0 - - + -
244C TYR* 3.7 17.5 + - + +
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Residues in contact with THR 126 (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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122C LEU* 2.6 35.8 + - + +
123C GLU* 4.7 2.7 - - - -
125C LEU* 1.3 83.9 - - + +
127C HIS* 1.3 64.3 + - - +
128C GLY 3.3 5.1 + - - +
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Residues in contact with HIS 127 (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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123C GLU* 3.1 39.0 + - + +
126C THR* 1.3 80.7 - - - +
128C GLY* 1.3 60.0 + - - +
129C THR* 4.1 4.1 + - - +
246C PRO 4.4 0.3 - - - +
247C GLY* 3.4 18.7 - - - -
248C GLY 4.3 2.9 + - - -
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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