Contacts of the helix formed by residues 143 - 149 (chain C) in PDB entry 1T4P
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 GLN 143 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67C VAL* 4.5 4.5 - - - +
128C ASP 3.4 5.8 - - - -
130C ASN 3.0 19.7 - - - +
132C PRO* 3.3 34.7 - - - +
135C THR* 3.4 29.2 + - + +
138C GLY* 3.6 9.5 + - - -
139C ASN 2.9 28.5 + - - +
140C LEU* 2.8 19.6 + - - +
142C GLY* 1.3 81.1 - - - +
144C PRO* 1.3 72.5 - - - +
146C ALA* 2.9 17.2 + - - +
147C PHE* 3.3 19.0 - - + -
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Residues in contact with PRO 144 (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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101C HIS 3.3 23.1 - - - +
102C SER* 3.8 6.3 - - - -
104C ALA* 4.4 4.0 - - + -
105C ILE* 3.7 23.0 - - + +
122C TRP* 3.8 19.7 - - + -
128C ASP* 3.4 11.9 - - + +
140C LEU 3.2 10.4 - - - +
141C HIS 3.2 16.8 - - - +
142C GLY 3.3 2.5 - - - -
143C GLN* 1.3 89.8 - - - +
145C VAL* 1.3 62.3 + - - +
147C PHE* 3.0 18.4 + - - +
148C LEU* 3.5 14.1 + - + +
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Residues in contact with VAL 145 (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 TRP* 3.8 33.4 - - + -
127C THR 3.7 3.8 - - - +
128C ASP 3.2 14.0 + - - +
129C ILE* 3.8 18.4 - - + -
144C PRO* 1.3 73.7 - - - +
146C ALA* 1.3 63.9 + - - +
148C LEU* 3.7 11.2 - - + -
149C LEU* 3.0 36.0 + - + +
169C ILE* 5.9 1.1 - - + -
174C ILE* 4.2 15.3 - - + -
176C TYR* 3.4 27.4 - - + +
195C ILE* 5.8 0.2 - - + -
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Residues in contact with ALA 146 (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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128C ASP 4.2 1.4 + - - -
129C ILE* 4.0 8.8 - - - +
130C ASN 3.1 33.0 - - - +
131C THR* 4.1 10.3 - - + -
143C GLN 2.9 7.5 + - - +
145C VAL* 1.3 79.0 - - - +
147C PHE* 1.3 66.5 + - + +
148C LEU 3.4 0.5 + - - -
149C LEU 4.0 4.2 + - - +
152C LEU* 3.7 31.8 - - + +
156C PHE* 3.8 16.1 - - + -
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Residues in contact with PHE 147 (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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105C ILE* 4.1 26.7 - - + -
132C PRO* 4.0 17.0 - - + -
140C LEU* 3.7 32.5 - - + -
143C GLN* 3.3 29.4 - - + -
144C PRO 3.0 8.0 + - - +
146C ALA* 1.3 77.0 - - + +
148C LEU* 1.3 60.0 + - - +
149C LEU 5.0 0.9 - - - -
156C PHE* 4.3 19.5 - + - -
159C VAL* 4.0 16.8 - - + -
162C PHE* 3.6 38.6 - + + -
165C VAL* 3.4 24.9 - - + +
167C PRO* 4.1 10.9 - - - +
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Residues in contact with LEU 148 (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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104C ALA 4.1 6.7 - - - +
105C ILE* 3.8 18.8 - - + +
108C ILE* 3.8 34.1 - - + -
109C SER* 3.6 26.5 - - - +
122C TRP* 5.0 3.8 - - + -
144C PRO* 3.6 16.4 - - + +
145C VAL* 3.1 15.1 + - + +
147C PHE* 1.3 84.1 - - + +
149C LEU* 1.3 65.0 + - - +
165C VAL* 5.0 2.2 - - + -
167C PRO* 3.1 19.0 - - - +
168C CYS* 3.2 22.4 + - - -
169C ILE* 3.4 21.7 - - + +
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Residues in contact with LEU 149 (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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129C ILE* 3.7 28.9 - - + -
145C VAL* 3.0 25.8 + - + +
146C ALA 4.0 3.2 + - - +
147C PHE 3.8 0.2 - - - -
148C LEU* 1.3 76.9 - - - +
150C LYS* 1.3 64.2 + - - +
151C GLU* 4.3 2.2 - - - +
152C LEU* 3.3 28.1 + - + +
153C LYS 3.8 5.0 + - - -
167C PRO* 3.5 7.8 - - - +
169C ILE* 3.3 24.5 - - + +
170C SER* 3.6 24.2 - - - +
171C ALA* 3.8 5.4 - - - +
174C ILE* 4.8 6.1 - - + -
193C LEU* 3.9 22.4 - - + -
195C ILE* 4.1 10.1 - - + -
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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