Contacts of the helix formed by residues 142 - 150 (chain A) in PDB entry 5T4S
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 PRO 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A SER* 3.7 24.2 - - - +
44A VAL* 5.9 0.2 - - + -
106A GLN* 3.8 1.8 - - - +
129A GLY 4.7 4.3 - - - +
130A MET 5.8 0.2 - - - -
131A GLY 3.8 15.3 - - - +
132A PHE 3.9 2.2 - - - +
133A ILE* 3.6 36.8 - - + +
140A VAL 3.2 7.2 - - - +
141A THR* 1.4 87.6 - - + +
143A ILE* 1.3 66.1 + - - +
144A PHE* 4.5 3.4 - - + +
145A ASP* 3.3 29.6 + - - +
146A ASN* 3.2 17.2 + - - -
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Residues in contact with ILE 143 (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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44A VAL* 4.0 11.6 - - + +
97A ILE* 3.9 26.0 - - + -
99A VAL* 4.0 12.8 - - + -
104A VAL* 3.7 28.0 - - + -
106A GLN* 3.2 28.2 - - + +
128A VAL* 3.4 35.7 - - + -
129A GLY 4.0 10.0 + - - +
130A MET* 4.4 6.5 - - + -
142A PRO* 1.3 70.9 - - - +
144A PHE* 1.3 59.0 + - - +
146A ASN* 3.2 4.0 + - - +
147A ILE* 2.9 35.9 + - + +
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Residues in contact with PHE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLY 5.2 0.6 + - - -
130A MET* 3.9 26.2 - - + +
131A GLY 6.0 0.9 - - - +
142A PRO* 3.3 3.1 - - + +
143A ILE* 1.3 77.9 - - - +
145A ASP* 1.3 58.2 + - - +
147A ILE* 3.1 11.0 + - + +
148A ILE* 2.8 41.0 + - + +
153A LEU* 3.6 27.4 - - + -
156A ASP* 3.5 24.7 - - - -
157A VAL 3.4 27.1 - - - -
158A PHE* 3.7 32.5 - + + -
178A LEU* 4.0 14.6 - - + -
329A ARG* 3.8 23.8 - - - +
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Residues in contact with ASP 145 (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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131A GLY 4.5 0.2 - - - +
133A ILE* 4.5 11.7 - - - +
141A THR* 3.7 15.9 - - + +
142A PRO* 3.3 36.4 + - - +
144A PHE* 1.3 74.7 - - - +
146A ASN* 1.3 58.8 + - - +
148A ILE* 3.3 11.4 + - - +
149A SER* 3.1 30.5 + - - -
329A ARG* 2.7 44.1 + - - +
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Residues in contact with ASN 146 (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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104A VAL* 3.9 13.6 - - + +
105A THR 3.8 13.8 + - - +
106A GLN* 2.8 30.3 + - - +
107A MET 5.2 1.2 - - - +
141A THR* 3.7 30.6 + - - +
142A PRO 3.2 2.4 + - - +
143A ILE 3.2 9.9 + - - +
145A ASP* 1.3 77.9 - - - +
147A ILE* 1.3 62.1 + - - +
149A SER* 3.5 19.5 + - - -
150A GLN* 3.5 15.8 - - - +
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Residues in contact with ILE 147 (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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99A VAL* 4.2 24.9 - - + -
102A ILE* 4.0 22.7 - - + -
104A VAL* 3.7 21.5 - - + -
143A ILE* 2.9 29.2 + - + +
144A PHE* 3.1 15.7 + - + +
146A ASN* 1.3 74.6 - - - +
148A ILE* 1.3 64.0 + - - +
150A GLN* 3.4 18.7 + - - +
151A GLY 4.1 2.1 + - - -
152A VAL* 4.3 5.6 + - + +
153A LEU* 3.8 36.0 - - + +
178A LEU* 4.3 17.7 - - + -
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Residues in contact with ILE 148 (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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2A THR* 4.2 16.4 - - + +
3A LEU* 5.4 5.2 - - + -
144A PHE* 2.8 33.6 + - + +
145A ASP* 3.3 12.5 + - - +
147A ILE* 1.3 75.9 - - - +
149A SER* 1.3 62.3 + - - +
151A GLY* 3.1 16.1 + - - -
153A LEU* 3.8 20.9 - - + -
155A GLU 4.4 1.8 - - - +
156A ASP* 3.3 46.0 - - + +
329A ARG* 5.5 2.0 - - - +
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Residues in contact with SER 149 (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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2A THR* 4.5 10.7 - - - +
145A ASP 3.1 14.0 + - - -
146A ASN* 3.6 17.8 + - - -
147A ILE 3.4 0.6 - - - -
148A ILE* 1.3 76.6 - - - +
150A GLN* 1.3 61.5 + - - +
151A GLY* 3.3 1.2 + - - -
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Residues in contact with GLN 150 (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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102A ILE* 3.6 23.0 - - - +
103A THR 2.7 24.7 + - - +
104A VAL* 3.3 18.0 - - - +
105A THR 5.2 1.0 - - - +
146A ASN 3.5 13.5 - - - +
147A ILE 3.5 9.0 - - - +
148A ILE 3.1 0.6 - - - -
149A SER* 1.3 77.7 - - - +
151A GLY* 1.3 63.2 + - - +
152A VAL* 3.5 23.1 + - + +
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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