Contacts of the helix formed by residues 142 - 156 (chain A) in PDB entry 1T43
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 MET 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ALA* 3.9 22.9 - - + +
140A ASP* 3.2 5.2 + - - +
141A ARG* 1.3 96.7 - - - +
143A PRO* 1.3 60.4 - - + +
144A ASP* 2.8 16.4 + - - +
145A ALA* 3.0 18.5 + - + +
146A VAL* 3.3 9.7 + - - +
205A THR* 2.9 47.3 - - - +
206A ALA 3.9 4.7 - - - +
300A SAH 3.6 37.2 - - + +
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Residues in contact with PRO 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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141A ARG 4.0 5.4 - - - +
142A MET* 1.3 84.2 - - + +
144A ASP* 1.3 68.7 + - - +
146A VAL* 3.0 28.3 - - + +
147A SER* 3.2 10.6 + - - -
165A GLN* 4.6 19.7 - - - +
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Residues in contact with ASP 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER* 4.9 5.3 + - - +
87A ALA* 3.3 29.5 - - + +
142A MET* 2.8 7.7 + - - +
143A PRO* 1.3 76.6 - - - +
145A ALA* 1.3 54.7 + - - +
147A SER* 2.8 9.0 + - - -
148A LEU* 2.6 37.0 + - - +
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Residues in contact with ALA 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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87A ALA* 4.5 2.7 - - - +
88A THR* 2.6 31.9 - - - +
118A THR* 5.6 0.4 - - - -
119A GLY 3.1 15.1 - - - +
140A ASP* 3.7 22.4 - - - +
142A MET* 3.0 12.1 + - + +
144A ASP* 1.3 76.9 - - - +
146A VAL* 1.4 55.0 + - - +
148A LEU* 3.0 4.9 + - - -
149A ALA* 2.7 33.5 + - - +
300A SAH 4.2 1.8 - - - +
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 5.9 1.3 - - - -
140A ASP* 3.9 24.6 - - + +
142A MET 3.4 7.2 - - - +
143A PRO* 3.0 34.8 - - + +
145A ALA* 1.4 78.6 - - - +
147A SER* 1.3 48.8 + - - +
149A ALA* 3.5 3.6 + - - +
150A GLN* 2.8 39.1 + - - +
163A ILE* 3.2 30.6 - - + +
164A LEU* 4.2 9.9 - - - +
165A GLN* 4.2 15.5 - - + +
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Residues in contact with SER 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A PRO 3.2 7.3 + - - -
144A ASP* 2.8 13.7 + - - -
146A VAL* 1.3 75.5 - - - +
148A LEU* 1.3 68.7 + - - +
149A ALA 3.1 1.3 - - - -
150A GLN* 2.7 25.6 + - - +
151A ARG* 2.6 44.4 + - - +
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Residues in contact with LEU 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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83A PHE* 3.4 34.8 - - + +
84A VAL* 4.0 5.4 - - - -
85A SER* 3.2 41.1 - - - +
88A THR* 4.0 12.3 - - - +
120A THR* 3.6 27.6 - - + -
144A ASP 2.6 22.0 + - - +
145A ALA* 3.2 6.3 - - - +
147A SER* 1.3 75.6 + - - +
149A ALA* 1.3 63.1 + - - +
151A ARG* 3.2 17.2 + - + +
152A ASN* 2.8 27.2 + - - +
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Residues in contact with ALA 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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118A THR* 4.1 12.3 - - + -
120A THR 2.8 31.7 + - - +
121A GLY* 3.9 6.5 - - - +
125A LEU* 5.1 1.4 - - + +
145A ALA 2.7 15.0 + - - +
146A VAL 3.6 8.5 - - - +
148A LEU* 1.3 71.0 - - - +
150A GLN* 1.3 65.7 + - - +
151A ARG 2.7 2.3 + - - -
152A ASN* 2.9 4.0 + - - +
153A ALA* 2.7 24.9 + - - +
163A ILE* 4.0 17.0 - - + -
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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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146A VAL* 2.8 24.7 - - - +
147A SER* 2.7 38.3 + - - +
149A ALA* 1.3 76.0 - - - +
151A ARG* 1.3 61.2 + - - +
153A ALA* 3.4 9.5 - - - +
154A GLN* 3.3 19.4 + - - +
163A ILE* 2.8 37.3 - - + +
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Residues in contact with ARG 151 (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* 5.1 26.1 - - + -
147A SER* 2.6 19.5 + - - +
148A LEU* 3.3 19.1 - - + +
149A ALA 2.7 3.2 + - - -
150A GLN* 1.3 67.3 - - - +
152A ASN* 1.3 60.3 + - - +
153A ALA 3.1 1.1 - - - -
154A GLN* 2.7 29.8 + - - +
155A HIS* 3.0 32.4 + - + +
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Residues in contact with ASN 152 (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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81A PRO 4.6 0.6 - - - +
82A LEU* 3.3 14.1 - - + -
83A PHE* 2.4 56.2 + - - +
120A THR* 3.2 23.6 + - - +
125A LEU* 4.3 11.4 - - + -
148A LEU* 2.8 26.8 + - - +
149A ALA 2.9 6.5 + - - +
151A ARG* 1.3 76.5 - - - +
153A ALA* 1.3 64.0 - - - +
155A HIS* 2.9 20.8 + - - +
156A LEU* 2.9 21.4 - - + +
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Residues in contact with ALA 153 (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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125A LEU* 4.5 5.1 - - + +
149A ALA 2.7 17.5 + - - +
150A GLN* 3.4 12.8 - - - +
152A ASN* 1.3 78.1 - - - +
154A GLN* 1.3 58.9 + - - +
157A ALA 3.4 2.3 + - - -
158A ILE* 3.0 43.7 + - + +
161A ILE* 4.0 25.6 - - + -
163A ILE* 5.5 2.7 - - + -
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Residues in contact with GLN 154 (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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150A GLN 3.3 9.7 + - - +
151A ARG* 2.7 15.0 + - - +
153A ALA* 1.3 79.6 - - - +
155A HIS* 1.3 66.5 + - + +
157A ALA* 3.0 17.9 + - - +
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Residues in contact with HIS 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PRO* 5.7 5.6 + - + +
83A PHE* 4.0 36.4 + + - +
151A ARG* 3.0 26.3 + - + +
152A ASN* 2.9 14.7 + - - +
154A GLN* 1.3 76.3 - - + +
156A LEU* 1.3 62.8 + - + +
157A ALA* 2.8 10.7 + - - +
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Residues in contact with LEU 156 (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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80A LEU* 4.0 34.5 - - + -
81A PRO* 4.1 26.2 - - + +
82A LEU* 4.4 9.0 - - + -
125A LEU* 4.7 8.7 - - + +
129A SER* 5.5 1.6 - - - -
152A ASN* 2.9 30.7 - - + +
153A ALA 4.2 2.7 - - - +
155A HIS* 1.3 78.1 - - + +
157A ALA* 1.3 72.4 + - - +
158A ILE* 3.7 36.0 - - + +
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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