Contacts of the helix formed by residues 144 - 151 (chain A) in PDB entry 1R1H
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 ASN 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ARG 3.3 16.2 + - - +
141A SER* 4.2 6.7 - - - +
142A CYS 3.3 3.0 - - - -
143A ILE* 1.3 75.8 - - + +
145A GLU* 1.3 58.8 + - - +
146A SER* 2.8 19.8 + - - -
147A ALA* 3.1 9.1 + - + +
148A ILE* 3.3 24.8 + - - +
503A GLU 4.9 4.8 + - - +
752A NAG 1.4 70.9 + - - +
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Residues in contact with GLU 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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142A CYS 5.2 0.9 - - - +
143A ILE 3.0 12.9 + - - +
144A ASN* 1.3 70.7 - - - +
146A SER* 1.3 60.8 + - - +
148A ILE* 3.7 10.1 - - + +
149A ASP* 2.8 42.7 + - - +
384A ARG* 3.3 26.2 + - - -
387A LYS* 5.4 3.8 - - - -
406A THR* 2.8 37.6 + - + -
409A ARG* 5.7 0.9 - - - -
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Residues in contact with SER 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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144A ASN* 2.8 12.2 + - - -
145A GLU* 1.3 79.9 - - - +
147A ALA* 1.3 72.8 + - - +
149A ASP* 3.4 4.8 + - - +
150A SER* 3.0 25.8 + - - -
752A NAG 3.8 13.2 + - - -
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Residues in contact with ALA 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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141A SER 5.9 0.7 - - - +
144A ASN* 3.1 15.6 + - + +
146A SER* 1.3 84.0 + - - +
148A ILE* 1.3 63.6 + - + +
150A SER* 3.5 10.3 + - - -
151A ARG* 3.5 22.8 - - - +
503A GLU 5.5 0.2 - - - +
504A ASP* 4.6 19.3 - - + +
752A NAG 3.5 33.7 - - - +
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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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141A SER 3.9 10.1 - - - +
142A CYS 3.8 20.2 - - - +
144A ASN 3.3 17.1 + - - +
145A GLU* 3.7 9.2 - - + +
146A SER 3.2 0.6 - - - -
147A ALA* 1.3 75.9 - - + +
149A ASP* 1.3 67.7 + - - +
151A ARG* 3.0 24.1 + - - +
152A GLY 3.8 4.5 + - - +
381A SER* 3.8 11.4 - - - +
382A LEU* 3.4 31.6 - - - +
383A SER* 4.1 3.6 - - - -
387A LYS* 5.7 4.7 - - - -
506A TYR* 4.0 32.5 - - + +
507A PHE 5.8 0.2 - - - +
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Residues in contact with ASP 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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145A GLU* 2.8 32.8 + - - +
146A SER* 4.0 5.5 - - - +
148A ILE* 1.3 74.6 - - - +
150A SER* 1.3 62.9 + - - +
151A ARG 3.1 1.0 + - - -
152A GLY* 3.2 10.4 + - - -
382A LEU 4.6 0.9 - - - +
383A SER* 3.5 14.4 - - - -
384A ARG* 3.1 39.9 + - - +
387A LYS* 5.4 2.3 - - - +
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Residues in contact with SER 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 SER 3.0 18.9 + - - -
147A ALA* 3.6 9.6 - - - -
148A ILE 3.1 0.2 - - - -
149A ASP* 1.3 76.9 - - - +
151A ARG* 1.3 61.5 + - - +
152A GLY 3.3 0.6 + - - -
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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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147A ALA 3.5 18.2 - - - +
148A ILE* 3.0 12.7 + - - +
150A SER* 1.3 80.9 - - - +
152A GLY* 1.3 65.0 + - - +
154A GLU* 3.0 33.6 + - + +
155A PRO* 3.7 30.7 - - + +
258A GLU* 4.4 0.9 - - - +
504A ASP 4.2 9.4 - - - -
505A GLU* 2.8 29.2 + - - +
506A TYR 6.0 0.4 - - - +
507A PHE* 5.4 1.8 - - - +
508A GLU* 2.6 32.5 + - - -
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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