Contacts of the helix formed by residues 138 - 150 (chain A) in PDB entry 3RC3
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 ASP 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A GLN* 4.0 20.7 + - - +
130A TYR* 5.5 2.6 + - - -
137A LEU* 1.3 76.3 - - - +
139A VAL* 1.3 66.2 + - + +
140A ASP* 3.4 18.2 + - - +
141A ILE* 3.4 10.0 - - + +
142A HIS* 3.1 19.4 + - - +
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Residues in contact with VAL 139 (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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137A LEU 3.5 2.5 + - - -
138A ASP* 1.3 72.6 - - + +
140A ASP* 1.3 64.4 + - + +
142A HIS* 3.4 6.6 + - + +
143A ILE* 3.0 44.5 + - + +
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Residues in contact with ASP 140 (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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138A ASP* 3.6 16.9 - - - +
139A VAL* 1.3 82.5 - - + +
141A ILE* 1.3 78.1 + - - +
143A ILE* 3.6 7.6 + - - +
144A VAL* 3.3 27.3 + - + +
161A PHE* 3.5 27.1 - - + -
164A ARG* 4.1 11.1 + - - -
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Residues in contact with ILE 141 (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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127A PHE* 4.0 22.2 - - + -
130A TYR* 6.1 3.4 - - + -
131A ILE* 4.3 15.0 - - + -
137A LEU* 3.8 23.6 - - + -
138A ASP* 3.4 20.6 - - + +
140A ASP* 1.3 82.4 + - - +
142A HIS* 1.3 67.4 + - - +
144A VAL* 3.1 3.1 + - - +
145A LEU* 3.0 31.2 + - + +
158A LEU* 4.2 9.9 - - + -
161A PHE* 3.8 44.6 - - + -
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Residues in contact with HIS 142 (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 PRO* 3.7 21.7 - - - +
88A LEU* 3.6 30.8 + - + +
137A LEU* 4.3 30.1 - - + +
138A ASP 3.1 17.4 + - - +
139A VAL* 3.4 9.2 + - + +
141A ILE* 1.3 78.8 - - - +
143A ILE* 1.3 63.3 + - + +
145A LEU* 3.4 4.8 + - - +
146A ASN* 3.0 39.8 + - - +
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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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139A VAL* 3.0 40.8 + - + +
140A ASP* 4.0 7.2 - - - +
141A ILE 3.3 0.2 - - - -
142A HIS* 1.3 76.1 - - + +
144A VAL* 1.3 59.2 + - + +
146A ASN* 3.4 10.1 + - + +
147A ASP* 2.8 46.9 + - - +
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Residues in contact with VAL 144 (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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140A ASP 3.3 14.5 + - - +
141A ILE 3.1 8.2 + - - +
143A ILE* 1.3 79.3 - - + +
145A LEU* 1.3 53.1 + - - +
147A ASP* 3.3 6.6 + - - +
148A ILE* 2.8 59.3 + - + +
153A ALA* 5.1 2.7 - - + -
157A ASP* 4.0 29.6 - - + +
158A LEU* 4.4 6.1 - - + +
161A PHE* 3.9 22.9 - - + -
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Residues in contact with LEU 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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88A LEU* 3.7 22.0 - - + -
93A VAL* 4.6 20.2 - - + -
96A VAL* 5.2 6.5 - - + -
97A LEU* 5.0 1.1 - - + -
131A ILE* 3.9 20.4 - - + -
137A LEU* 3.7 29.2 - - + -
141A ILE* 3.0 31.7 + - + +
142A HIS 3.7 0.7 - - - +
144A VAL* 1.3 74.3 - - - +
146A ASN* 1.3 59.3 + - - +
148A ILE* 3.2 7.1 + - + +
149A CYS* 2.9 37.1 + - - -
158A LEU* 3.8 32.3 - - + -
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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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87A PRO* 3.7 21.4 - - - +
88A LEU* 3.2 18.9 - - - +
142A HIS* 3.0 33.9 + - - +
143A ILE* 3.4 12.6 - - - +
145A LEU* 1.3 76.7 - - - +
147A ASP* 1.3 66.7 + - - +
150A PHE* 2.8 46.3 + - + +
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Residues in contact with ASP 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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143A ILE* 2.8 36.3 + - - +
144A VAL* 3.6 6.5 - - - +
145A LEU 3.3 0.4 - - - -
146A ASN* 1.3 83.6 - - - +
148A ILE* 1.3 61.3 + - - +
150A PHE* 3.8 1.6 - - - +
151A GLY 3.2 0.9 + - - -
152A ALA* 2.8 35.6 + - + +
153A ALA* 2.8 35.4 + - + +
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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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96A VAL* 3.7 30.9 - - + +
144A VAL* 2.8 45.6 + - + +
145A LEU* 3.2 7.1 + - - +
147A ASP* 1.3 70.1 - - - +
149A CYS* 1.3 68.4 + - - +
150A PHE 3.2 0.5 + - - -
151A GLY* 3.3 10.9 + - - -
153A ALA* 3.4 16.3 - - + +
154A HIS 3.7 15.9 - - - +
155A ALA* 4.0 28.5 - - + +
158A LEU* 4.2 27.6 - - + +
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Residues in contact with CYS 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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88A LEU* 5.3 2.5 - - - -
89A ASP* 4.9 3.6 - - + -
92A GLU* 4.1 30.6 - - + +
93A VAL* 4.1 27.4 - - - -
96A VAL* 4.2 15.3 - - - -
145A LEU* 2.9 25.5 + - - +
146A ASN* 5.1 0.2 - - - -
148A ILE* 1.3 79.2 - - - +
150A PHE* 1.3 82.2 + - + +
151A GLY 3.7 0.7 + - - -
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Residues in contact with PHE 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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87A PRO 5.1 7.2 - - - -
88A LEU* 5.8 0.4 - - + -
89A ASP* 5.3 15.9 - - + -
146A ASN* 2.8 48.1 + - + +
147A ASP* 3.9 2.0 - - - +
149A CYS* 1.3 92.9 - - + +
151A GLY* 1.3 56.0 + - - +
152A ALA* 3.3 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