Contacts of the helix formed by residues 151 - 165 (chain A) in PDB entry 1RC7
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 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A LYS 3.3 3.8 + - - +
150A LYS* 1.3 74.0 - - - +
152A TYR* 1.3 60.6 + - + +
153A LYS* 3.3 5.7 + - - +
154A THR* 2.4 40.9 + - - -
155A ILE* 2.8 31.5 + - - +
207A GLN* 2.9 30.6 + - - +
26D G 3.5 25.8 + - - +
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Residues in contact with TYR 152 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A ASP* 1.3 72.6 - - + +
153A LYS* 1.3 57.3 - - - +
155A ILE* 3.0 10.6 + - + +
156A LEU* 2.7 36.4 + - - +
207A GLN* 3.3 32.2 + - + +
210A ALA* 3.9 2.0 - - - -
211A GLU* 2.6 62.8 + - + +
214A ILE* 3.7 14.9 - - + +
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Residues in contact with LYS 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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151A ASP* 3.3 7.3 + - - +
152A TYR* 1.3 75.7 - - - +
154A THR* 1.3 62.6 + - - +
156A LEU* 3.4 1.9 + - - +
157A GLN* 3.1 24.1 + - - +
168A PRO* 5.5 0.5 - - - +
170A TYR* 3.8 41.0 + - - +
203A LYS* 4.6 3.3 - - + +
206A GLU* 2.8 37.7 + - + +
207A GLN* 3.2 35.1 + - + +
210A ALA* 3.9 4.0 - - + +
25D C 3.5 26.9 + - - +
26D G 2.8 28.1 + - - +
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Residues in contact with THR 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 LYS* 4.5 14.8 - - + -
151A ASP* 2.4 32.3 + - - -
152A TYR 3.2 0.6 - - - -
153A LYS* 1.3 76.9 - - - +
155A ILE* 1.3 64.4 + - - +
157A GLN* 3.4 5.3 + - - +
158A GLU* 3.1 42.8 + - + +
24D G 6.3 0.2 - - - +
25D C 3.1 27.5 + - - +
26D G 3.4 7.8 + - - -
36E G 5.1 4.9 + - - +
37E C 5.6 4.0 - - - +
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Residues in contact with ILE 155 (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 LYS* 3.7 32.8 - - + +
151A ASP 2.8 24.7 + - - +
152A TYR* 3.5 15.0 - - + +
154A THR* 1.3 73.4 - - - +
156A LEU* 1.3 66.7 + - - +
158A GLU* 3.3 9.6 + - - +
159A ILE* 3.1 35.3 + - + +
214A ILE* 3.8 18.6 - - + -
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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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152A TYR 2.7 19.5 + - - +
153A LYS 3.6 4.3 - - - +
155A ILE* 1.3 73.5 - - - +
157A GLN* 1.3 64.0 + - - +
159A ILE* 2.9 8.3 + - + +
160A THR* 2.9 40.0 + - + +
168A PRO* 3.6 24.0 - - + -
170A TYR* 3.3 24.7 - - + +
188A ALA* 4.6 0.2 - - + -
210A ALA* 3.9 16.2 - - + -
213A LEU* 3.9 31.6 - - + -
214A ILE* 4.1 19.0 - - + +
217A LEU* 4.0 11.4 - - + -
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Residues in contact with GLN 157 (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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153A LYS 3.1 13.5 + - - +
154A THR* 3.7 6.7 - - - +
155A ILE 3.3 0.2 - - - -
156A LEU* 1.3 79.0 - - - +
158A GLU* 1.3 58.7 + - + +
160A THR* 3.2 7.4 + - - -
161A GLN* 2.8 56.7 + - + +
167A ARG* 3.9 11.8 - - + +
168A PRO* 4.1 10.1 - - + +
24D G 2.6 62.7 + - - +
25D C 2.9 20.3 + - - -
38E G 3.6 8.8 - - - +
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Residues in contact with GLU 158 (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 LYS* 2.9 39.8 + - - +
154A THR* 3.1 29.3 + - + +
155A ILE* 3.7 6.7 - - - +
156A LEU 3.3 0.4 - - - -
157A GLN* 1.3 77.7 - - + +
159A ILE* 1.3 63.4 - - + +
161A GLN* 4.1 0.9 - - - +
162A LYS* 3.2 25.1 + - - +
37E C 3.0 20.5 + - - +
38E G 3.8 35.4 + - - +
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Residues in contact with ILE 159 (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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155A ILE* 3.1 31.7 + - + +
156A LEU* 2.9 11.1 + - - +
158A GLU* 1.3 77.8 - - + +
160A THR* 1.3 65.7 + - - +
162A LYS* 3.1 6.0 + - - +
163A ARG* 3.0 31.2 + - + +
164A TRP* 5.3 2.7 - - + -
214A ILE* 4.1 23.1 - - + +
217A LEU* 4.0 26.2 - - + -
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Residues in contact with THR 160 (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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156A LEU* 2.9 34.5 + - + +
157A GLN 3.2 5.7 + - - -
159A ILE* 1.3 72.5 - - - +
161A GLN* 1.3 57.9 + - - +
164A TRP* 3.0 39.5 + - + +
165A LYS 3.3 3.1 + - - -
166A GLU 2.7 27.0 + - - +
168A PRO* 3.2 18.5 - - + +
190A ILE* 3.6 36.3 - - + -
217A LEU* 4.4 4.5 - - + -
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Residues in contact with GLN 161 (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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157A GLN* 2.8 33.7 + - - +
158A GLU 4.2 0.2 - - - +
160A THR* 1.3 74.6 + - - +
162A LYS* 1.3 57.6 + - - +
165A LYS* 2.9 32.3 + - - +
166A GLU* 3.4 20.6 - - - +
167A ARG* 3.1 22.8 - - + +
38E G 2.8 70.9 + - - +
39E C 3.2 21.7 + - - +
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Residues in contact with LYS 162 (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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158A GLU 3.2 18.8 + - - +
159A ILE* 3.1 5.4 + - - +
161A GLN* 1.3 80.9 - - - +
163A ARG* 1.3 62.9 + - + +
164A TRP 3.3 0.9 + - - -
165A LYS* 4.1 14.6 - - - +
38E G 6.0 0.7 - - - +
39E C 4.8 13.2 - - - +
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Residues in contact with ARG 163 (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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159A ILE* 3.0 19.8 + - + +
162A LYS* 1.3 80.5 - - + +
164A TRP* 1.3 118.8 + - + +
165A LYS* 5.7 0.2 - - - -
193A TYR* 3.9 17.0 + - - -
217A LEU* 4.6 17.6 + - - +
220A SER 4.2 16.0 + - - -
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Residues in contact with TRP 164 (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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159A ILE* 5.3 0.9 - - + -
160A THR* 3.0 30.5 + - + +
162A LYS 3.3 0.2 - - - -
163A ARG* 1.3 136.5 + - + +
165A LYS* 1.3 77.9 + - - +
166A GLU* 3.0 28.1 + - + +
190A ILE* 3.5 34.1 - - + -
191A LYS* 3.3 32.3 - - + +
193A TYR* 3.8 28.0 - + - -
217A LEU* 3.9 10.5 - - + -
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Residues in contact with LYS 165 (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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160A THR 3.3 0.6 + - - -
161A GLN* 2.9 34.0 + - - +
162A LYS* 4.1 14.1 - - - +
164A TRP* 1.3 80.4 - - - +
166A GLU* 1.3 62.4 + - - +
39E C 3.4 31.2 + - - +
40E C 2.8 31.5 + - - +
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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